diff --git a/cl-base.owl b/cl-base.owl index 006392d2f..d6e4617c6 100644 --- a/cl-base.owl +++ b/cl-base.owl @@ -22,7 +22,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + An ontology of cell types. Cell Ontology @@ -38,7 +38,7 @@ See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo. - 2024-07-10 + 2024-08-16 @@ -401,6 +401,12 @@ + + + + + + @@ -5952,23 +5958,29 @@ Covers cells actively being cultured or stored in a quiescent state for future u - The output neuron of the cerebellar cortex. + An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress. BTO:0001011 CALOHA:TS-0845 FMA:67969 ZFA:0009071 Purkinje neuron - Purkinje's cell cerebellar Purkinje cell - cerebellum Purkinje cell + PC + PN + Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024). Purkinje cell - The output neuron of the cerebellar cortex. + An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress. MESH:D011689 + PMID:12907269 + PMID:14568361 + PMID:31424738 + PMID:33288911 + PMID:38168772 @@ -5976,6 +5988,41 @@ Covers cells actively being cultured or stored in a quiescent state for future u ZFA:0009071 + + + + Purkinje neuron + PMID:28821816 + + + + + cerebellar Purkinje cell + https://doi.org/10.1016/j.proghi.2004.07.002 + + + + + PC + PMID:38168772 + + + + + + PN + PMID:28821816 + + + + + + Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024). + PMID:17535929 + PMID:27215193 + PMID:37426070 + https://doi.org/10.1016/j.stem.2023.11.013 + @@ -7376,9 +7423,26 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - A cell of the epithelial lining that produce and secrete mucins. + + + + + + + + + + + + + + + + + + + + A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane. BTO:0001540 FMA:13148 ZFA:0009094 @@ -7386,12 +7450,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u chalice cell goblet cell + https://upload.wikimedia.org/wikipedia/commons/thumb/c/c4/404_Goblet_Cell_new.jpg/800px-404_Goblet_Cell_new.jpg - A cell of the epithelial lining that produce and secrete mucins. + A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane. MESH:D020397 + http://en.wikipedia.org/wiki/Goblet_cell @@ -7399,6 +7465,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u ZFA:0009094 + + + + https://upload.wikimedia.org/wikipedia/commons/thumb/c/c4/404_Goblet_Cell_new.jpg/800px-404_Goblet_Cell_new.jpg + + + @@ -12609,14 +12682,15 @@ The modern definition of neurosecretion has evolved to include the release of an + - - + + - A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. + An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development. FMA:83028 trophoblastic cell trophoblast cell @@ -12630,9 +12704,17 @@ The modern definition of neurosecretion has evolved to include the release of an - A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. + An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development. GOC:tfm MESH:D014327 + PMID:37630754 + doi:10.1007/978-3-030-84725-8 + + + + + trophoblastic cell + doi:10.1007/978-3-030-84725-8 @@ -14657,20 +14739,20 @@ The modern definition of neurosecretion has evolved to include the release of an - + A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods. somatic stem cell FBbt:00004903 follicle stem cell (sensu Arthropoda) - + - + https://github.com/obophenotype/cell-ontology/issues/1943 @@ -15798,7 +15880,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -15811,14 +15893,14 @@ The modern definition of neurosecretion has evolved to include the release of an FBbt:00004904 follicle cell of egg chamber - + - + @@ -16656,7 +16738,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -16755,24 +16837,11 @@ The modern definition of neurosecretion has evolved to include the release of an - - A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it. - ZFA:0009233 - paracrine cell + + The term paracrine describes a role of a secreted hormone. There are a vast number of cell types that could fit this description, however it is difficult to know every case where a secreted hormone has paracrine effects. + obsolete paracrine cell + true - - - - A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it. - GOC:tfm - ISBN:0198529171 - - - - - ZFA:0009233 - - @@ -17279,19 +17348,19 @@ The modern definition of neurosecretion has evolved to include the release of an - + A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed. ZFA:0009242 primary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -17406,19 +17475,19 @@ The modern definition of neurosecretion has evolved to include the release of an - + A neuron of teleosts that develops later than a primary neuron, typically during the larval stages. ZFA:0009246 secondary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -20719,7 +20788,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -20767,7 +20836,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -23148,7 +23217,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -23937,7 +24005,6 @@ The modern definition of neurosecretion has evolved to include the release of an neuroglioblast (sensu Nematoda) - false @@ -26587,7 +26654,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -26618,7 +26685,7 @@ radial glial cells acting as neural progenitors throughout life. FMB cone bipolar cell type 2 cone bipolar cell (sensu Mus) - + @@ -26638,7 +26705,7 @@ radial glial cells acting as neural progenitors throughout life. - + PMID:27565351 @@ -56538,27 +56605,41 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + - A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree. + A multi-ciliated epithelial cell located in the trachea and bronchi, characterized by a columnar shape and motile cilia on its apical surface. These cilia facilitate mucociliary clearance by moving mucus and trapped particles toward the pharynx. 2010-08-24T03:38:29Z FMA:70542 + These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles. ciliated columnar cell of tracheobronchial tree - A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree. + A multi-ciliated epithelial cell located in the trachea and bronchi, characterized by a columnar shape and motile cilia on its apical surface. These cilia facilitate mucociliary clearance by moving mucus and trapped particles toward the pharynx. GOC:tfm - ISBN:0517223651 + PMID:28400610 + + + + + These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles. + + PMID:25386990 @@ -56658,39 +56739,36 @@ radial glial cells acting as neural progenitors throughout life. - + - + - + - + - An epithelial cell of the uterus. + An epithelial cell of the uterus. This cell has a mesodermal origin. 2010-08-24T10:45:54Z FMA:256161 epithelial cell of uterus - - - - - true - - An epithelial cell of the uterus. + An epithelial cell of the uterus. This cell has a mesodermal origin. GOC:tfm + PMID:11331626 + PMID:16960017 + PMID:21698266 @@ -56754,14 +56832,26 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + - + - A columnar cell of the cervix uteri. + A simple columnar epithelial cell located in the endocervix. 2010-08-24T10:47:47Z FMA:86486 @@ -56770,9 +56860,10 @@ radial glial cells acting as neural progenitors throughout life. - A columnar cell of the cervix uteri. + A simple columnar epithelial cell located in the endocervix. GOC:tfm ISBN:0721662544 + doi:/10.1016/j.autneu.2015.04.008 @@ -57511,22 +57602,21 @@ radial glial cells acting as neural progenitors throughout life. - + - + + + + + + - - - - - - - A mucous cell in the epithelium of the stomach. + An epithelial cell of the stomach. This cell produces mucous. 2010-08-25T03:38:51Z FMA:63464 @@ -57535,7 +57625,7 @@ radial glial cells acting as neural progenitors throughout life. - A mucous cell in the epithelium of the stomach. + An epithelial cell of the stomach. This cell produces mucous. GOC:tfm @@ -57571,18 +57661,6 @@ radial glial cells acting as neural progenitors throughout life. mucus neck cell of gastric gland mucous neck cell of gastric gland - - - - - true - - - - - - true - @@ -57596,8 +57674,14 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. 2010-08-25T03:45:10Z @@ -57629,8 +57713,7 @@ radial glial cells acting as neural progenitors throughout life. - - + @@ -57764,22 +57847,37 @@ radial glial cells acting as neural progenitors throughout life. - An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. + + + + + + + An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. 2010-08-26T10:59:44Z BTO:0004632 FMA:70970 + Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. glomerular endothelial cell - An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. + An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. GOC:tfm PMID:15840009 + + + + Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. + PMID:18480313 + PMID:19129259 + PMID:33123011 + @@ -59563,9 +59661,25 @@ radial glial cells acting as neural progenitors throughout life. - - - A nonstratified squamous cell located in the ectocervix. + + + + + + + + + + + + + + + + + + + A stratified squamous epithelial cell located in the ectocervix. 2010-09-08T09:12:23Z FMA:86483 @@ -59575,8 +59689,10 @@ radial glial cells acting as neural progenitors throughout life. - A nonstratified squamous cell located in the ectocervix. + A stratified squamous epithelial cell located in the ectocervix. GOC:tfm + PMID:32644501 + doi:/10.1016/j.autneu.2015.04.008 http://www.bu.edu/histology/p/19404loa.htm @@ -61240,7 +61356,7 @@ radial glial cells acting as neural progenitors throughout life. - + A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum. 2010-09-13T03:39:17Z @@ -61249,14 +61365,14 @@ radial glial cells acting as neural progenitors throughout life. Type A cells are usually round and located in the upper part of the synovial intima. type A synovial cell - + - + PMID:10770586 @@ -69086,8 +69202,10 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte that produces pigment within the hair follicle. + 2010-12-03T03:17:09Z + hair follicle melanocyte @@ -71121,7 +71239,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -72229,9 +72347,11 @@ radial glial cells acting as neural progenitors throughout life. An epidermal cell that is part of the germinal matrix. + 2011-03-01T04:31:06Z trichocyte + hair germinal matrix cell @@ -72624,6 +72744,7 @@ radial glial cells acting as neural progenitors throughout life. BTO:0001220 CALOHA:TS-0898 MESH:D012583 + neurolemmocyte A myelinating Schwann cell wraps around a single axon. Myelination occurs in larger diameter axons, while a process called ensheathment occurs on smaller diameter axons in which a single cell wraps around multiple small, unmyelinated axons separating them with a thin layer of cytoplasm. The structure formed is called a Remak bundle. @@ -72636,6 +72757,13 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:16807057 + + + + neurolemmocyte + PMID:32119275 + PMID:38638689 + @@ -75418,16 +75546,17 @@ radial glial cells acting as neural progenitors throughout life. - + + - + A glandular epithelial cell of the endometrium. @@ -75547,14 +75676,9 @@ radial glial cells acting as neural progenitors throughout life. 2011-07-11T01:20:35Z CALOHA:TS-1284 FMA:86554 - glandular cell of stomach + glandular cell of stomach + glandular epithelial cell of stomach - - - - - true - @@ -81510,18 +81634,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + A skeletal muscle satellite cell that has become mitotically active - typically following muscle damage. activated skeletal muscle satellite cell - + - + More accurately - transformation_of ? @@ -83822,8 +83946,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + - A goblet cell that is located in the colon. goblet cell of colon @@ -85303,7 +85427,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -86675,19 +86799,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + Any photoreceptor cell that is part of some camera-type eye. camera type eye photoreceptor cell camera-type eye photoreceptor cell - + - + https://github.com/obophenotype/cell-ontology/issues/2245 @@ -88796,11 +88920,9 @@ plexiform layer using GABA. A hillock cell that is part of the prostatic urethra. - 2022-10-13T13:58:15Z hillock cell of prostatic urethra - hillock cell of prostatic urethral epithelium @@ -90055,7 +90177,6 @@ plexiform layer using GABA. - Any goblet cell that is part of some lung epithelium. lung goblet cell @@ -91993,7 +92114,7 @@ plexiform layer using GABA. - + @@ -92098,7 +92219,7 @@ plexiform layer using GABA. - + @@ -92188,7 +92309,12 @@ plexiform layer using GABA. - + + + + + + A goblet cell that is part of the epithelium proper of duodenum. FMA:263063 @@ -92313,7 +92439,23 @@ plexiform layer using GABA. - + + + + + + + + + + + + + + + + + A goblet cell that is part of the epithelium proper of appendix. FMA:263069 goblet cell of epithelium proper of appendix @@ -97125,8 +97267,14 @@ plexiform layer using GABA. + - + + + + + + A goblet cell that is part of the small intestine. FMA:86929 goblet cell of epithelium of small intestine @@ -99073,7 +99221,7 @@ plexiform layer using GABA. - + @@ -99081,7 +99229,7 @@ plexiform layer using GABA. - + @@ -99089,18 +99237,12 @@ plexiform layer using GABA. - Any kidney blood vessel cell that is part of some kidney capillary. + An endothelial cell that is part of the capillary of the kidney. KUPO:0001030 kidney capillary endothelial cell - - - - Any kidney blood vessel cell that is part of some kidney capillary. - FBC:Autogenerated - @@ -99259,7 +99401,6 @@ plexiform layer using GABA. - @@ -99268,19 +99409,13 @@ plexiform layer using GABA. - Any kidney capillary endothelial cell that is part of some glomerular capillary endothelium. + An endothelial cell that is part of the glomerular capillary of the kidney. KUPO:0001037 glomerular capillary endothelial cell - - - - Any kidney capillary endothelial cell that is part of some glomerular capillary endothelium. - FBC:Autogenerated - @@ -99306,7 +99441,7 @@ plexiform layer using GABA. - Any kidney arterial blood vessel cell that is part of some renal afferent arteriole. + An endothelial cell which is part of the afferent arteriole in the kidney. This cell is responsible for maintaining renal blood flow and glomerular filtration rate. KUPO:0001038 kidney afferent arteriole cell @@ -99319,8 +99454,11 @@ plexiform layer using GABA. - Any kidney arterial blood vessel cell that is part of some renal afferent arteriole. - FBC:Autogenerated + An endothelial cell which is part of the afferent arteriole in the kidney. This cell is responsible for maintaining renal blood flow and glomerular filtration rate. + PMID:16990493 + PMID:22733355 + PMID:24066938 + PMID:25834230 @@ -99453,12 +99591,12 @@ plexiform layer using GABA. - + - + @@ -99466,18 +99604,25 @@ plexiform layer using GABA. - An endothelial cell that is part of some peritubular capillary. + An endothelial cell that is part of the peritubular capillary of the kidney. This cell is highly fenestrated and plays a vital role in the kidney's filtration process, enabling the exchange of materials between the blood and the renal tubules. KUPO:0001065 + Peritubular capillary endothelial cells feature fenestrations measuring 60-70 nm in diameter, each traversed by a thin diaphragm. peritubular capillary endothelial cell - - - true + + An endothelial cell that is part of the peritubular capillary of the kidney. This cell is highly fenestrated and plays a vital role in the kidney's filtration process, enabling the exchange of materials between the blood and the renal tubules. + PMID:19129259 + + + + + Peritubular capillary endothelial cells feature fenestrations measuring 60-70 nm in diameter, each traversed by a thin diaphragm. + PMID:19129259 @@ -99488,7 +99633,7 @@ plexiform layer using GABA. - + @@ -99497,8 +99642,8 @@ plexiform layer using GABA. - - + + @@ -99512,7 +99657,7 @@ plexiform layer using GABA. - + true @@ -99655,24 +99800,21 @@ plexiform layer using GABA. - Any endothelial cell that is part of some renal afferent arteriole. + An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration. KUPO:0001039 kidney afferent arteriole endothelial cell - - - - - true - - Any endothelial cell that is part of some renal afferent arteriole. - FBC:Autogenerated + An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration. + PMID:16990493 + PMID:22733355 + PMID:24066938 + PMID:25834230 @@ -99694,15 +99836,18 @@ plexiform layer using GABA. - Any smooth muscle cell that is part of some renal afferent arteriole. + A smooth muscle cell found in the wall of the afferent arteriole. This cell contracts and relaxes in response to changes in blood pressure, a process known as a myogenic response, to alter artery diameter and regulate blood flow into the glomeruli. KUPO:0001040 kidney afferent arteriole smooth muscle cell - Any smooth muscle cell that is part of some renal afferent arteriole. - FBC:Autogenerated + A smooth muscle cell found in the wall of the afferent arteriole. This cell contracts and relaxes in response to changes in blood pressure, a process known as a myogenic response, to alter artery diameter and regulate blood flow into the glomeruli. + PMID:16990493 + PMID:22733355 + PMID:24066938 + PMID:25834230 @@ -99981,28 +100126,10 @@ plexiform layer using GABA. - Any peritubular capillary endothelial cell that is part of some outer renal medulla peritubular capillary. + An endothelial cell that is part of the peritubular capillary of the outer renal medulla. KUPO:0001066 kidney outer medulla peritubular capillary cell - - - - - true - - - - - - true - - - - - Any peritubular capillary endothelial cell that is part of some outer renal medulla peritubular capillary. - FBC:Autogenerated - @@ -100028,16 +100155,10 @@ plexiform layer using GABA. - Any peritubular capillary endothelial cell that is part of some renal cortex peritubular capillary. + An endothelial cell that is part of the peritubular capillary of the renal cortex. KUPO:0001067 kidney cortex peritubular capillary cell - - - - Any peritubular capillary endothelial cell that is part of some renal cortex peritubular capillary. - FBC:Autogenerated - @@ -100056,6 +100177,7 @@ plexiform layer using GABA. + @@ -100103,6 +100225,7 @@ plexiform layer using GABA. + @@ -100455,12 +100578,6 @@ plexiform layer using GABA. KUPO:0001079 arcuate artery endothelial cell - - - - - true - @@ -105627,19 +105744,13 @@ plexiform layer using GABA. - + - - - - - - Any capillary endothelial cell that is part of a placenta. @@ -107339,17 +107450,17 @@ plexiform layer using GABA. - L2/3 bipolar vip interneuron (Mus) - A vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar vip cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer vip cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar vip cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar vip cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper vip cells. + L2/3 bipolar VIP interneuron (Mus) + A VIP GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar VIP cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer VIP cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar VIP cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar VIP cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper VIP cells. L2/3 bipolar Vip (Mus musculus) - L2/3 bipolar vip GABAergic interneuron (Mmus) + L2/3 bipolar VIP GABAergic interneuron (Mmus) - A vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar vip cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer vip cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar vip cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar vip cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper vip cells. + A VIP GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar VIP cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer VIP cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar VIP cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar VIP cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper VIP cells. PMID:26420784 @@ -107654,17 +107765,17 @@ plexiform layer using GABA. - L5 vip interneuron (Mus) - A vip GABAergic cortical interneuron with a soma found in L5. L5 vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 vip cells show particularly low resting membrane potential. + L5 VIP interneuron (Mus) + A VIP GABAergic cortical interneuron with a soma found in L5. L5 VIP cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical VIP subclass cells that tend to show high input resistance. L5 VIP cells show particularly low resting membrane potential. L5 VIP (Mus musculus) - L5 vip GABAergic interneuron (Mmus) + L5 VIP GABAergic interneuron (Mmus) - A vip GABAergic cortical interneuron with a soma found in L5. L5 vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 vip cells show particularly low resting membrane potential. + A VIP GABAergic cortical interneuron with a soma found in L5. L5 VIP cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical VIP subclass cells that tend to show high input resistance. L5 VIP cells show particularly low resting membrane potential. PMID:26420784 PMID:26612957 @@ -107747,13 +107858,13 @@ plexiform layer using GABA. - vip cortical interneuron + VIP cortical interneuron A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide ILX:0770151 - vip GABAergic cortical interneuron + VIP GABAergic cortical interneuron @@ -107883,16 +107994,16 @@ plexiform layer using GABA. - A vip GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization. + A VIP GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization. L5/6 CCK Vip (Mus musculus) - L5/6 cck, vip GABAergic interneuron (Mmus) + L5/6 cck, VIP GABAergic interneuron (Mmus) - A vip GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization. + A VIP GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization. PMID:33184512 @@ -109157,9 +109268,9 @@ plexiform layer using GABA. - - - + + + A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. VLMC (Mus musculus) @@ -109167,34 +109278,34 @@ plexiform layer using GABA. vascular leptomeningeal cell (Mmus) - + - + - + - + PMID:30096314 - + PMID:30096314 - + PMID:30096314 @@ -112599,6 +112710,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell. 2022-03-03T10:39:31Z @@ -112631,6 +112748,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -113925,23 +114048,33 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - + + + + + - + + - A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium. + + + + + + + A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucus across the endometrial surface. 