From fb50180791186c82404e245c56d35c9603392dcd Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Thu, 14 Nov 2024 15:19:53 +0000 Subject: [PATCH 1/3] definition and refs --- src/ontology/uberon-edit.obo | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 4018c5421..4834ae8a9 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224694,6 +224694,18 @@ is_a: UBERON:0004693 ! Peyer's patch epithelium relationship: dc-contributor https://orcid.org/0009-0005-7919-4905 property_value: dcterms-date "2024-11-07T11:44:27Z" xsd:dateTime +[Term] +id: UBERON:8700003 +name: stratum corneum of esophageal epithelium +def: "The outermost layer of the stratified squamous epithelium lining the esophagus, composed of several layers of flattened, anucleated keratinocytes called corneocytes. It forms the primary protective barrier against mechanical, chemical, and microbial insults, while regulating permeability and contributing to tissue integrity. This layer is characterized by corneocytes embedded in a lipid-rich extracellular matrix, providing mechanical reinforcement and maintaining essential barrier functions of the esophageal lining." [] +xref: DOI:10.1038/gimo15 +xref: PMID:21126700 +xref: PMID:26019440 +is_a: UBERON:0010304 ! non-keratinized stratified squamous epithelium +relationship: dc-contributor https://orcid.org/0009-0005-7919-4905 +relationship: part_of UBERON:0001043 ! esophagus +property_value: dcterms-date "2024-11-14T15:10:48Z" xsd:dateTime + [Term] id: UBERON:8850000 name: lumen of pulmonary alveolus From 5b80ca2b23a1229a04817b500c373c0f069ac6e6 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Tue, 17 Dec 2024 12:03:31 +0000 Subject: [PATCH 2/3] fixed dbxrefs --- src/ontology/uberon-edit.obo | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 791a39802..1829df02c 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -45,9 +45,6 @@ synonymtypedef: PENDING_REVIEW "expert consultation and attribution required" synonymtypedef: SENSU "taxonomic disambiguation" synonymtypedef: SYSTEMATIC "a systematic synonym used as the base name for design patterns" default-namespace: uberon -idspace: EFO http://www.ebi.ac.uk/efo/EFO_ -idspace: NIF_Subcellular http://www.neurolex.org/wiki/ -idspace: NIFEXT http://uri.neuinfo.org/nif/nifstd/nifext_ treat-xrefs-as-equivalent: AEO treat-xrefs-as-equivalent: BILA treat-xrefs-as-equivalent: BSPO @@ -72993,8 +72990,8 @@ id: UBERON:0003532 name: hindlimb skin def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] synonym: "hind limb skin" EXACT [OBOL:automatic] -synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "lower limb skin" EXACT [FMA:23102] +synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "skin of hind limb" EXACT [OBOL:automatic] synonym: "skin of hindlimb" EXACT [OBOL:automatic] synonym: "skin of lower extremity" EXACT [OBOL:automatic] @@ -224728,10 +224725,7 @@ property_value: dcterms-date "2024-11-14T15:00:21Z" xsd:dateTime [Term] id: UBERON:8700003 name: stratum corneum of esophageal epithelium -def: "The outermost layer of the stratified squamous epithelium lining the esophagus, composed of several layers of flattened, anucleated keratinocytes called corneocytes. It forms the primary protective barrier against mechanical, chemical, and microbial insults, while regulating permeability and contributing to tissue integrity. This layer is characterized by corneocytes embedded in a lipid-rich extracellular matrix, providing mechanical reinforcement and maintaining essential barrier functions of the esophageal lining." [] -xref: DOI:10.1038/gimo15 -xref: PMID:21126700 -xref: PMID:26019440 +def: "The outermost layer of the stratified squamous epithelium lining the esophagus, composed of several layers of flattened, anucleated keratinocytes called corneocytes. It forms the primary protective barrier against mechanical, chemical, and microbial insults, while regulating permeability and contributing to tissue integrity. This layer is characterized by corneocytes embedded in a lipid-rich extracellular matrix, providing mechanical reinforcement and maintaining essential barrier functions of the esophageal lining." [doi:10.1038/gimo15, PMID:21126700, PMID:26019440] is_a: UBERON:0010304 ! non-keratinized stratified squamous epithelium relationship: dc-contributor https://orcid.org/0009-0005-7919-4905 relationship: part_of UBERON:0001043 ! esophagus From 395347ce4e3cd9fac56da7a4a9928ba36ec5959b Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Thu, 23 Jan 2025 09:45:32 +0000 Subject: [PATCH 3/3] Update uberon-edit.obo def and ref update --- src/ontology/uberon-edit.obo | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 730772c14..7e08371b1 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -36856,7 +36856,7 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002187 ! terminal bronchiole relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 ! Aleix Puig-Barbé relationship: has_part CL:0000158 {source="FMA"} ! club cell -relationship: has_part CL:1000271 ! lung ciliated cell +relationship: has_part CL:1000271 ! lung multiciliated epithelial cell property_value: taxon_notes "A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]" xsd:string [Term] @@ -39644,8 +39644,8 @@ intersection_of: part_of UBERON:0002186 ! bronchiole relationship: contributes_to_morphology_of UBERON:0002186 ! bronchiole relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 ! Aleix Puig-Barbé relationship: has_part CL:0000158 ! club cell -relationship: has_part CL:0002145 {source="FMA"} ! ciliated columnar cell of tracheobronchial tree -relationship: has_part CL:1000271 ! lung ciliated cell +relationship: has_part CL:0002145 {source="FMA"} ! multiciliated columnar cell of tracheobronchial tree +relationship: has_part CL:1000271 ! lung multiciliated epithelial cell relationship: part_of UBERON:0005039 ! mucosa of bronchiole [Term] @@ -47868,7 +47868,7 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002183 ! lobar bronchus relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 ! Aleix Puig-Barbé relationship: has_part CL:0002329 ! basal epithelial cell of tracheobronchial tree -relationship: has_part CL:0002332 ! ciliated cell of the bronchus +relationship: has_part CL:0002332 ! multiciliated epithelial cell of the bronchus relationship: has_part CL:0017000 ! pulmonary ionocyte [Term] @@ -47925,10 +47925,10 @@ relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 ! Aleix Puig- relationship: has_part CL:0000158 ! club cell relationship: has_part CL:0002208 ! brush cell of bronchus relationship: has_part CL:0002329 ! basal epithelial cell of tracheobronchial tree -relationship: has_part CL:0002332 ! ciliated cell of the bronchus +relationship: has_part CL:0002332 ! multiciliated epithelial cell of the bronchus relationship: has_part CL:0017000 ! pulmonary ionocyte relationship: has_part CL:1000143 ! lung goblet cell -relationship: has_part CL:1000223 ! lung neuroendocrine cell +relationship: has_part CL:1000223 ! pulmonary neuroendocrine cell relationship: part_of UBERON:0002184 ! segmental bronchus [Term] @@ -72969,8 +72969,8 @@ id: UBERON:0003532 name: hindlimb skin def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] synonym: "hind limb skin" EXACT [OBOL:automatic] -synonym: "lower limb skin" EXACT [FMA:23102] synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] +synonym: "lower limb skin" EXACT [FMA:23102] synonym: "skin of hind limb" EXACT [OBOL:automatic] synonym: "skin of hindlimb" EXACT [OBOL:automatic] synonym: "skin of lower extremity" EXACT [OBOL:automatic] @@ -116143,7 +116143,7 @@ xref: NCIT:C45715 xref: UMLS:C0682578 {source="ncithesaurus:Glandular_Epithelium"} xref: UMLS:C1708242 {source="ncithesaurus:Glandular_Epithelial_Tissue"} intersection_of: UBERON:0000483 ! epithelium -intersection_of: composed_primarily_of CL:0000150 ! glandular epithelial cell +intersection_of: composed_primarily_of CL:0000150 ! glandular secretory epithelial cell disjoint_from: UBERON:0011952 ! non-glandular epithelium property_value: editor_note "consider splitting epithelium from epithelial tissue" xsd:string @@ -117486,14 +117486,14 @@ xref: FMA:64800 xref: NCIT:C13182 xref: UMLS:C0225337 {source="ncithesaurus:Columnar_Epithelium"} intersection_of: UBERON:0000485 ! simple columnar epithelium -intersection_of: composed_primarily_of CL:0000150 ! glandular epithelial cell +intersection_of: composed_primarily_of CL:0000150 ! glandular secretory epithelial cell [Term] id: UBERON:0006930 name: glandular cuboidal epithelium xref: FMA:66809 intersection_of: UBERON:0000484 ! simple cuboidal epithelium -intersection_of: composed_primarily_of CL:0000150 ! glandular epithelial cell +intersection_of: composed_primarily_of CL:0000150 ! glandular secretory epithelial cell [Term] id: UBERON:0006931 @@ -134921,7 +134921,7 @@ synonym: "pulmonary neuroepithelial body" EXACT [MP:0010921] xref: EMAPA:37943 {source="MA:th"} is_a: UBERON:0000061 {source="MP"} ! anatomical structure relationship: contributes_to_morphology_of UBERON:0000115 ! lung epithelium -relationship: has_part CL:1000223 ! lung neuroendocrine cell +relationship: has_part CL:1000223 ! pulmonary neuroendocrine cell relationship: part_of UBERON:0000115 ! lung epithelium relationship: part_of UBERON:8600018 ! neuroendocrine system @@ -224710,7 +224710,7 @@ property_value: dcterms-date "2024-11-14T15:00:21Z" xsd:dateTime [Term] id: UBERON:8700003 name: stratum corneum of esophageal epithelium -def: "The outermost layer of the stratified squamous epithelium lining the esophagus, composed of several layers of flattened, anucleated keratinocytes called corneocytes. It forms the primary protective barrier against mechanical, chemical, and microbial insults, while regulating permeability and contributing to tissue integrity. This layer is characterized by corneocytes embedded in a lipid-rich extracellular matrix, providing mechanical reinforcement and maintaining essential barrier functions of the esophageal lining." [doi:10.1038/gimo15, PMID:21126700, PMID:26019440] +def: "The outermost layer of the stratified squamous epithelium lining the esophagus, composed of several layers of flattened epithelial cells that are partially or non-keratinized. This layer provides a protective barrier against mechanical and chemical insults, contributing to tissue integrity and regulating permeability through its apical cell membranes and intercellular junctional complexes." [doi:10.1038/gimo15, doi:10.1152/ajpgi.00088.2015, https://en.wikipedia.org/wiki/Stratified_squamous_epithelium, PMID:21126700, PMID:26019440] is_a: UBERON:0010304 ! non-keratinized stratified squamous epithelium relationship: dc-contributor https://orcid.org/0009-0005-7919-4905 relationship: part_of UBERON:0001043 ! esophagus