From 6ef435dc62ea9462c54b04552f6d75636362b9f0 Mon Sep 17 00:00:00 2001 From: Jasmine Belfiore <166385424+JABelfiore@users.noreply.github.com> Date: Mon, 28 Oct 2024 15:47:35 +0000 Subject: [PATCH] Fixes #2409 Stomach neuroendocrine cells now classified under grouping term (#2533) * Update cl-edit.owl * G cells, EC cells and D cells under this category * Update cl-edit.owl Some more tweaks to fix hierarchy * type g cell of stomach Updated definition to reflect location and created new term for type g cell of stomach * Refs update, logical def amend * references added, def amended * removed an axiom --------- Co-authored-by: David Osumi-Sutherland Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com> Co-authored-by: Caroline Eastwood --- src/ontology/cl-edit.owl | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 9825cfc25..79155c801 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3085,6 +3085,7 @@ Declaration(Class(obo:CL_4047011)) Declaration(Class(obo:CL_4047012)) Declaration(Class(obo:CL_4047018)) Declaration(Class(obo:CL_4047019)) +Declaration(Class(obo:CL_4047025)) Declaration(Class(obo:CL_4047051)) Declaration(Class(obo:CL_4047052)) Declaration(Class(obo:CL_4047101)) @@ -7762,6 +7763,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000502 "FMA:62935") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000502 "D cell") AnnotationAssertion(rdfs:label obo:CL_0000502 "type D enteroendocrine cell") SubClassOf(obo:CL_0000502 obo:CL_0000164) +SubClassOf(obo:CL_0000502 obo:CL_0000165) SubClassOf(obo:CL_0000502 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0070253)) # Class: obo:CL_0000503 (theca cell) @@ -7803,15 +7805,15 @@ SubClassOf(obo:CL_0000507 obo:CL_0000167) # Class: obo:CL_0000508 (type G enteroendocrine cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation(oboInOwl:hasDbXref "MESH:D019863") obo:IAO_0000115 obo:CL_0000508 "An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation(oboInOwl:hasDbXref "MESH:D019863") Annotation(oboInOwl:hasDbXref "PMID:10700044") Annotation(oboInOwl:hasDbXref "PMID:35674015") Annotation(oboInOwl:hasDbXref "PMID:37240181") obo:IAO_0000115 obo:CL_0000508 "An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000508 "BTO:0004108") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000508 "FMA:67609") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000508 "G cell") AnnotationAssertion(rdfs:label obo:CL_0000508 "type G enteroendocrine cell") SubClassOf(obo:CL_0000508 obo:CL_0000164) +SubClassOf(obo:CL_0000508 obo:CL_0000165) SubClassOf(obo:CL_0000508 obo:CL_0000506) SubClassOf(obo:CL_0000508 obo:CL_0000509) -SubClassOf(obo:CL_0000508 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004997)) # Class: obo:CL_0000509 (gastrin secreting cell) @@ -8477,6 +8479,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000577 "argentaffin cell") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000577 "enterochromaffin cell") AnnotationAssertion(rdfs:label obo:CL_0000577 "type EC enteroendocrine cell") SubClassOf(obo:CL_0000577 obo:CL_0000164) +SubClassOf(obo:CL_0000577 obo:CL_0000165) SubClassOf(obo:CL_0000577 obo:CL_0000166) SubClassOf(obo:CL_0000577 obo:CL_0000458) SubClassOf(obo:CL_0000577 obo:CL_0000506) @@ -16523,7 +16526,7 @@ AnnotationAssertion(terms:contributor obo:CL_0002264 ) +AnnotationAssertion(terms:date obo:CL_4047025 "2024-10-24T10:43:22Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:CL_4047025 "type G cell of stomach"@en) +EquivalentClasses(obo:CL_4047025 ObjectIntersectionOf(obo:CL_0000508 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001276))) + # Class: obo:CL_4047051 (small intestine BEST4+ enterocyte) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047051 "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium.")