2023-02-09T11:25:14Z ciliated cell of the uterus uterine ciliated cell @@ -113953,7 +114086,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium. + A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucus across the endometrial surface. + PMID:31290979 + PMID:37999981 + doi:10.1016/j.coemr.2024.100503 doi:10.1038/s41591-020-1040-z https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells @@ -113976,14 +114112,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A ciliated cell of the endometrial luminal epithelium. + A ciliated cell of the endometrial luminal epithelium. This cell is characterized by the presence of motile cilia on its apical surface. 2023-02-09T11:34:42Z luminal endometrial ciliated epithelial cell - A ciliated cell of the endometrial luminal epithelium. + A ciliated cell of the endometrial luminal epithelium. This cell is characterized by the presence of motile cilia on its apical surface. doi:10.1038/s41591-020-1040-z @@ -113999,14 +114135,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A ciliated cell of the endometrial glandular epithelium. + A ciliated cell of the endometrial glandular epithelium. This cell is characterized by the presence of motile cilia on its apical surface. 2023-02-09T11:37:30Z glandular endometrial ciliated epithelial cell - A ciliated cell of the endometrial glandular epithelium. + A ciliated cell of the endometrial glandular epithelium. This cell is characterized by the presence of motile cilia on its apical surface. doi:10.1038/s41591-020-1040-z @@ -115144,21 +115280,21 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion. https://orcid.org/0000-0002-1425-877X 2023-10-13T11:22:42Z UB cell ureteric bud cell - + - + PMID:9374839 @@ -115321,12 +115457,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An epithelial cell of the urethra that has an expression profile similar to lung club cells. Club-like cells of the urethra epithelium are similar to lung club cells in their expression of SCGB1A1 and in their enrichment of immunomodulatory programs. The term "club-like" is used to disambiguate from club cells which CL defines as a type of bronchial epithelial cell. This seems to reflect common usage of club cell when used without location (club cell seems to mean bronchial club cell, unless it is proceded or preceded by something that says it is not bronchial). In the literature, the name "club-like" isn't used. - club cell of the urethra epithelium club-like cell of the prostatic urethra epithelium prostate club cell - Club cells typically refer to bronchiolar exocrine cells found in the lungs. This cell type is given the name club cell due to their similarity to club cells in the lungs. club-like cell of the urethral epithelium @@ -117845,8 +117979,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - @@ -118085,7 +118217,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - @@ -118142,7 +118273,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - @@ -118404,6 +118534,712 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) B cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating B cell + cycling B cell + + + + + A(n) B cell that is cycling. + PMID:31348891 + + + + + proliferating B cell + PMID:31348891 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) T cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating T cell + cycling T cell + + + + + A(n) T cell that is cycling. + PMID:37291214 + + + + + proliferating T cell + PMID:37291214 + + + + + + + + + + + + + + + + + + + + + + + + + A(n) dendritic cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating dendritic cell + cycling dendritic cell + + + + + A(n) dendritic cell that is cycling. + PMID:32066951 + + + + + proliferating dendritic cell + PMID:32066951 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) natural killer cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating natural killer cell + cycling natural killer cell + + + + + A(n) natural killer cell that is cycling. + PMID:34062119 + + + + + proliferating natural killer cell + PMID:34062119 + + + + + + + + + + + + + + + + + + + + + + + + + A(n) gamma-delta T cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating gamma-delta T cell + cycling gamma-delta T cell + + + + + A(n) gamma-delta T cell that is cycling. + PMID:32066951 + + + + + proliferating gamma-delta T cell + PMID:32066951 + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) monocyte that is cycling. + + 2024-07-02T09:14:23Z + proliferating monocyte + cycling monocyte + + + + + A(n) monocyte that is cycling. + PMID:31348891 + + + + + proliferating monocyte + PMID:31348891 + + + + + + + + + + + + + + + + + + + + + + + + + A(n) CD8-positive, alpha-beta T cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating CD8-positive, alpha-beta T cell + cycling CD8-positive, alpha-beta T cell + + + + + A(n) CD8-positive, alpha-beta T cell that is cycling. + PMID:34062119 + + + + + proliferating CD8-positive, alpha-beta T cell + PMID:34062119 + + + + + + + + + + + + + + + + + + + + + + + + + A(n) CD4-positive, alpha-beta T cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating CD4-positive, alpha-beta T cell + cycling CD4-positive, alpha-beta T cell + + + + + A(n) CD4-positive, alpha-beta T cell that is cycling. + PMID:34062119 + + + + + proliferating CD4-positive, alpha-beta T cell + PMID:34062119 + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) macrophage that is cycling. + + 2024-07-02T09:14:23Z + proliferating macrophage + cycling macrophage + + + + + A(n) macrophage that is cycling. + PMID:33208946 + + + + + proliferating macrophage + PMID:33208946 + + + + + + + + + + + + + + + + + + + + + + + + + A(n) alveolar macrophage that is cycling. + + 2024-07-02T09:14:23Z + proliferating alveolar macrophage + cycling alveolar macrophage + + + + + A(n) alveolar macrophage that is cycling. + PMID:37291214 + + + + + proliferating alveolar macrophage + PMID:37291214 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) mononuclear phagocyte that is cycling. + + 2024-07-02T09:14:23Z + proliferating mononuclear phagocyte + cycling mononuclear phagocyte + + + + + A(n) mononuclear phagocyte that is cycling. + PMID:37468583 + + + + + proliferating mononuclear phagocyte + PMID:37468583 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) endothelial cell of lymphatic vessel that is cycling. + + 2024-07-02T09:14:23Z + proliferating endothelial cell of lymphatic vessel + cycling endothelial cell of lymphatic vessel + + + + + A(n) endothelial cell of lymphatic vessel that is cycling. + PMID:37291214 + + + + + proliferating endothelial cell of lymphatic vessel + PMID:37291214 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) pulmonary alveolar type 2 cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating pulmonary alveolar type 2 cell + cycling pulmonary alveolar type 2 cell + + + + + A(n) pulmonary alveolar type 2 cell that is cycling. + PMID:37291214 + + + + + proliferating pulmonary alveolar type 2 cell + PMID:37291214 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) myeloid cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating myeloid cell + cycling myeloid cell + + + + + A(n) myeloid cell that is cycling. + PMID:38301653 + + + + + proliferating myeloid cell + PMID:38301653 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) basal cell that is cycling. + + 2024-07-02T09:14:23Z + proliferating basal cell + cycling basal cell + + + + + A(n) basal cell that is cycling. + PMID:33208946 + + + + + proliferating basal cell + PMID:33208946 + + + + @@ -119257,6 +120093,414 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + A VIP GABAergic cortical interneuron with a soma located in L1-3 of some neocortex in Mmus. This neuron has a multipolar morphology with spiny dendrites concentrating on L1 of the cortex, and has a burst firing electrophysiological signature with highly dynamic dendritic spines. + + 2024-07-11T12:09:53Z + superficial VIP-positive spiny neuron + multipolar VIP neuron + spiny VIP neuron + + + + + A VIP GABAergic cortical interneuron with a soma located in L1-3 of some neocortex in Mmus. This neuron has a multipolar morphology with spiny dendrites concentrating on L1 of the cortex, and has a burst firing electrophysiological signature with highly dynamic dendritic spines. + PMID:35418660 + + + + + superficial VIP-positive spiny neuron + PMID:35418660 + + + + + multipolar VIP neuron + PMID:35418660 + + + + + + + + + + + + + + + + + + + + A VIP GABAergic cortical interneuron expressing vasoactive intestinal polypeptide and choline acetyltransferase in the Mmus neocortex. This interneuron releases both γ-aminobutyric acid and acetylcholine. + + 2024-07-11T12:22:48Z + VIP+/ChAT+ interneuron + VIP/ChAT interneuron + VChI + VIP+/ChAT+ cell + Work in the mouse barrel cortex and somatosensory cortex shows that a VIP-ChAT interneuron is predominantely located in L2/3 and more rarely in the deeper layers of the cortex (Dudai et al., 2021; Dudai et al., 2020). This neuronal type could be transcriptomically distinct as transcriptomic studies have identified VIP neurons expressing ChAT in a whole brain mouse transcriptomic study (Tasic et al., 2018). + VIP-ChAT interneuron + + + + + A VIP GABAergic cortical interneuron expressing vasoactive intestinal polypeptide and choline acetyltransferase in the Mmus neocortex. This interneuron releases both γ-aminobutyric acid and acetylcholine. + PMID:30382198 + PMID:31754098 + PMID:32027647 + PMID:33301603 + + + + + VIP+/ChAT+ interneuron + PMID:33301603 + + + + + VIP/ChAT interneuron + PMID:32027647 + + + + + VChI + PMID:32027647 + + + + + + VIP+/ChAT+ cell + PMID:33301603 + + + + + Work in the mouse barrel cortex and somatosensory cortex shows that a VIP-ChAT interneuron is predominantely located in L2/3 and more rarely in the deeper layers of the cortex (Dudai et al., 2021; Dudai et al., 2020). This neuronal type could be transcriptomically distinct as transcriptomic studies have identified VIP neurons expressing ChAT in a whole brain mouse transcriptomic study (Tasic et al., 2018). + PMID:30382198 + PMID:32027647 + PMID:33301603 + + + + + + + + + + + + + + + + + + + + + + A serous secreting cell that is part of a submucosal gland in the nasal cavity respiratory epithelium. + + 2024-07-12T10:58:06Z + https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ + nasal mucous secretory cell + nasal serous secreting cell + + + + + A serous secreting cell that is part of a submucosal gland in the nasal cavity respiratory epithelium. + PMID:37291214 + + + + + nasal mucous secretory cell + PMID:11005715 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) stromal cell that is cycling. + + 2024-07-19T09:14:23Z + proliferating stromal cell + cycling stromal cell + + + + + A(n) stromal cell that is cycling. + PMID:34497389 + + + + + proliferating stromal cell + PMID:34497389 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) glial cell that is cycling. + + 2024-07-19T09:14:23Z + proliferating glial cell + cycling glial cell + + + + + A(n) glial cell that is cycling. + PMID:34497389 + + + + + proliferating glial cell + PMID:34497389 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) plasma cell that is cycling. + + 2024-07-19T09:14:23Z + proliferating plasma cell + cycling plasma cell + + + + + A(n) plasma cell that is cycling. + PMID:34497389 + + + + + proliferating plasma cell + PMID:34497389 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) type EC enteroendocrine cell that is cycling. + + 2024-07-19T09:14:23Z + proliferating type EC enteroendocrine cell + cycling type EC enteroendocrine cell + + + + + A(n) type EC enteroendocrine cell that is cycling. + PMID:34497389 + + + + + proliferating type EC enteroendocrine cell + PMID:34497389 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A(n) neuroblast (sensu Vertebrata) that is cycling. + + 2024-07-19T09:14:23Z + proliferating neuroblast (sensu Vertebrata) + cycling neuroblast (sensu Vertebrata) + + + + + A(n) neuroblast (sensu Vertebrata) that is cycling. + PMID:34497389 + + + + + proliferating neuroblast (sensu Vertebrata) + PMID:34497389 + + + + @@ -119938,6 +121182,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -120124,6 +121374,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -120334,6 +121590,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -121036,6 +122298,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -121336,6 +122610,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -123208,12 +124488,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -123298,12 +124572,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -123658,12 +124926,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -125506,6 +126768,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -126094,12 +127362,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -126388,6 +127650,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -126784,6 +128052,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -126820,6 +128094,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -127180,6 +128466,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + - + @@ -46320,7 +46315,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -46336,7 +46331,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -46418,7 +46413,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -46426,7 +46421,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -46439,7 +46434,7 @@ plexiform layer. - + Obol @@ -46514,7 +46509,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46522,7 +46517,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -46535,7 +46530,7 @@ plexiform layer. - + AEO @@ -46774,7 +46769,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -46784,14 +46779,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -46819,7 +46814,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46836,14 +46831,14 @@ plexiform layer. vascular system - + - + MA @@ -46964,7 +46959,7 @@ plexiform layer. - + @@ -46981,14 +46976,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47084,7 +47079,7 @@ plexiform layer. - + @@ -47100,14 +47095,14 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + ZFA @@ -47140,14 +47135,14 @@ plexiform layer. - + - + @@ -47172,24 +47167,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -47235,7 +47230,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47243,14 +47238,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47273,7 +47268,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47283,14 +47278,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -47346,14 +47341,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -47366,7 +47361,7 @@ plexiform layer. - + EHDAA2 @@ -47507,7 +47502,7 @@ plexiform layer. - + @@ -47530,14 +47525,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -47578,8 +47573,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -47593,11 +47588,11 @@ plexiform layer. midbrain basal plate - + - + @@ -47610,13 +47605,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -47645,7 +47640,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -47654,14 +47649,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -47908,10 +47903,10 @@ plexiform layer. UBERON:0010427 ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png - https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/eye-female-left/v1.3/assets/3d-vh-f-eye-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/eye-female-right/v1.3/assets/3d-vh-f-eye-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/eye-male-left/v1.3/assets/3d-vh-m-eye-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/eye-male-right/v1.3/assets/3d-vh-m-eye-r.glb @@ -47964,8 +47959,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -47977,11 +47972,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -47994,13 +47989,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -48061,7 +48056,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48071,7 +48066,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48084,7 +48079,7 @@ plexiform layer. - + cjm @@ -48206,7 +48201,7 @@ plexiform layer. - + AAO:0010038 EMAPA:18808 FMA:49150 @@ -48216,14 +48211,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -48485,7 +48480,7 @@ plexiform layer. - + @@ -48527,7 +48522,7 @@ plexiform layer. anterior uvea - + @@ -48540,7 +48535,7 @@ plexiform layer. - + MP @@ -49333,7 +49328,7 @@ plexiform layer. - + @@ -49356,7 +49351,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -49369,7 +49364,7 @@ plexiform layer. - + AEO diff --git a/src/ontology/subsets/eye_upper_slim.tsv b/src/ontology/subsets/eye_upper_slim.tsv index f6a93c692..af5171f4d 100644 --- a/src/ontology/subsets/eye_upper_slim.tsv +++ b/src/ontology/subsets/eye_upper_slim.tsv @@ -1,315 +1,315 @@ ?x ?label -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1001 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1016 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1022 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1031 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1037 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1043 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1051 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1058 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1065 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1074 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1088 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+_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid760 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid779 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid795 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid802 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid813 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid819 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid836 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid842 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid851 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid861 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid909 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid959 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid969 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid976 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid983 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "cell" "neural crest derived fibroblast" "neuronal receptor cell" diff --git a/src/ontology/subsets/general_cell_types_upper_slim.json b/src/ontology/subsets/general_cell_types_upper_slim.json index a7dcbb071..31ba38f2e 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.json +++ b/src/ontology/subsets/general_cell_types_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-07-10" + "val" : "2024-08-16" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", diff --git a/src/ontology/subsets/general_cell_types_upper_slim.obo b/src/ontology/subsets/general_cell_types_upper_slim.obo index ce6d8abd7..90957720c 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.obo +++ b/src/ontology/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-07-10/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2024-08-16/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -95,7 +95,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-07-10" xsd:string +property_value: owl:versionInfo "2024-08-16" xsd:string [Term] id: CL:0000000 diff --git a/src/ontology/subsets/general_cell_types_upper_slim.owl b/src/ontology/subsets/general_cell_types_upper_slim.owl index 4354de63c..0df0a51ec 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.owl +++ b/src/ontology/subsets/general_cell_types_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-07-10 + + 2024-08-16 diff --git a/src/ontology/subsets/general_cell_types_upper_slim.tsv b/src/ontology/subsets/general_cell_types_upper_slim.tsv index e12af28b8..36fc6b05d 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.tsv +++ b/src/ontology/subsets/general_cell_types_upper_slim.tsv @@ -1,279 +1,279 @@ ?x ?label -_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid1005 -_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid1012 -_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid1018 -_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid1059 -_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid1074 -_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid1080 -_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid1091 -_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid1098 -_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid1105 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--- a/src/ontology/subsets/kidney_upper_slim.json +++ b/src/ontology/subsets/kidney_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-07-10" + "val" : "2024-08-16" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/kidney_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -1801,6 +1801,34 @@ "val" : "2010-08-24T02:06:40Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0002144", + "lbl" : "capillary endothelial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An endothelial cell found in capillaries.", + "xrefs" : [ "GOC:tfm" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "BTO:0004956" + }, { + "val" : "CALOHA:TS-0112" + }, { + "val" : "FMA:67756" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-08-24T10:15:00Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002173", "lbl" : "extraglomerular mesangial cell", @@ -1839,9 +1867,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate.", + "val" : "An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate.", "xrefs" : [ "GOC:tfm", "PMID:15840009" ] }, + "comments" : [ "Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes." ], "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], "xrefs" : [ { "val" : "BTO:0004632" @@ -2085,6 +2114,23 @@ "val" : "KUPO:0001016" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0002653", + "lbl" : "squamous endothelial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A squamous shaped endothelial cell.