From 01a8ba7f16a42da3b4f50b4cf7449e26014de61a Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Mon, 3 Feb 2025 12:09:58 +0000 Subject: [PATCH 1/2] Fixes #2925 Conjunctiva goblet cell Fixes #2925 - Improved textual and logical definition - Added references --- src/ontology/cl-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 8ccb5c431..ef3a665e1 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -29136,12 +29136,12 @@ EquivalentClasses(obo:CL_2000083 ObjectIntersectionOf(obo:CL_0000346 ObjectSomeV # Class: obo:CL_2000084 (conjunctiva goblet cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") obo:IAO_0000115 obo:CL_2000084 "Any goblet cell that is part of a conjunctiva.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") Annotation(oboInOwl:hasDbXref "PMID:27091323") Annotation(oboInOwl:hasDbXref "PMID:28475124") Annotation(oboInOwl:hasDbXref "PMID:31734511") obo:IAO_0000115 obo:CL_2000084 "A goblet cell that is part of the conjunctival epithelium, characterized by apical accumulation of mucin granules (MUC5AC in humans; Muc5ac/Muc5b in mice). These gel-forming mucins support tear film stability, ocular lubrication, and pathogen defence. The conjunctival goblet cell forms tight junctions with neighbouring epithelial cells via species-specific claudins (claudin-10 in humans, claudin-2 in mice) and regulates immune homeostasis by facilitating soluble antigen transport to dendritic cells through goblet cell-associated antigen passages (GAPs) (Barbosa et al., 2017). The transcription factor SPDEF is essential for its differentiation.") AnnotationAssertion(terms:contributor obo:CL_2000084 ) AnnotationAssertion(oboInOwl:creation_date obo:CL_2000084 "2014-12-02T19:28:38Z"^^xsd:dateTime) -AnnotationAssertion(oboInOwl:id obo:CL_2000084 "CL:2000084") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31734511") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_2000084 "CGCs") AnnotationAssertion(rdfs:label obo:CL_2000084 "conjunctiva goblet cell") -EquivalentClasses(obo:CL_2000084 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001811))) +EquivalentClasses(obo:CL_2000084 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0006763))) # Class: obo:CL_2000085 (mononuclear cell of umbilical cord) From 7e4d8ca7d3118af438303abd50e80b52c761e8a9 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Tue, 11 Feb 2025 12:04:34 +0000 Subject: [PATCH 2/2] updated definition and synonym --- src/ontology/cl-edit.owl | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index e06991be7..d1c8b62ba 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3398,7 +3398,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to") -# Annotation Property: obo:IAO_0000700 (preferred_root) +# Annotation Property: obo:IAO_0000700 (has ontology root term) AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root") @@ -3488,11 +3488,11 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") -# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym) +# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") -# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) +# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") @@ -5185,7 +5185,6 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "BTO:0001780") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "FMA:62901") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") oboInOwl:hasExactSynonym obo:CL_0000162 "gastric parietal cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") Annotation(oboInOwl:hasDbXref "PMID:31613538") rdfs:comment obo:CL_0000162 "Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function.") AnnotationAssertion(rdfs:label obo:CL_0000162 "parietal cell") SubClassOf(obo:CL_0000162 obo:CL_0000151) @@ -29138,10 +29137,10 @@ EquivalentClasses(obo:CL_2000083 ObjectIntersectionOf(obo:CL_0000346 ObjectSomeV # Class: obo:CL_2000084 (conjunctiva goblet cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") Annotation(oboInOwl:hasDbXref "PMID:27091323") Annotation(oboInOwl:hasDbXref "PMID:28475124") Annotation(oboInOwl:hasDbXref "PMID:31734511") obo:IAO_0000115 obo:CL_2000084 "A goblet cell that is part of the conjunctival epithelium, characterized by apical accumulation of mucin granules (MUC5AC in humans; Muc5ac/Muc5b in mice). These gel-forming mucins support tear film stability, ocular lubrication, and pathogen defence. The conjunctival goblet cell forms tight junctions with neighbouring epithelial cells via species-specific claudins (claudin-10 in humans, claudin-2 in mice) and regulates immune homeostasis by facilitating soluble antigen transport to dendritic cells through goblet cell-associated antigen passages (GAPs) (Barbosa et al., 2017). The transcription factor SPDEF is essential for its differentiation.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") Annotation(oboInOwl:hasDbXref "PMID:27091323") Annotation(oboInOwl:hasDbXref "PMID:28475124") Annotation(oboInOwl:hasDbXref "PMID:31734511") obo:IAO_0000115 obo:CL_2000084 "A goblet cell that is part of the conjunctival epithelium, characterized by apical accumulation of mucin granules (containing MUC5AC in humans; Muc5ac/Muc5b in mice). These gel-forming mucins support tear film stability, ocular lubrication, and pathogen defence. The conjunctival goblet cell forms tight junctions with neighbouring epithelial cells via species-specific claudins (claudin-10 in humans, claudin-2 in mice) and regulates immune homeostasis by facilitating soluble antigen transport to dendritic cells through goblet cell-associated antigen passages (GAPs) (Barbosa et al., 2017). The transcription factor SPDEF is essential for its differentiation.") AnnotationAssertion(terms:contributor obo:CL_2000084 ) AnnotationAssertion(oboInOwl:creation_date obo:CL_2000084 "2014-12-02T19:28:38Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31734511") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_2000084 "CGCs") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31734511") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_2000084 "CGC") AnnotationAssertion(rdfs:label obo:CL_2000084 "conjunctiva goblet cell") EquivalentClasses(obo:CL_2000084 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0006763)))