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-07-08T03:31:25Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002681", "lbl" : "kidney cortical cell", @@ -2663,8 +2709,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any kidney blood vessel cell that is part of some kidney capillary.", - "xrefs" : [ "FBC:Autogenerated" ] + "val" : "An endothelial cell that is part of the capillary of the kidney." }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], "xrefs" : [ { @@ -2759,6 +2804,23 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_2000008", + "lbl" : "microvascular endothelial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any blood vessel endothelial cell that is part of a microvascular endothelium.", + "xrefs" : [ "GOC:TermGenie" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://www.wikidata.org/entity/Q35563349" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-06-04T15:07:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_4030031", "lbl" : "interstitial cell", @@ -6561,6 +6623,35 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0036053", + "lbl" : "glomerular endothelium fenestra", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes.", + "xrefs" : [ "GOC:cjm", "MP:0011454", "PMID:19129259" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "GEnC fenestration", + "xrefs" : [ "PMID:19129259" ] + }, { + "pred" : "hasExactSynonym", + "val" : "glomerular endothelial cell fenestration", + "xrefs" : [ "PMID:19129259" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "bf" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-12-12T10:53:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0040011", "lbl" : "locomotion", @@ -7192,6 +7283,33 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0046930", + "lbl" : "pore complex", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "pore" + }, { + "pred" : "hasRelatedSynonym", + "val" : "channel-forming toxin activity" + }, { + "pred" : "hasRelatedSynonym", + "val" : "pore-forming toxin activity" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/20452" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0048103", "lbl" : "somatic stem cell division", @@ -8725,6 +8843,21 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0098796", + "lbl" : "membrane protein complex", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any protein complex that is part of a membrane.", + "xrefs" : [ "GOC:dos" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_metagenomics" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0098801", "lbl" : "regulation of renal system process", @@ -14067,16 +14200,16 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" @@ -16017,13 +16150,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" } ] } }, { @@ -17384,10 +17514,10 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" } ] } }, { @@ -17506,16 +17636,16 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" @@ -17993,10 +18123,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-female/v1.2/assets/3d-vh-f-urinary-bladder.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" @@ -18987,6 +19117,55 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001915", + "lbl" : "endothelium of capillary", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An endothelium that is part of a capillary [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blood capillary endothelium", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "capillary endothelium" + }, { + "pred" : "hasExactSynonym", + "val" : "capillary vessel endothelium", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "endothelium of blood capillary", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "endothelium of capillary vessel", + "xrefs" : [ "OBOL:automatic" ] + } ], + "xrefs" : [ { + "val" : "BTO:0004954" + }, { + "val" : "CALOHA:TS-0112" + }, { + "val" : "EMAPA:36292" + }, { + "val" : "FMA:62114" + }, { + "val" : "MA:0000711" + }, { + "val" : "NCIT:C49215" + }, { + "val" : "UMLS:C0006904" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0001969", "lbl" : "blood plasma", @@ -19589,10 +19768,10 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" } ] } }, { @@ -22502,10 +22681,10 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" @@ -23239,16 +23418,16 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" @@ -23689,10 +23868,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" } ] } }, { @@ -26997,6 +27176,22 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0008339", + "lbl" : "microvascular endothelium", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "BTO:0003122" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2186" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0008987", "lbl" : "renal parenchyma", @@ -34482,6 +34677,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002139", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000115" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002144", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0002653" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002144", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_2000008" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002144", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001915" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002173", "pred" : "is_a", @@ -34516,6 +34723,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000074" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002188", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0036053" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002242", "pred" : "is_a", @@ -34634,6 +34845,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002653", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000115" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002681", "pred" : "is_a", @@ -35001,7 +35216,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000892", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000071" + "obj" : "http://purl.obolibrary.org/obo/CL_0002144" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000892", "pred" : "is_a", @@ -35092,6 +35307,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_1001318", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1000500" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_2000008", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000071" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_2000008", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0008339" }, { "sub" : "http://purl.obolibrary.org/obo/CL_4030031", "pred" : "is_a", @@ -36274,6 +36497,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0035592", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0071692" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0036053", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0046930" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0040011", "pred" : "is_a", @@ -36450,6 +36677,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0046903", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0006810" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0046930", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0098796" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0048103", "pred" : "is_a", @@ -36966,6 +37197,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098794", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0045202" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098796", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098796", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0016020" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098801", "pred" : "is_a", @@ -39381,7 +39620,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "pred" : "http://purl.obolibrary.org/obo/RO_0002131", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006542", "meta" : { "basicPropertyValues" : [ { @@ -39389,6 +39628,10 @@ "val" : "MA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", + "pred" : "http://purl.obolibrary.org/obo/RO_0002131", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006853" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", "pred" : "http://purl.obolibrary.org/obo/RO_0002150", @@ -39591,6 +39834,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001851", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001915", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0008339" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001915", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001982" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -42786,6 +43037,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0007832", "pred" : "http://purl.obolibrary.org/obo/RO_0002576", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001271" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0008339", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004638" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0008339", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_8410081" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0008987", "pred" : "is_a", @@ -45411,6 +45670,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002202", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000222" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0002144", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000071" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001915" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0002173", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0002320" ], @@ -45679,7 +45945,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_1000892", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_1000854" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0003527" @@ -45726,6 +45992,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0005215" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_2000008", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000071" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0008339" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_4030031", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], @@ -46380,6 +46653,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005604" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098796", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098801", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -46689,6 +46969,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0013756" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0001915", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001986" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001982" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0001969", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ], @@ -47364,6 +47651,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002576", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001271" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0008339", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001986" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_8410081" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0008987", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000353" ], diff --git a/src/ontology/subsets/kidney_upper_slim.obo b/src/ontology/subsets/kidney_upper_slim.obo index 3f10ccd90..467009d20 100644 --- a/src/ontology/subsets/kidney_upper_slim.obo +++ b/src/ontology/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-07-10/subsets/kidney_upper_slim.owl +data-version: cl/releases/2024-08-16/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -95,7 +95,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-07-10" xsd:string +property_value: owl:versionInfo "2024-08-16" xsd:string [Term] id: CL:0000000 @@ -1321,6 +1321,24 @@ is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z +[Term] +id: CL:0002144 +name: capillary endothelial cell +def: "An endothelial cell found in capillaries." [GOC:tfm] +subset: cellxgene_subset +subset: human_reference_atlas +xref: BTO:0004956 +xref: CALOHA:TS-0112 +xref: FMA:67756 +is_a: CL:0002653 ! squamous endothelial cell +is_a: CL:2000008 ! microvascular endothelial cell +intersection_of: CL:0000071 ! blood vessel endothelial cell +intersection_of: part_of UBERON:0001915 ! endothelium of capillary +relationship: part_of UBERON:0001915 ! endothelium of capillary +property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +creation_date: 2010-08-24T10:15:00Z + [Term] id: CL:0002173 name: extraglomerular mesangial cell @@ -1342,7 +1360,8 @@ creation_date: 2010-08-25T02:20:55Z [Term] id: CL:0002188 name: glomerular endothelial cell -def: "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." [GOC:tfm, PMID:15840009] +def: "An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." [GOC:tfm, PMID:15840009] +comment: Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. {xref="PMID:33123011", xref="PMID:18480313", xref="PMID:19129259"} subset: cellxgene_subset subset: kidney_upper_slim xref: BTO:0004632 @@ -1351,6 +1370,7 @@ is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus +relationship: has_part GO:0036053 ! glomerular endothelium fenestra relationship: part_of UBERON:0000074 ! renal glomerulus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T10:59:44Z @@ -1494,6 +1514,14 @@ is_a: CL:0002681 {is_inferred="true"} ! kidney cortical cell intersection_of: CL:0002518 ! kidney epithelial cell intersection_of: part_of UBERON:0001225 ! cortex of kidney +[Term] +id: CL:0002653 +name: squamous endothelial cell +def: "A squamous shaped endothelial cell." [GOC:dos] +is_a: CL:0000115 ! endothelial cell +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +creation_date: 2011-07-08T03:31:25Z + [Term] id: CL:0002681 name: kidney cortical cell @@ -1910,13 +1938,13 @@ relationship: part_of UBERON:0003644 ! kidney arterial blood vessel [Term] id: CL:1000892 name: kidney capillary endothelial cell -def: "Any kidney blood vessel cell that is part of some kidney capillary." [FBC:Autogenerated] +def: "An endothelial cell that is part of the capillary of the kidney." [] subset: cellxgene_subset subset: kidney_upper_slim xref: KUPO:0001030 -is_a: CL:0000071 ! blood vessel endothelial cell +is_a: CL:0002144 ! capillary endothelial cell is_a: CL:1000854 ! kidney blood vessel cell -intersection_of: CL:1000854 ! kidney blood vessel cell +intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003527 ! kidney capillary relationship: part_of UBERON:0003527 ! kidney capillary @@ -1991,6 +2019,17 @@ intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0005215 ! kidney interstitium property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: CL:2000008 +name: microvascular endothelial cell +def: "Any blood vessel endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] +is_a: CL:0000071 ! blood vessel endothelial cell +intersection_of: CL:0000071 ! blood vessel endothelial cell +intersection_of: part_of UBERON:0008339 ! microvascular endothelium +relationship: part_of UBERON:0008339 ! microvascular endothelium +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 +creation_date: 2014-06-04T15:07:42Z + [Term] id: CL:4030031 name: interstitial cell @@ -4118,6 +4157,17 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region created_by: bf creation_date: 2010-11-09T10:25:08Z +[Term] +id: GO:0036053 +name: glomerular endothelium fenestra +namespace: cellular_component +def: "A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes." [GOC:cjm, MP:0011454, PMID:19129259] +synonym: "GEnC fenestration" EXACT [PMID:19129259] +synonym: "glomerular endothelial cell fenestration" EXACT [PMID:19129259] +is_a: GO:0046930 ! pore complex +created_by: bf +creation_date: 2011-12-12T10:53:24Z + [Term] id: GO:0040011 name: locomotion @@ -4461,6 +4511,17 @@ def: "The controlled release of a substance by a cell or a tissue." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport +[Term] +id: GO:0046930 +name: pore complex +namespace: cellular_component +def: "A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids." [ISBN:0198506732] +synonym: "channel-forming toxin activity" RELATED [] +synonym: "pore" EXACT [] +synonym: "pore-forming toxin activity" RELATED [] +is_a: GO:0098796 ! membrane protein complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20452" xsd:anyURI + [Term] id: GO:0048103 name: somatic stem cell division @@ -5293,6 +5354,17 @@ is_a: GO:0110165 ! cellular anatomical entity relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse +[Term] +id: GO:0098796 +name: membrane protein complex +namespace: cellular_component +def: "Any protein complex that is part of a membrane." [GOC:dos] +subset: goslim_metagenomics +is_a: GO:0032991 ! protein-containing complex +intersection_of: GO:0032991 ! protein-containing complex +intersection_of: part_of GO:0016020 ! membrane +relationship: part_of GO:0016020 ! membrane + [Term] id: GO:0098801 name: regulation of renal system process @@ -7838,10 +7910,10 @@ relationship: capable_of_part_of GO:0070295 ! renal water absorption relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -8802,9 +8874,8 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -9535,8 +9606,8 @@ intersection_of: RO:0002179 UBERON:0002113 ! drains kidney relationship: RO:0002179 UBERON:0002113 ! drains kidney relationship: RO:0002376 UBERON:0001072 ! tributary of inferior vena cava property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -9604,10 +9675,10 @@ intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -9843,8 +9914,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018707 {source="BTO"} ! bladder organ relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-female/v1.2/assets/3d-vh-f-urinary-bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -10029,9 +10100,10 @@ xref: Wikipedia:Proximal_straight_tubule xref: ZFA:0005291 is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0009035 {source="MA"} ! renal straight tubule +relationship: overlaps UBERON:0006542 {source="MA"} ! outer medulla outer stripe loop of Henle +relationship: overlaps UBERON:0006853 ! renal cortex tubule relationship: part_of UBERON:0001289 {source="MA"} ! descending limb of loop of Henle relationship: part_of UBERON:0004134 ! proximal tubule -relationship: part_of UBERON:0006542 {source="MA"} ! outer medulla outer stripe loop of Henle relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule relationship: RO:0002150 UBERON:0005096 ! continuous with descending thin limb property_value: IAO:0000116 "TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)" xsd:string @@ -10372,6 +10444,28 @@ xref: Wikipedia:Cortex_(anatomy) is_a: UBERON:0000064 ! organ part relationship: bounding_layer_of UBERON:0000062 ! organ +[Term] +id: UBERON:0001915 +name: endothelium of capillary +namespace: uberon +def: "An endothelium that is part of a capillary [Automatically generated definition]." [OBOL:automatic] +synonym: "blood capillary endothelium" EXACT [OBOL:automatic] +synonym: "capillary endothelium" EXACT [] +synonym: "capillary vessel endothelium" EXACT [OBOL:automatic] +synonym: "endothelium of blood capillary" EXACT [OBOL:automatic] +synonym: "endothelium of capillary vessel" EXACT [OBOL:automatic] +xref: BTO:0004954 +xref: CALOHA:TS-0112 +xref: EMAPA:36292 +xref: FMA:62114 +xref: MA:0000711 +xref: NCIT:C49215 +xref: UMLS:C0006904 {source="ncithesaurus:Capillary_Endothelium"} +is_a: UBERON:0008339 ! microvascular endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0001982 ! capillary +relationship: part_of UBERON:0001982 ! capillary + [Term] id: UBERON:0001969 name: blood plasma @@ -10707,8 +10801,8 @@ is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035554 ! right cardiac chamber relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -12226,8 +12320,8 @@ xref: Wikipedia:Venae_cavae is_a: UBERON:0003479 ! thoracic cavity vein is_a: UBERON:0013768 ! great vessel of heart property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI [Term] @@ -12569,10 +12663,10 @@ xref: Wikipedia:Renal_pyramids is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000362 ! renal medulla relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -12798,8 +12892,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -14551,6 +14645,17 @@ relationship: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI property_value: IAO:0000116 "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string +[Term] +id: UBERON:0008339 +name: microvascular endothelium +namespace: uberon +xref: BTO:0003122 +is_a: UBERON:0004638 ! blood vessel endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:8410081 ! blood microvessel +relationship: part_of UBERON:8410081 ! blood microvessel +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string + [Term] id: UBERON:0008987 name: renal parenchyma diff --git a/src/ontology/subsets/kidney_upper_slim.owl b/src/ontology/subsets/kidney_upper_slim.owl index 06b276c12..68c9d4c93 100644 --- a/src/ontology/subsets/kidney_upper_slim.owl +++ b/src/ontology/subsets/kidney_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-07-10 + + 2024-08-16 @@ -8869,6 +8869,48 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + An endothelial cell found in capillaries. + + + 2010-08-24T10:15:00Z + BTO:0004956 + CALOHA:TS-0112 + FMA:67756 + + + capillary endothelial cell + + + + + An endothelial cell found in capillaries. + GOC:tfm + + + + @@ -8941,22 +8983,37 @@ Each of these 3 primitives can be composed to yield a cross-product of different - An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. + + + + + + + An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. 2010-08-26T10:59:44Z BTO:0004632 FMA:70970 + Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. glomerular endothelial cell - An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. + An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. GOC:tfm PMID:15840009 + + + + Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. + PMID:18480313 + PMID:19129259 + PMID:33123011 + @@ -9360,6 +9417,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A squamous shaped endothelial cell. + + 2011-07-08T03:31:25Z + squamous endothelial cell + + + + + A squamous shaped endothelial cell. + GOC:dos + + + + @@ -10608,7 +10683,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10616,7 +10691,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10624,18 +10699,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any kidney blood vessel cell that is part of some kidney capillary. + An endothelial cell that is part of the capillary of the kidney. KUPO:0001030 kidney capillary endothelial cell - - - - Any kidney blood vessel cell that is part of some kidney capillary. - FBC:Autogenerated - @@ -10867,6 +10936,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + Any blood vessel endothelial cell that is part of a microvascular endothelium. + + 2014-06-04T15:07:42Z + CL:2000008 + microvascular endothelial cell + + + + + Any blood vessel endothelial cell that is part of a microvascular endothelium. + GOC:TermGenie + + + + @@ -12162,32 +12267,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -16301,6 +16406,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes. + bf + 2011-12-12T10:53:24Z + GEnC fenestration + glomerular endothelial cell fenestration + cellular_component + GO:0036053 + glomerular endothelium fenestra + + + + + A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes. + GOC:cjm + MP:0011454 + PMID:19129259 + + + + + GEnC fenestration + PMID:19129259 + + + + + glomerular endothelial cell fenestration + PMID:19129259 + + + + @@ -17147,6 +17288,28 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids. + https://github.com/geneontology/go-ontology/issues/20452 + pore + cellular_component + channel-forming toxin activity + pore-forming toxin activity + GO:0046930 + pore complex + + + + + A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids. + ISBN:0198506732 + + + + @@ -19428,6 +19591,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + Any protein complex that is part of a membrane. + cellular_component + GO:0098796 + + membrane protein complex + + + + + Any protein complex that is part of a membrane. + GOC:dos + + + + @@ -23181,7 +23380,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23235,14 +23434,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -23292,7 +23491,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23340,14 +23539,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - + - + Wikipedia @@ -23854,7 +24053,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23904,14 +24103,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -24174,14 +24373,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -24213,24 +24412,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different metanephros - + - + - + GO - + ISBN:9780878932504 @@ -24345,8 +24544,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. BTO:0001646 EHDAA2:0002140 @@ -24370,11 +24569,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureteric bud - + - + @@ -24387,13 +24586,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 - + ISBN:9780878932504 @@ -24774,7 +24973,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -24810,14 +25009,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -25077,8 +25276,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -25104,24 +25303,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -25162,8 +25361,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -25181,24 +25380,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -25221,7 +25420,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25260,14 +25459,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -25549,15 +25748,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -25594,34 +25793,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -25880,10 +26079,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Note that 'renal medulla' is not synonymous with 'medullary region of kidney'. The former is composed of kidney pyramids only, while the latter covers kidney pyramids and renal columns, which are histologically different. renal medulla - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg @@ -26963,7 +27162,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27005,14 +27204,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27370,7 +27569,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27405,14 +27604,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different abdomen - + - + MA @@ -27641,7 +27840,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27676,14 +27875,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27723,7 +27922,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27758,14 +27957,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -27806,7 +28005,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -27847,14 +28046,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28020,7 +28219,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28063,7 +28262,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -28076,7 +28275,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -28138,7 +28337,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28206,18 +28405,17 @@ Each of these 3 primitives can be composed to yield a cross-product of different Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart - https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -29071,7 +29269,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29121,14 +29319,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29194,7 +29392,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29239,7 +29437,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -29253,7 +29451,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -29450,7 +29648,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29484,14 +29682,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -29938,8 +30136,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb @@ -29982,14 +30180,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -30041,24 +30239,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -30104,7 +30302,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30134,20 +30332,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different cortex of kidney - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -30183,7 +30381,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30228,14 +30426,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -30309,7 +30507,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30351,14 +30549,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -30448,10 +30646,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -30495,7 +30693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron tubule - + @@ -30504,14 +30702,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + GO MA ZFA @@ -30525,7 +30723,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -30739,7 +30937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30782,11 +30980,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different urinary bladder - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-female/v1.2/assets/3d-vh-f-urinary-bladder.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + @@ -30799,7 +30997,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -30929,7 +31127,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30942,7 +31140,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. @@ -30973,24 +31171,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + - + FMA - + Bgee:AN @@ -31041,14 +31239,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -31084,11 +31282,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + @@ -31101,13 +31299,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GO - + Wikipedia @@ -31239,7 +31437,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31266,7 +31464,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -31279,7 +31477,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -31303,14 +31501,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + + + + + + + @@ -31349,12 +31553,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal straight tubule - + - - + + @@ -31366,13 +31570,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + MA - + MA @@ -31414,7 +31618,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31450,7 +31654,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -31463,7 +31667,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EMAPA GO MA-modified-from-isa @@ -31738,7 +31942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31761,14 +31965,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -31809,7 +32013,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -31846,14 +32050,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -32228,6 +32432,83 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a capillary [Automatically generated definition]. + BTO:0004954 + CALOHA:TS-0112 + EMAPA:36292 + FMA:62114 + MA:0000711 + NCIT:C49215 + UMLS:C0006904 + blood capillary endothelium + capillary endothelium + capillary vessel endothelium + endothelium of blood capillary + endothelium of capillary vessel + uberon + UBERON:0001915 + endothelium of capillary + + + + + An endothelium that is part of a capillary [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C0006904 + ncithesaurus:Capillary_Endothelium + + + + + blood capillary endothelium + OBOL:automatic + + + + + capillary vessel endothelium + OBOL:automatic + + + + + endothelium of blood capillary + OBOL:automatic + + + + + endothelium of capillary vessel + OBOL:automatic + + + + @@ -32489,8 +32770,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -32503,7 +32784,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32557,34 +32838,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -33067,8 +33348,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different right cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb @@ -33441,7 +33722,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33493,14 +33774,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney - + - + FMA @@ -33535,8 +33816,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -33574,11 +33855,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -33591,13 +33872,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + ZFA @@ -33924,7 +34205,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33943,7 +34224,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -33965,24 +34246,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different juxtaglomerular apparatus - + - + - + MA - + GO @@ -34106,8 +34387,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -34124,24 +34405,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -34283,9 +34564,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -34333,15 +34614,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -34360,19 +34641,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34412,8 +34693,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -34451,11 +34732,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -34468,13 +34749,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -34534,8 +34815,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. BTO:0003940 @@ -34553,24 +34834,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different macula densa - + - + - + MA - + GO @@ -34595,22 +34876,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -34643,45 +34924,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -35045,7 +35326,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35098,14 +35379,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -35323,7 +35604,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -35346,14 +35627,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -35394,8 +35675,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. AAO:0011088 NCIT:C34279 @@ -35414,11 +35695,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -35431,13 +35712,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Wikipedia - + XAO @@ -35543,9 +35824,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -35584,34 +35865,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -35720,7 +36001,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct @@ -35749,7 +36030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -35762,7 +36043,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -35816,9 +36097,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -35847,34 +36128,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -35914,7 +36195,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -35940,7 +36221,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -35953,7 +36234,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -36000,7 +36281,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36040,7 +36321,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36053,7 +36334,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -36103,15 +36384,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -36128,15 +36409,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -36149,19 +36430,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -36190,8 +36471,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -36215,11 +36496,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -36238,13 +36519,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -36489,7 +36770,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36515,14 +36796,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -37210,7 +37491,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -37225,14 +37506,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -37456,8 +37737,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different vena cava http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png @@ -37812,8 +38093,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -37830,24 +38111,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal tubule - + - + - + GO - + GO @@ -37906,7 +38187,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -37916,14 +38197,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004136 intermediate tubule - + - + FMA @@ -37999,8 +38280,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -38012,24 +38293,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -38082,7 +38363,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -38101,14 +38382,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -38330,8 +38611,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -38341,24 +38622,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different comma-shaped body - + - + - + cjm - + ZFA @@ -38380,8 +38661,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 @@ -38393,24 +38674,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different S-shaped body - + - + - + cjm - + GO @@ -38479,10 +38760,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney pyramid - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png @@ -38822,7 +39103,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38860,14 +39141,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -39229,8 +39510,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004537 blood vasculature - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb @@ -39407,7 +39688,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39444,14 +39725,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -39811,7 +40092,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -39825,14 +40106,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -39859,7 +40140,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39898,14 +40179,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -40203,7 +40484,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40224,14 +40505,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -40297,9 +40578,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -40319,34 +40600,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -40821,7 +41102,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -40829,14 +41110,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005095 kidney rudiment - + - + GO @@ -40952,7 +41233,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -40970,14 +41251,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -41708,7 +41989,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -41724,14 +42005,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -41848,7 +42129,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -41866,14 +42147,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -41901,7 +42182,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41928,7 +42209,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different gonad primordium - + @@ -41941,7 +42222,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -42000,14 +42281,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 @@ -42025,24 +42306,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -42089,7 +42370,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42106,14 +42387,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular tuft - + - + Wikipedia @@ -42363,7 +42644,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42391,14 +42672,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -42483,7 +42764,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -42493,7 +42774,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -42512,7 +42793,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -42609,7 +42890,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42648,14 +42929,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -42689,7 +42970,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -42703,7 +42984,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -42716,7 +42997,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -42744,7 +43025,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -42761,14 +43042,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -43312,7 +43593,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -43322,14 +43603,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0006853 renal cortex tubule - + - + MA @@ -44001,7 +44282,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44027,7 +44308,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -44043,7 +44324,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -44204,7 +44485,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -44212,7 +44493,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -44225,7 +44506,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -44439,7 +44720,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -44456,14 +44737,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -44601,7 +44882,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44639,14 +44920,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -44684,6 +44965,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + BTO:0003122 + uberon + UBERON:0008339 + microvascular endothelium + https://github.com/obophenotype/uberon/issues/2186 + + + + @@ -44699,7 +45010,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -44710,7 +45021,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0008987 renal parenchyma - + @@ -44723,7 +45034,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -44793,7 +45104,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44810,14 +45121,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -44936,7 +45247,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -44944,14 +45255,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45050,7 +45361,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45060,14 +45371,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -45388,7 +45699,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45406,14 +45717,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010227 future cardiac atrium - + - + ZFA @@ -45556,7 +45867,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45570,7 +45881,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010377 mesenchyme from somatopleure - + @@ -45583,7 +45894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -45599,7 +45910,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -45609,14 +45920,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -45649,7 +45960,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45665,7 +45976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010532 primitive nephron - + @@ -45678,7 +45989,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -45694,7 +46005,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45705,7 +46016,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010536 nephron progenitor - + @@ -45718,7 +46029,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -45961,8 +46272,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -45974,11 +46285,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -45991,13 +46302,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -46058,7 +46369,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46068,7 +46379,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46081,7 +46392,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46105,7 +46416,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46130,14 +46441,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different upper urinary tract - + - + FMA @@ -46455,7 +46766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46470,14 +46781,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -46500,20 +46811,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -46523,20 +46834,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -46563,7 +46874,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46583,14 +46894,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeleton of pelvic complex - + - + FMA @@ -46642,7 +46953,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The precursor of the urethra. SCTID:361531004 Wikipedia:Urethral_groove @@ -46653,14 +46964,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -47231,7 +47542,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47254,7 +47565,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -47267,7 +47578,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -47678,7 +47989,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -47689,14 +48000,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis/ureter - + - + NCIT diff --git a/src/ontology/subsets/kidney_upper_slim.tsv b/src/ontology/subsets/kidney_upper_slim.tsv index 684848508..2bd85ec1d 100644 --- a/src/ontology/subsets/kidney_upper_slim.tsv +++ b/src/ontology/subsets/kidney_upper_slim.tsv @@ -1,332 +1,337 @@ ?x ?label -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1000 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1006 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1013 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1018 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1023 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1029 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1034 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1040 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1046 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1053 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+_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid842 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid848 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid855 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid863 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid869 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid876 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid883 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid889 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid898 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid904 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid913 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid921 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid934 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid946 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid952 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid958 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid964 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid970 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid976 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid982 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid989 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid997 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -400,6 +405,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "ecto-epithelial cell" "meso-epithelial cell" "endothelial cell of vascular tree" + "capillary endothelial cell" "extraglomerular mesangial cell" "glomerular endothelial cell" "nucleate cell" @@ -412,6 +418,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "kidney epithelial cell" "embryonic blood vessel endothelial progenitor cell" "renal cortical epithelial cell" + "squamous endothelial cell" "kidney cortical cell" "renal principal cell" "premigratory neural crest cell" @@ -455,6 +462,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "kidney loop of Henle descending limb epithelial cell" "kidney collecting duct cell" "renal interstitial pericyte" + "microvascular endothelial cell" "interstitial cell" "perivascular cell" "mitotic cell cycle" @@ -603,6 +611,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "tube morphogenesis" "tube development" "establishment of protein localization to extracellular region" + "glomerular endothelium fenestra" "locomotion" "embryonic cleavage" "fluid transport" @@ -630,6 +639,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "establishment of protein localization" "synapse" "secretion" + "pore complex" "somatic stem cell division" "organelle fission" "mesoderm morphogenesis" @@ -695,6 +705,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "basement membrane collagen trimer" "presynapse" "postsynapse" + "membrane protein complex" "regulation of renal system process" "anterograde trans-synaptic signaling" "supramolecular complex" @@ -945,6 +956,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "artery" "vein" "cortex" + "endothelium of capillary" "blood plasma" "venule" "arteriole" @@ -1139,6 +1151,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "vascular system" "appendage girdle region" "pelvic girdle skeleton" + "microvascular endothelium" "renal parenchyma" "renal straight tubule" "entire embryonic mesenchyme" diff --git a/subsets/blood_and_immune_upper_slim.json b/subsets/blood_and_immune_upper_slim.json index 7c2d36189..0f8e1a3e4 100644 --- a/subsets/blood_and_immune_upper_slim.json +++ b/subsets/blood_and_immune_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-07-10" + "val" : "2024-08-16" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/blood_and_immune_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/blood_and_immune_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -21768,13 +21768,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" } ] } }, { @@ -25311,10 +25308,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" } ] } }, { diff --git a/subsets/blood_and_immune_upper_slim.obo b/subsets/blood_and_immune_upper_slim.obo index ad7ec0937..0cc054eb5 100644 --- a/subsets/blood_and_immune_upper_slim.obo +++ b/subsets/blood_and_immune_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-07-10/subsets/blood_and_immune_upper_slim.owl +data-version: cl/releases/2024-08-16/subsets/blood_and_immune_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -95,7 +95,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/blood_and_immune_upper_slim -property_value: owl:versionInfo "2024-07-10" xsd:string +property_value: owl:versionInfo "2024-08-16" xsd:string [Term] id: CL:0000000 @@ -12030,9 +12030,8 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -13930,8 +13929,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] diff --git a/subsets/blood_and_immune_upper_slim.owl b/subsets/blood_and_immune_upper_slim.owl index bb770b572..b38f201de 100644 --- a/subsets/blood_and_immune_upper_slim.owl +++ b/subsets/blood_and_immune_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-07-10 + + 2024-08-16 @@ -37884,9 +37884,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart - https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb @@ -42861,8 +42860,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004537 blood vasculature - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb - 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+_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid754 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid775 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid790 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid845 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid877 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid922 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid936 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid951 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid968 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid986 +_:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "cell" "early embryonic cell (metazoa)" "stem cell" diff --git a/subsets/eye_upper_slim.json b/subsets/eye_upper_slim.json index c7df74eb0..b921f2954 100644 --- a/subsets/eye_upper_slim.json +++ b/subsets/eye_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-07-10" + "val" : "2024-08-16" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/eye_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/eye_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -16166,13 +16166,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" } ] } }, { @@ -16291,10 +16288,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb" } ] } }, { @@ -16424,6 +16421,12 @@ }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb" } ] } }, { @@ -20670,10 +20673,10 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb" } ] } }, { @@ -21668,10 +21671,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" } ] } }, { @@ -21908,10 +21911,10 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-female/v1.1/assets/3d-vh-f-spinal-cord.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-male/v1.1/assets/3d-vh-m-spinal-cord.glb" } ] } }, { @@ -25536,10 +25539,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" } ] } }, { @@ -29106,16 +29109,16 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/eye-female-left/v1.3/assets/3d-vh-f-eye-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/eye-female-right/v1.3/assets/3d-vh-f-eye-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/eye-male-left/v1.3/assets/3d-vh-m-eye-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/eye-male-right/v1.3/assets/3d-vh-m-eye-r.glb" } ] } }, { @@ -40663,10 +40666,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001456", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001444" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001456", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000165" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001456", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", diff --git a/subsets/eye_upper_slim.obo b/subsets/eye_upper_slim.obo index afc802901..6947ccb4b 100644 --- a/subsets/eye_upper_slim.obo +++ b/subsets/eye_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-07-10/subsets/eye_upper_slim.owl +data-version: cl/releases/2024-08-16/subsets/eye_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -95,7 +95,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/eye_upper_slim -property_value: owl:versionInfo "2024-07-10" xsd:string +property_value: owl:versionInfo "2024-08-16" xsd:string [Term] id: CL:0000000 @@ -8882,9 +8882,8 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -8950,8 +8949,8 @@ relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous s relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0006238 {source="Bgee:AN"} ! immediate transformation of future brain -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb" xsd:anyURI property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -9021,6 +9020,8 @@ intersection_of: part_of UBERON:0001894 ! diencephalon relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0001908 ! optic tract property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb" xsd:anyURI [Term] id: UBERON:0000964 @@ -9822,7 +9823,6 @@ xref: SCTID:302549007 xref: UMLS:C0015450 {source="ncithesaurus:Face"} xref: Wikipedia:Face is_a: UBERON:0001444 ! subdivision of head -relationship: has_part UBERON:0000165 ! mouth relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI @@ -11181,8 +11181,8 @@ relationship: part_of UBERON:0003931 ! diencephalic white matter relationship: RO:0002134 UBERON:0000966 ! innervates retina relationship: RO:0002433 UBERON:0003544 ! contributes to morphology of brain white matter property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb" xsd:anyURI property_value: IAO:0000116 "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11709,8 +11709,8 @@ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11836,8 +11836,8 @@ relationship: RO:0002202 UBERON:0003076 ! develops from posterior neural tube relationship: RO:0002254 UBERON:0003853 ! has developmental contribution from spinal cord neural crest relationship: RO:0002495 UBERON:0006241 ! immediate transformation of future spinal cord property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-female/v1.1/assets/3d-vh-f-spinal-cord.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-male/v1.1/assets/3d-vh-m-spinal-cord.glb" xsd:anyURI property_value: IAO:0000116 "TODO - add superclass to unify with VNC?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -13688,8 +13688,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -15584,10 +15584,10 @@ is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001775 ! ciliary body property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/eye-female-left/v1.3/assets/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/eye-female-right/v1.3/assets/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/eye-male-left/v1.3/assets/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/eye-male-right/v1.3/assets/3d-vh-m-eye-r.glb" xsd:anyURI [Term] id: UBERON:0010912 diff --git a/subsets/eye_upper_slim.owl b/subsets/eye_upper_slim.owl index 96eb56261..69be33e39 100644 --- a/subsets/eye_upper_slim.owl +++ b/subsets/eye_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-07-10 + + 2024-08-16 @@ -28372,9 +28372,8 @@ plexiform layer. Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart - https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb @@ -28500,8 +28499,8 @@ plexiform layer. brain - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb @@ -28706,6 +28705,8 @@ plexiform layer. optic chiasma http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg + https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb @@ -30726,12 +30727,6 @@ plexiform layer. - - - - - - @@ -30811,7 +30806,7 @@ plexiform layer. - + A tube extending from the mouth to the anus. @@ -30848,14 +30843,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -30910,7 +30905,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -30933,7 +30928,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -30952,7 +30947,7 @@ plexiform layer. - + FMA @@ -31070,7 +31065,7 @@ plexiform layer. - + @@ -31116,14 +31111,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -31389,7 +31384,7 @@ plexiform layer. - + @@ -31428,14 +31423,14 @@ plexiform layer. iris - + - + XAO @@ -31489,7 +31484,7 @@ plexiform layer. - + @@ -31538,14 +31533,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -31633,15 +31628,15 @@ plexiform layer. - - + + - + @@ -31676,34 +31671,34 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + FMA - + ZFA - + ISBN:0781772214 @@ -31745,7 +31740,7 @@ plexiform layer. - + @@ -31783,14 +31778,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -31828,14 +31823,14 @@ plexiform layer. - + - + @@ -31896,24 +31891,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -32106,9 +32101,9 @@ plexiform layer. - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -32128,15 +32123,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -32149,19 +32144,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -32277,7 +32272,7 @@ plexiform layer. - + @@ -32335,14 +32330,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -32418,7 +32413,7 @@ plexiform layer. - + @@ -32450,14 +32445,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -32950,7 +32945,7 @@ plexiform layer. - + @@ -33006,7 +33001,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -33019,7 +33014,7 @@ plexiform layer. - + FMA @@ -33073,7 +33068,7 @@ plexiform layer. - + @@ -33128,14 +33123,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -33825,7 +33820,7 @@ plexiform layer. - + @@ -33857,14 +33852,14 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + FMA @@ -33908,7 +33903,7 @@ plexiform layer. - + @@ -33938,14 +33933,14 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA @@ -33982,9 +33977,9 @@ plexiform layer. - - - + + + @@ -34032,15 +34027,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -34053,19 +34048,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -34223,7 +34218,7 @@ plexiform layer. - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -34269,14 +34264,14 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + Bgee:AN @@ -34677,8 +34672,8 @@ plexiform layer. optic tract http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb @@ -34747,7 +34742,7 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. MTg @@ -34786,14 +34781,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -34961,8 +34956,8 @@ plexiform layer. - - + + @@ -34975,7 +34970,7 @@ plexiform layer. - + @@ -35029,34 +35024,34 @@ plexiform layer. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -35385,7 +35380,7 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -35428,14 +35423,14 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + Bgee:AN @@ -36066,7 +36061,7 @@ plexiform layer. - + Vasculature that is part of the eye region. FMA:74743 @@ -36085,17 +36080,17 @@ plexiform layer. vasculature of eye - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb - + - + ISBN:0781772214 @@ -36299,7 +36294,7 @@ plexiform layer. - + @@ -36370,17 +36365,17 @@ plexiform layer. spinal cord http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-female/v1.1/assets/3d-vh-f-spinal-cord.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-male/v1.1/assets/3d-vh-m-spinal-cord.glb - + - + ZFA @@ -36835,9 +36830,9 @@ plexiform layer. - - - + + + @@ -36885,15 +36880,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -36912,19 +36907,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -36964,8 +36959,8 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -37003,11 +36998,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -37020,13 +37015,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -37088,22 +37083,22 @@ plexiform layer. - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -37136,45 +37131,45 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -37460,7 +37455,7 @@ plexiform layer. - + @@ -37513,14 +37508,14 @@ plexiform layer. hematopoietic system - + - + FMA @@ -37560,8 +37555,8 @@ plexiform layer. - - + + @@ -37587,11 +37582,11 @@ plexiform layer. iris epithelium - + - + @@ -37604,13 +37599,13 @@ plexiform layer. - + MA - + MP @@ -37749,7 +37744,7 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode ectodermal placode @@ -37766,7 +37761,7 @@ plexiform layer. cranial placode - + @@ -37779,7 +37774,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -37979,7 +37974,7 @@ plexiform layer. - + @@ -37992,7 +37987,7 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure AAO:0011064 @@ -38021,24 +38016,24 @@ plexiform layer. midbrain-hindbrain boundary - + - + - + ZFA - + ZFA @@ -38160,7 +38155,7 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -38183,14 +38178,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -38357,7 +38352,7 @@ plexiform layer. - + @@ -38394,7 +38389,7 @@ plexiform layer. eye primordium - + @@ -38407,7 +38402,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -38457,8 +38452,8 @@ plexiform layer. - - + + @@ -38486,24 +38481,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -38559,7 +38554,7 @@ plexiform layer. - + @@ -38597,7 +38592,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -38610,7 +38605,7 @@ plexiform layer. - + ZFA @@ -38649,9 +38644,9 @@ plexiform layer. - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -38680,34 +38675,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -38782,7 +38777,7 @@ plexiform layer. - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -38808,7 +38803,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38821,7 +38816,7 @@ plexiform layer. - + Bgee:AN @@ -38897,7 +38892,7 @@ plexiform layer. - + @@ -38937,7 +38932,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38950,7 +38945,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -39000,15 +38995,15 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -39025,15 +39020,15 @@ plexiform layer. heart primordium - + - + - + @@ -39046,19 +39041,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -39087,8 +39082,8 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -39112,11 +39107,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -39135,13 +39130,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -39462,7 +39457,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -39474,14 +39469,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -40256,7 +40251,7 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -40271,14 +40266,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -40371,7 +40366,7 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. AAO:0011095 @@ -40402,14 +40397,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -40662,7 +40657,7 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure ependymal layer @@ -40679,7 +40674,7 @@ plexiform layer. neural tube ventricular layer - + @@ -40692,7 +40687,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -41094,9 +41089,9 @@ plexiform layer. - - - + + + @@ -41128,34 +41123,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -41251,8 +41246,8 @@ plexiform layer. - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -41264,24 +41259,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -41334,7 +41329,7 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -41353,14 +41348,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -41437,7 +41432,7 @@ plexiform layer. - + @@ -41453,14 +41448,14 @@ plexiform layer. eye muscle - + - + MA @@ -41643,7 +41638,7 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. EMAPA:18804 @@ -41672,14 +41667,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -42054,8 +42049,8 @@ plexiform layer. UBERON:0004537 blood vasculature - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb @@ -42429,7 +42424,7 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -42443,14 +42438,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -42477,7 +42472,7 @@ plexiform layer. - + @@ -42516,14 +42511,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -43375,7 +43370,7 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. EFO:0003492 EHDAA2:0000732 @@ -43396,14 +43391,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -43461,7 +43456,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -43477,14 +43472,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -43999,7 +43994,7 @@ plexiform layer. - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -44007,7 +44002,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -44026,7 +44021,7 @@ plexiform layer. - + ZFA @@ -44049,7 +44044,7 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44067,14 +44062,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -44264,7 +44259,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44274,7 +44269,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -44293,7 +44288,7 @@ plexiform layer. - + AEO-modified-relation @@ -44350,8 +44345,8 @@ plexiform layer. - - + + @@ -44368,11 +44363,11 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + @@ -44385,13 +44380,13 @@ plexiform layer. - + FMA - + HPO:pr @@ -44633,7 +44628,7 @@ plexiform layer. - + @@ -44656,14 +44651,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -44839,7 +44834,7 @@ plexiform layer. - + @@ -44863,14 +44858,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -44907,7 +44902,7 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44921,7 +44916,7 @@ plexiform layer. notochordal plate - + @@ -44934,7 +44929,7 @@ plexiform layer. - + EHDAA2 @@ -44962,7 +44957,7 @@ plexiform layer. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44979,14 +44974,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -46027,8 +46022,8 @@ plexiform layer. - - + + @@ -46054,24 +46049,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -46122,7 +46117,7 @@ plexiform layer. - + @@ -46141,14 +46136,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -46294,7 +46289,7 @@ plexiform layer. - + @@ -46320,7 +46315,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -46336,7 +46331,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -46418,7 +46413,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -46426,7 +46421,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -46439,7 +46434,7 @@ plexiform layer. - + Obol @@ -46514,7 +46509,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46522,7 +46517,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -46535,7 +46530,7 @@ plexiform layer. - + AEO @@ -46774,7 +46769,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -46784,14 +46779,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -46819,7 +46814,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46836,14 +46831,14 @@ plexiform layer. vascular system - + - + MA @@ -46964,7 +46959,7 @@ plexiform layer. - + @@ -46981,14 +46976,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47084,7 +47079,7 @@ plexiform layer. - + @@ -47100,14 +47095,14 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + ZFA @@ -47140,14 +47135,14 @@ plexiform layer. - + - + @@ -47172,24 +47167,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -47235,7 +47230,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47243,14 +47238,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47273,7 +47268,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47283,14 +47278,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -47346,14 +47341,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -47366,7 +47361,7 @@ plexiform layer. - + EHDAA2 @@ -47507,7 +47502,7 @@ plexiform layer. - + @@ -47530,14 +47525,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -47578,8 +47573,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -47593,11 +47588,11 @@ plexiform layer. midbrain basal plate - + - + @@ -47610,13 +47605,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -47645,7 +47640,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -47654,14 +47649,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -47908,10 +47903,10 @@ plexiform layer. UBERON:0010427 ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png - https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/eye-female-left/v1.3/assets/3d-vh-f-eye-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/eye-female-right/v1.3/assets/3d-vh-f-eye-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/eye-male-left/v1.3/assets/3d-vh-m-eye-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/eye-male-right/v1.3/assets/3d-vh-m-eye-r.glb @@ -47964,8 +47959,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -47977,11 +47972,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -47994,13 +47989,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -48061,7 +48056,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48071,7 +48066,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48084,7 +48079,7 @@ plexiform layer. - + cjm @@ -48206,7 +48201,7 @@ plexiform layer. - + AAO:0010038 EMAPA:18808 FMA:49150 @@ -48216,14 +48211,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -48485,7 +48480,7 @@ plexiform layer. - + @@ -48527,7 +48522,7 @@ plexiform layer. anterior uvea - + @@ -48540,7 +48535,7 @@ plexiform layer. - + MP @@ -49333,7 +49328,7 @@ plexiform layer. - + @@ -49356,7 +49351,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -49369,7 +49364,7 @@ plexiform layer. - + AEO diff --git a/subsets/eye_upper_slim.tsv b/subsets/eye_upper_slim.tsv index f6a93c692..af5171f4d 100644 --- a/subsets/eye_upper_slim.tsv +++ b/subsets/eye_upper_slim.tsv @@ -1,315 +1,315 @@ ?x ?label -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1001 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1016 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1022 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1031 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1037 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1043 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1051 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1058 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1065 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1074 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1088 -_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid1097 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+_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid779 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid795 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid802 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid813 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid819 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid836 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid842 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid851 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid861 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid909 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid959 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid969 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid976 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid983 +_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "cell" "neural crest derived fibroblast" "neuronal receptor cell" diff --git a/subsets/general_cell_types_upper_slim.json b/subsets/general_cell_types_upper_slim.json index a7dcbb071..31ba38f2e 100644 --- a/subsets/general_cell_types_upper_slim.json +++ b/subsets/general_cell_types_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-07-10" + "val" : "2024-08-16" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", diff --git a/subsets/general_cell_types_upper_slim.obo b/subsets/general_cell_types_upper_slim.obo index ce6d8abd7..90957720c 100644 --- a/subsets/general_cell_types_upper_slim.obo +++ b/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-07-10/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2024-08-16/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -95,7 +95,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-07-10" xsd:string +property_value: owl:versionInfo "2024-08-16" xsd:string [Term] id: CL:0000000 diff --git a/subsets/general_cell_types_upper_slim.owl b/subsets/general_cell_types_upper_slim.owl index 4354de63c..0df0a51ec 100644 --- a/subsets/general_cell_types_upper_slim.owl +++ b/subsets/general_cell_types_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-07-10 + + 2024-08-16 diff --git a/subsets/general_cell_types_upper_slim.tsv b/subsets/general_cell_types_upper_slim.tsv 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+_:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid857 +_:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid864 +_:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid874 +_:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid901 +_:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid918 +_:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid927 +_:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid977 +_:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid985 +_:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "cell" "neuronal receptor cell" "early embryonic cell (metazoa)" diff --git a/subsets/kidney_upper_slim.json b/subsets/kidney_upper_slim.json index a1c0d3fe7..5bc36508b 100644 --- a/subsets/kidney_upper_slim.json +++ b/subsets/kidney_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-07-10" + "val" : "2024-08-16" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/kidney_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -1801,6 +1801,34 @@ "val" : "2010-08-24T02:06:40Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0002144", + "lbl" : "capillary endothelial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An endothelial cell found in capillaries.", + "xrefs" : [ "GOC:tfm" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "BTO:0004956" + }, { + "val" : "CALOHA:TS-0112" + }, { + "val" : "FMA:67756" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-08-24T10:15:00Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002173", "lbl" : "extraglomerular mesangial cell", @@ -1839,9 +1867,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate.", + "val" : "An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate.", "xrefs" : [ "GOC:tfm", "PMID:15840009" ] }, + "comments" : [ "Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes." ], "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], "xrefs" : [ { "val" : "BTO:0004632" @@ -2085,6 +2114,23 @@ "val" : "KUPO:0001016" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0002653", + "lbl" : "squamous endothelial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A squamous shaped endothelial cell.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-07-08T03:31:25Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002681", "lbl" : "kidney cortical cell", @@ -2663,8 +2709,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any kidney blood vessel cell that is part of some kidney capillary.", - "xrefs" : [ "FBC:Autogenerated" ] + "val" : "An endothelial cell that is part of the capillary of the kidney." }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], "xrefs" : [ { @@ -2759,6 +2804,23 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_2000008", + "lbl" : "microvascular endothelial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any blood vessel endothelial cell that is part of a microvascular endothelium.", + "xrefs" : [ "GOC:TermGenie" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://www.wikidata.org/entity/Q35563349" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-06-04T15:07:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_4030031", "lbl" : "interstitial cell", @@ -6561,6 +6623,35 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0036053", + "lbl" : "glomerular endothelium fenestra", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes.", + "xrefs" : [ "GOC:cjm", "MP:0011454", "PMID:19129259" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "GEnC fenestration", + "xrefs" : [ "PMID:19129259" ] + }, { + "pred" : "hasExactSynonym", + "val" : "glomerular endothelial cell fenestration", + "xrefs" : [ "PMID:19129259" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "bf" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-12-12T10:53:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0040011", "lbl" : "locomotion", @@ -7192,6 +7283,33 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0046930", + "lbl" : "pore complex", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "pore" + }, { + "pred" : "hasRelatedSynonym", + "val" : "channel-forming toxin activity" + }, { + "pred" : "hasRelatedSynonym", + "val" : "pore-forming toxin activity" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/20452" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0048103", "lbl" : "somatic stem cell division", @@ -8725,6 +8843,21 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0098796", + "lbl" : "membrane protein complex", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any protein complex that is part of a membrane.", + "xrefs" : [ "GOC:dos" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_metagenomics" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0098801", "lbl" : "regulation of renal system process", @@ -14067,16 +14200,16 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" @@ -16017,13 +16150,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" } ] } }, { @@ -17384,10 +17514,10 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" } ] } }, { @@ -17506,16 +17636,16 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" @@ -17993,10 +18123,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-female/v1.2/assets/3d-vh-f-urinary-bladder.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" @@ -18987,6 +19117,55 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001915", + "lbl" : "endothelium of capillary", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An endothelium that is part of a capillary [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blood capillary endothelium", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "capillary endothelium" + }, { + "pred" : "hasExactSynonym", + "val" : "capillary vessel endothelium", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "endothelium of blood capillary", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "endothelium of capillary vessel", + "xrefs" : [ "OBOL:automatic" ] + } ], + "xrefs" : [ { + "val" : "BTO:0004954" + }, { + "val" : "CALOHA:TS-0112" + }, { + "val" : "EMAPA:36292" + }, { + "val" : "FMA:62114" + }, { + "val" : "MA:0000711" + }, { + "val" : "NCIT:C49215" + }, { + "val" : "UMLS:C0006904" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0001969", "lbl" : "blood plasma", @@ -19589,10 +19768,10 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" } ] } }, { @@ -22502,10 +22681,10 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" @@ -23239,16 +23418,16 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" @@ -23689,10 +23868,10 @@ "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" } ] } }, { @@ -26997,6 +27176,22 @@ "val" : "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0008339", + "lbl" : "microvascular endothelium", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "BTO:0003122" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2186" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0008987", "lbl" : "renal parenchyma", @@ -34482,6 +34677,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002139", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000115" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002144", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0002653" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002144", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_2000008" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002144", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001915" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002173", "pred" : "is_a", @@ -34516,6 +34723,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000074" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002188", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0036053" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002242", "pred" : "is_a", @@ -34634,6 +34845,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002653", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000115" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002681", "pred" : "is_a", @@ -35001,7 +35216,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000892", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000071" + "obj" : "http://purl.obolibrary.org/obo/CL_0002144" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000892", "pred" : "is_a", @@ -35092,6 +35307,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_1001318", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1000500" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_2000008", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000071" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_2000008", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0008339" }, { "sub" : "http://purl.obolibrary.org/obo/CL_4030031", "pred" : "is_a", @@ -36274,6 +36497,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0035592", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0071692" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0036053", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0046930" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0040011", "pred" : "is_a", @@ -36450,6 +36677,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0046903", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0006810" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0046930", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0098796" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0048103", "pred" : "is_a", @@ -36966,6 +37197,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098794", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0045202" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098796", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098796", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0016020" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098801", "pred" : "is_a", @@ -39381,7 +39620,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "pred" : "http://purl.obolibrary.org/obo/RO_0002131", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006542", "meta" : { "basicPropertyValues" : [ { @@ -39389,6 +39628,10 @@ "val" : "MA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", + "pred" : "http://purl.obolibrary.org/obo/RO_0002131", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006853" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", "pred" : "http://purl.obolibrary.org/obo/RO_0002150", @@ -39591,6 +39834,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001851", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001915", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0008339" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001915", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001982" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -42786,6 +43037,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0007832", "pred" : "http://purl.obolibrary.org/obo/RO_0002576", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001271" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0008339", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004638" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0008339", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_8410081" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0008987", "pred" : "is_a", @@ -45411,6 +45670,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002202", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000222" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0002144", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000071" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001915" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0002173", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0002320" ], @@ -45679,7 +45945,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_1000892", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_1000854" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0003527" @@ -45726,6 +45992,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0005215" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_2000008", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000071" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0008339" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_4030031", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], @@ -46380,6 +46653,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005604" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098796", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098801", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -46689,6 +46969,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0013756" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0001915", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001986" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001982" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0001969", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ], @@ -47364,6 +47651,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002576", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001271" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0008339", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001986" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_8410081" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0008987", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000353" ], diff --git a/subsets/kidney_upper_slim.obo b/subsets/kidney_upper_slim.obo index 3f10ccd90..467009d20 100644 --- a/subsets/kidney_upper_slim.obo +++ b/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-07-10/subsets/kidney_upper_slim.owl +data-version: cl/releases/2024-08-16/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -95,7 +95,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-07-10" xsd:string +property_value: owl:versionInfo "2024-08-16" xsd:string [Term] id: CL:0000000 @@ -1321,6 +1321,24 @@ is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z +[Term] +id: CL:0002144 +name: capillary endothelial cell +def: "An endothelial cell found in capillaries." [GOC:tfm] +subset: cellxgene_subset +subset: human_reference_atlas +xref: BTO:0004956 +xref: CALOHA:TS-0112 +xref: FMA:67756 +is_a: CL:0002653 ! squamous endothelial cell +is_a: CL:2000008 ! microvascular endothelial cell +intersection_of: CL:0000071 ! blood vessel endothelial cell +intersection_of: part_of UBERON:0001915 ! endothelium of capillary +relationship: part_of UBERON:0001915 ! endothelium of capillary +property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +creation_date: 2010-08-24T10:15:00Z + [Term] id: CL:0002173 name: extraglomerular mesangial cell @@ -1342,7 +1360,8 @@ creation_date: 2010-08-25T02:20:55Z [Term] id: CL:0002188 name: glomerular endothelial cell -def: "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." [GOC:tfm, PMID:15840009] +def: "An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." [GOC:tfm, PMID:15840009] +comment: Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. {xref="PMID:33123011", xref="PMID:18480313", xref="PMID:19129259"} subset: cellxgene_subset subset: kidney_upper_slim xref: BTO:0004632 @@ -1351,6 +1370,7 @@ is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus +relationship: has_part GO:0036053 ! glomerular endothelium fenestra relationship: part_of UBERON:0000074 ! renal glomerulus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T10:59:44Z @@ -1494,6 +1514,14 @@ is_a: CL:0002681 {is_inferred="true"} ! kidney cortical cell intersection_of: CL:0002518 ! kidney epithelial cell intersection_of: part_of UBERON:0001225 ! cortex of kidney +[Term] +id: CL:0002653 +name: squamous endothelial cell +def: "A squamous shaped endothelial cell." [GOC:dos] +is_a: CL:0000115 ! endothelial cell +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +creation_date: 2011-07-08T03:31:25Z + [Term] id: CL:0002681 name: kidney cortical cell @@ -1910,13 +1938,13 @@ relationship: part_of UBERON:0003644 ! kidney arterial blood vessel [Term] id: CL:1000892 name: kidney capillary endothelial cell -def: "Any kidney blood vessel cell that is part of some kidney capillary." [FBC:Autogenerated] +def: "An endothelial cell that is part of the capillary of the kidney." [] subset: cellxgene_subset subset: kidney_upper_slim xref: KUPO:0001030 -is_a: CL:0000071 ! blood vessel endothelial cell +is_a: CL:0002144 ! capillary endothelial cell is_a: CL:1000854 ! kidney blood vessel cell -intersection_of: CL:1000854 ! kidney blood vessel cell +intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003527 ! kidney capillary relationship: part_of UBERON:0003527 ! kidney capillary @@ -1991,6 +2019,17 @@ intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0005215 ! kidney interstitium property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: CL:2000008 +name: microvascular endothelial cell +def: "Any blood vessel endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] +is_a: CL:0000071 ! blood vessel endothelial cell +intersection_of: CL:0000071 ! blood vessel endothelial cell +intersection_of: part_of UBERON:0008339 ! microvascular endothelium +relationship: part_of UBERON:0008339 ! microvascular endothelium +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 +creation_date: 2014-06-04T15:07:42Z + [Term] id: CL:4030031 name: interstitial cell @@ -4118,6 +4157,17 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region created_by: bf creation_date: 2010-11-09T10:25:08Z +[Term] +id: GO:0036053 +name: glomerular endothelium fenestra +namespace: cellular_component +def: "A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes." [GOC:cjm, MP:0011454, PMID:19129259] +synonym: "GEnC fenestration" EXACT [PMID:19129259] +synonym: "glomerular endothelial cell fenestration" EXACT [PMID:19129259] +is_a: GO:0046930 ! pore complex +created_by: bf +creation_date: 2011-12-12T10:53:24Z + [Term] id: GO:0040011 name: locomotion @@ -4461,6 +4511,17 @@ def: "The controlled release of a substance by a cell or a tissue." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport +[Term] +id: GO:0046930 +name: pore complex +namespace: cellular_component +def: "A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids." [ISBN:0198506732] +synonym: "channel-forming toxin activity" RELATED [] +synonym: "pore" EXACT [] +synonym: "pore-forming toxin activity" RELATED [] +is_a: GO:0098796 ! membrane protein complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20452" xsd:anyURI + [Term] id: GO:0048103 name: somatic stem cell division @@ -5293,6 +5354,17 @@ is_a: GO:0110165 ! cellular anatomical entity relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse +[Term] +id: GO:0098796 +name: membrane protein complex +namespace: cellular_component +def: "Any protein complex that is part of a membrane." [GOC:dos] +subset: goslim_metagenomics +is_a: GO:0032991 ! protein-containing complex +intersection_of: GO:0032991 ! protein-containing complex +intersection_of: part_of GO:0016020 ! membrane +relationship: part_of GO:0016020 ! membrane + [Term] id: GO:0098801 name: regulation of renal system process @@ -7838,10 +7910,10 @@ relationship: capable_of_part_of GO:0070295 ! renal water absorption relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -8802,9 +8874,8 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -9535,8 +9606,8 @@ intersection_of: RO:0002179 UBERON:0002113 ! drains kidney relationship: RO:0002179 UBERON:0002113 ! drains kidney relationship: RO:0002376 UBERON:0001072 ! tributary of inferior vena cava property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -9604,10 +9675,10 @@ intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -9843,8 +9914,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018707 {source="BTO"} ! bladder organ relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-female/v1.2/assets/3d-vh-f-urinary-bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -10029,9 +10100,10 @@ xref: Wikipedia:Proximal_straight_tubule xref: ZFA:0005291 is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0009035 {source="MA"} ! renal straight tubule +relationship: overlaps UBERON:0006542 {source="MA"} ! outer medulla outer stripe loop of Henle +relationship: overlaps UBERON:0006853 ! renal cortex tubule relationship: part_of UBERON:0001289 {source="MA"} ! descending limb of loop of Henle relationship: part_of UBERON:0004134 ! proximal tubule -relationship: part_of UBERON:0006542 {source="MA"} ! outer medulla outer stripe loop of Henle relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule relationship: RO:0002150 UBERON:0005096 ! continuous with descending thin limb property_value: IAO:0000116 "TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)" xsd:string @@ -10372,6 +10444,28 @@ xref: Wikipedia:Cortex_(anatomy) is_a: UBERON:0000064 ! organ part relationship: bounding_layer_of UBERON:0000062 ! organ +[Term] +id: UBERON:0001915 +name: endothelium of capillary +namespace: uberon +def: "An endothelium that is part of a capillary [Automatically generated definition]." [OBOL:automatic] +synonym: "blood capillary endothelium" EXACT [OBOL:automatic] +synonym: "capillary endothelium" EXACT [] +synonym: "capillary vessel endothelium" EXACT [OBOL:automatic] +synonym: "endothelium of blood capillary" EXACT [OBOL:automatic] +synonym: "endothelium of capillary vessel" EXACT [OBOL:automatic] +xref: BTO:0004954 +xref: CALOHA:TS-0112 +xref: EMAPA:36292 +xref: FMA:62114 +xref: MA:0000711 +xref: NCIT:C49215 +xref: UMLS:C0006904 {source="ncithesaurus:Capillary_Endothelium"} +is_a: UBERON:0008339 ! microvascular endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0001982 ! capillary +relationship: part_of UBERON:0001982 ! capillary + [Term] id: UBERON:0001969 name: blood plasma @@ -10707,8 +10801,8 @@ is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035554 ! right cardiac chamber relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -12226,8 +12320,8 @@ xref: Wikipedia:Venae_cavae is_a: UBERON:0003479 ! thoracic cavity vein is_a: UBERON:0013768 ! great vessel of heart property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI [Term] @@ -12569,10 +12663,10 @@ xref: Wikipedia:Renal_pyramids is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000362 ! renal medulla relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -12798,8 +12892,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -14551,6 +14645,17 @@ relationship: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI property_value: IAO:0000116 "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string +[Term] +id: UBERON:0008339 +name: microvascular endothelium +namespace: uberon +xref: BTO:0003122 +is_a: UBERON:0004638 ! blood vessel endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:8410081 ! blood microvessel +relationship: part_of UBERON:8410081 ! blood microvessel +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string + [Term] id: UBERON:0008987 name: renal parenchyma diff --git a/subsets/kidney_upper_slim.owl b/subsets/kidney_upper_slim.owl index 06b276c12..68c9d4c93 100644 --- a/subsets/kidney_upper_slim.owl +++ b/subsets/kidney_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-07-10 + + 2024-08-16 @@ -8869,6 +8869,48 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + An endothelial cell found in capillaries. + + + 2010-08-24T10:15:00Z + BTO:0004956 + CALOHA:TS-0112 + FMA:67756 + + + capillary endothelial cell + + + + + An endothelial cell found in capillaries. + GOC:tfm + + + + @@ -8941,22 +8983,37 @@ Each of these 3 primitives can be composed to yield a cross-product of different - An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. + + + + + + + An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. 2010-08-26T10:59:44Z BTO:0004632 FMA:70970 + Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. glomerular endothelial cell - An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. + An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. GOC:tfm PMID:15840009 + + + + Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. + PMID:18480313 + PMID:19129259 + PMID:33123011 + @@ -9360,6 +9417,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A squamous shaped endothelial cell. + + 2011-07-08T03:31:25Z + squamous endothelial cell + + + + + A squamous shaped endothelial cell. + GOC:dos + + + + @@ -10608,7 +10683,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10616,7 +10691,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10624,18 +10699,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any kidney blood vessel cell that is part of some kidney capillary. + An endothelial cell that is part of the capillary of the kidney. KUPO:0001030 kidney capillary endothelial cell - - - - Any kidney blood vessel cell that is part of some kidney capillary. - FBC:Autogenerated - @@ -10867,6 +10936,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + Any blood vessel endothelial cell that is part of a microvascular endothelium. + + 2014-06-04T15:07:42Z + CL:2000008 + microvascular endothelial cell + + + + + Any blood vessel endothelial cell that is part of a microvascular endothelium. + GOC:TermGenie + + + + @@ -12162,32 +12267,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -16301,6 +16406,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes. + bf + 2011-12-12T10:53:24Z + GEnC fenestration + glomerular endothelial cell fenestration + cellular_component + GO:0036053 + glomerular endothelium fenestra + + + + + A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes. + GOC:cjm + MP:0011454 + PMID:19129259 + + + + + GEnC fenestration + PMID:19129259 + + + + + glomerular endothelial cell fenestration + PMID:19129259 + + + + @@ -17147,6 +17288,28 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids. + https://github.com/geneontology/go-ontology/issues/20452 + pore + cellular_component + channel-forming toxin activity + pore-forming toxin activity + GO:0046930 + pore complex + + + + + A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids. + ISBN:0198506732 + + + + @@ -19428,6 +19591,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + Any protein complex that is part of a membrane. + cellular_component + GO:0098796 + + membrane protein complex + + + + + Any protein complex that is part of a membrane. + GOC:dos + + + + @@ -23181,7 +23380,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23235,14 +23434,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -23292,7 +23491,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23340,14 +23539,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - + - + Wikipedia @@ -23854,7 +24053,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23904,14 +24103,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -24174,14 +24373,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -24213,24 +24412,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different metanephros - + - + - + GO - + ISBN:9780878932504 @@ -24345,8 +24544,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. BTO:0001646 EHDAA2:0002140 @@ -24370,11 +24569,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureteric bud - + - + @@ -24387,13 +24586,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 - + ISBN:9780878932504 @@ -24774,7 +24973,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -24810,14 +25009,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -25077,8 +25276,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -25104,24 +25303,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -25162,8 +25361,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -25181,24 +25380,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -25221,7 +25420,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25260,14 +25459,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -25549,15 +25748,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -25594,34 +25793,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -25880,10 +26079,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Note that 'renal medulla' is not synonymous with 'medullary region of kidney'. The former is composed of kidney pyramids only, while the latter covers kidney pyramids and renal columns, which are histologically different. renal medulla - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg @@ -26963,7 +27162,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27005,14 +27204,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27370,7 +27569,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27405,14 +27604,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different abdomen - + - + MA @@ -27641,7 +27840,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27676,14 +27875,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27723,7 +27922,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27758,14 +27957,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -27806,7 +28005,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -27847,14 +28046,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28020,7 +28219,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28063,7 +28262,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -28076,7 +28275,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -28138,7 +28337,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28206,18 +28405,17 @@ Each of these 3 primitives can be composed to yield a cross-product of different Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart - https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -29071,7 +29269,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29121,14 +29319,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29194,7 +29392,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29239,7 +29437,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -29253,7 +29451,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -29450,7 +29648,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29484,14 +29682,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -29938,8 +30136,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb @@ -29982,14 +30180,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -30041,24 +30239,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -30104,7 +30302,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30134,20 +30332,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different cortex of kidney - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -30183,7 +30381,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30228,14 +30426,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -30309,7 +30507,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30351,14 +30549,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -30448,10 +30646,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -30495,7 +30693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron tubule - + @@ -30504,14 +30702,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + GO MA ZFA @@ -30525,7 +30723,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -30739,7 +30937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30782,11 +30980,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different urinary bladder - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-female/v1.2/assets/3d-vh-f-urinary-bladder.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + @@ -30799,7 +30997,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -30929,7 +31127,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30942,7 +31140,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. @@ -30973,24 +31171,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + - + FMA - + Bgee:AN @@ -31041,14 +31239,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -31084,11 +31282,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + @@ -31101,13 +31299,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GO - + Wikipedia @@ -31239,7 +31437,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31266,7 +31464,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -31279,7 +31477,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -31303,14 +31501,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + + + + + + + @@ -31349,12 +31553,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal straight tubule - + - - + + @@ -31366,13 +31570,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + MA - + MA @@ -31414,7 +31618,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31450,7 +31654,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -31463,7 +31667,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EMAPA GO MA-modified-from-isa @@ -31738,7 +31942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31761,14 +31965,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -31809,7 +32013,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -31846,14 +32050,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -32228,6 +32432,83 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a capillary [Automatically generated definition]. + BTO:0004954 + CALOHA:TS-0112 + EMAPA:36292 + FMA:62114 + MA:0000711 + NCIT:C49215 + UMLS:C0006904 + blood capillary endothelium + capillary endothelium + capillary vessel endothelium + endothelium of blood capillary + endothelium of capillary vessel + uberon + UBERON:0001915 + endothelium of capillary + + + + + An endothelium that is part of a capillary [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C0006904 + ncithesaurus:Capillary_Endothelium + + + + + blood capillary endothelium + OBOL:automatic + + + + + capillary vessel endothelium + OBOL:automatic + + + + + endothelium of blood capillary + OBOL:automatic + + + + + endothelium of capillary vessel + OBOL:automatic + + + + @@ -32489,8 +32770,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -32503,7 +32784,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32557,34 +32838,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -33067,8 +33348,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different right cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb @@ -33441,7 +33722,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33493,14 +33774,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney - + - + FMA @@ -33535,8 +33816,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -33574,11 +33855,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -33591,13 +33872,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + ZFA @@ -33924,7 +34205,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33943,7 +34224,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -33965,24 +34246,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different juxtaglomerular apparatus - + - + - + MA - + GO @@ -34106,8 +34387,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -34124,24 +34405,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -34283,9 +34564,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -34333,15 +34614,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -34360,19 +34641,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34412,8 +34693,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -34451,11 +34732,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -34468,13 +34749,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -34534,8 +34815,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. BTO:0003940 @@ -34553,24 +34834,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different macula densa - + - + - + MA - + GO @@ -34595,22 +34876,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -34643,45 +34924,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -35045,7 +35326,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35098,14 +35379,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -35323,7 +35604,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -35346,14 +35627,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -35394,8 +35675,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. AAO:0011088 NCIT:C34279 @@ -35414,11 +35695,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -35431,13 +35712,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Wikipedia - + XAO @@ -35543,9 +35824,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -35584,34 +35865,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -35720,7 +36001,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct @@ -35749,7 +36030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -35762,7 +36043,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -35816,9 +36097,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -35847,34 +36128,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -35914,7 +36195,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -35940,7 +36221,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -35953,7 +36234,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -36000,7 +36281,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36040,7 +36321,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36053,7 +36334,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -36103,15 +36384,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -36128,15 +36409,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -36149,19 +36430,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -36190,8 +36471,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -36215,11 +36496,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -36238,13 +36519,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -36489,7 +36770,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36515,14 +36796,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -37210,7 +37491,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -37225,14 +37506,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -37456,8 +37737,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different vena cava http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png @@ -37812,8 +38093,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -37830,24 +38111,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal tubule - + - + - + GO - + GO @@ -37906,7 +38187,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -37916,14 +38197,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004136 intermediate tubule - + - + FMA @@ -37999,8 +38280,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -38012,24 +38293,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -38082,7 +38363,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -38101,14 +38382,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -38330,8 +38611,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -38341,24 +38622,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different comma-shaped body - + - + - + cjm - + ZFA @@ -38380,8 +38661,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 @@ -38393,24 +38674,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different S-shaped body - + - + - + cjm - + GO @@ -38479,10 +38760,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney pyramid - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-right/v1.3/assets/3d-vh-f-kidney-r.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-left/v1.3/assets/3d-vh-m-kidney-l.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png @@ -38822,7 +39103,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38860,14 +39141,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -39229,8 +39510,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004537 blood vasculature - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb - https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb + https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb @@ -39407,7 +39688,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39444,14 +39725,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -39811,7 +40092,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -39825,14 +40106,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -39859,7 +40140,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39898,14 +40179,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -40203,7 +40484,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40224,14 +40505,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -40297,9 +40578,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -40319,34 +40600,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -40821,7 +41102,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -40829,14 +41110,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005095 kidney rudiment - + - + GO @@ -40952,7 +41233,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -40970,14 +41251,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -41708,7 +41989,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -41724,14 +42005,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -41848,7 +42129,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -41866,14 +42147,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -41901,7 +42182,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41928,7 +42209,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different gonad primordium - + @@ -41941,7 +42222,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -42000,14 +42281,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 @@ -42025,24 +42306,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -42089,7 +42370,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42106,14 +42387,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular tuft - + - + Wikipedia @@ -42363,7 +42644,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42391,14 +42672,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -42483,7 +42764,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -42493,7 +42774,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -42512,7 +42793,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -42609,7 +42890,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42648,14 +42929,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -42689,7 +42970,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -42703,7 +42984,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -42716,7 +42997,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -42744,7 +43025,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -42761,14 +43042,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -43312,7 +43593,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -43322,14 +43603,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0006853 renal cortex tubule - + - + MA @@ -44001,7 +44282,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44027,7 +44308,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -44043,7 +44324,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -44204,7 +44485,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -44212,7 +44493,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -44225,7 +44506,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -44439,7 +44720,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -44456,14 +44737,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -44601,7 +44882,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44639,14 +44920,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -44684,6 +44965,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + BTO:0003122 + uberon + UBERON:0008339 + microvascular endothelium + https://github.com/obophenotype/uberon/issues/2186 + + + + @@ -44699,7 +45010,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -44710,7 +45021,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0008987 renal parenchyma - + @@ -44723,7 +45034,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -44793,7 +45104,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44810,14 +45121,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -44936,7 +45247,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -44944,14 +45255,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45050,7 +45361,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45060,14 +45371,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -45388,7 +45699,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45406,14 +45717,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010227 future cardiac atrium - + - + ZFA @@ -45556,7 +45867,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45570,7 +45881,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010377 mesenchyme from somatopleure - + @@ -45583,7 +45894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -45599,7 +45910,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -45609,14 +45920,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -45649,7 +45960,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45665,7 +45976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010532 primitive nephron - + @@ -45678,7 +45989,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -45694,7 +46005,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45705,7 +46016,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010536 nephron progenitor - + @@ -45718,7 +46029,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -45961,8 +46272,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -45974,11 +46285,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -45991,13 +46302,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -46058,7 +46369,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46068,7 +46379,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46081,7 +46392,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46105,7 +46416,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46130,14 +46441,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different upper urinary tract - + - + FMA @@ -46455,7 +46766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46470,14 +46781,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -46500,20 +46811,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -46523,20 +46834,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -46563,7 +46874,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46583,14 +46894,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeleton of pelvic complex - + - + FMA @@ -46642,7 +46953,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The precursor of the urethra. SCTID:361531004 Wikipedia:Urethral_groove @@ -46653,14 +46964,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -47231,7 +47542,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47254,7 +47565,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -47267,7 +47578,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -47678,7 +47989,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -47689,14 +48000,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis/ureter - + - + NCIT diff --git a/subsets/kidney_upper_slim.tsv b/subsets/kidney_upper_slim.tsv index 684848508..2bd85ec1d 100644 --- a/subsets/kidney_upper_slim.tsv +++ b/subsets/kidney_upper_slim.tsv @@ -1,332 +1,337 @@ ?x ?label -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1000 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1006 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1013 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1018 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1023 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1029 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1034 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1040 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1046 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1053 -_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid1061 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+_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid976 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid982 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid989 +_:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid997 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -400,6 +405,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "ecto-epithelial cell" "meso-epithelial cell" "endothelial cell of vascular tree" + "capillary endothelial cell" "extraglomerular mesangial cell" "glomerular endothelial cell" "nucleate cell" @@ -412,6 +418,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "kidney epithelial cell" "embryonic blood vessel endothelial progenitor cell" "renal cortical epithelial cell" + "squamous endothelial cell" "kidney cortical cell" "renal principal cell" "premigratory neural crest cell" @@ -455,6 +462,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "kidney loop of Henle descending limb epithelial cell" "kidney collecting duct cell" "renal interstitial pericyte" + "microvascular endothelial cell" "interstitial cell" "perivascular cell" "mitotic cell cycle" @@ -603,6 +611,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "tube morphogenesis" "tube development" "establishment of protein localization to extracellular region" + "glomerular endothelium fenestra" "locomotion" "embryonic cleavage" "fluid transport" @@ -630,6 +639,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "establishment of protein localization" "synapse" "secretion" + "pore complex" "somatic stem cell division" "organelle fission" "mesoderm morphogenesis" @@ -695,6 +705,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "basement membrane collagen trimer" "presynapse" "postsynapse" + "membrane protein complex" "regulation of renal system process" "anterograde trans-synaptic signaling" "supramolecular complex" @@ -945,6 +956,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "artery" "vein" "cortex" + "endothelium of capillary" "blood plasma" "venule" "arteriole" @@ -1139,6 +1151,7 @@ _:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "vascular system" "appendage girdle region" "pelvic girdle skeleton" + "microvascular endothelium" "renal parenchyma" "renal straight tubule" "entire embryonic mesenchyme"