BEST4 enterocyte and subtypes (#2465)

* class hierarchy revision - class hierarchy revision and 2 subclasses added * Fixes #2410 - logical definition updated best4 * fixed IDs and reserialized - Tweaks to textual and logical defs - renamed enterocyte of colon to colonocyte for consistency --------- Co-authored-by: David Osumi-Sutherland <[email protected]> Co-authored-by: CEastwood <[email protected]>
obophenotype · Sep 14, 2024 · 4adcd94 · 4adcd94
1 parent 29b9465
commit 4adcd94
Showing 1 changed file with 25 additions and 7 deletions.
diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl
@@ -3066,6 +3066,8 @@ Declaration(Class(obo:CL_4047006))
 Declaration(Class(obo:CL_4047007))
 Declaration(Class(obo:CL_4047011))
 Declaration(Class(obo:CL_4047012))
+Declaration(Class(obo:CL_4047051))
+Declaration(Class(obo:CL_4047052))
 Declaration(Class(obo:CL_4052001))
 Declaration(Class(obo:CL_4052002))
 Declaration(Class(obo:CP_0000000))
@@ -25557,13 +25559,14 @@ AnnotationAssertion(oboInOwl:hasNarrowSynonym obo:CL_1000346 "vacuolar absorptiv
 AnnotationAssertion(rdfs:label obo:CL_1000346 "enterocyte of epithelium proper of large intestine")
 SubClassOf(obo:CL_1000346 obo:CL_0002071)
 
-# Class: obo:CL_1000347 (enterocyte of colon)
+# Class: obo:CL_1000347 (colonocyte)
 
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") obo:IAO_0000115 obo:CL_1000347 "A columnar cell of the colon that is part of the colonic epithelium.")
 AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000347 "FMA:263114")
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34497389") oboInOwl:hasExactSynonym obo:CL_1000347 "colonocyte")
+AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_1000347 "enterocyte of colon")
 AnnotationAssertion(oboInOwl:hasNarrowSynonym obo:CL_1000347 "vacuolar absorptive cell of epithelium of colon")
-AnnotationAssertion(rdfs:label obo:CL_1000347 "enterocyte of colon")
+AnnotationAssertion(rdfs:label obo:CL_1000347 "colonocyte")
 EquivalentClasses(obo:CL_1000347 ObjectIntersectionOf(obo:CL_0002071 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000397)))
 SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000347 obo:CL_0002071)
 
@@ -30867,14 +30870,13 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16230044") rdfs:comment
 AnnotationAssertion(rdfs:label obo:CL_4030025 "renal cortical fibroblast")
 EquivalentClasses(obo:CL_4030025 ObjectIntersectionOf(obo:CL_0000057 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005270)))
 
-# Class: obo:CL_4030026 (BEST4+ intestinal epithelial cell, human)
+# Class: obo:CL_4030026 (BEST4+ enteroycte)
 
-AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://orcid.org/0000-0002-7431-4139>) Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:35176508") obo:IAO_0000115 obo:CL_4030026 "An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://orcid.org/0000-0002-7431-4139>) Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:35176508") obo:IAO_0000115 obo:CL_4030026 "An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels.")
 AnnotationAssertion(terms:date obo:CL_4030026 "2022-09-07T12:34:20Z"^^xsd:dateTime)
-AnnotationAssertion(rdfs:label obo:CL_4030026 "BEST4+ intestinal epithelial cell, human")
-SubClassOf(obo:CL_4030026 obo:CL_0000677)
+AnnotationAssertion(rdfs:label obo:CL_4030026 "BEST4+ enteroycte")
+EquivalentClasses(obo:CL_4030026 ObjectIntersectionOf(obo:CL_0000584 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q8NFU0)))
 SubClassOf(obo:CL_4030026 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_9606))
-SubClassOf(obo:CL_4030026 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q8NFU0))
 
 # Class: obo:CL_4030027 (GABAergic amacrine cell)
 
@@ -32378,6 +32380,22 @@ AnnotationAssertion(terms:date obo:CL_4047012 "2024-09-06T08:41:39Z"^^xsd:dateTi
 AnnotationAssertion(rdfs:label obo:CL_4047012 "angiogenic pericyte"@en)
 SubClassOf(obo:CL_4047012 obo:CL_0000669)
 
+# 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.")
+AnnotationAssertion(terms:contributor obo:CL_4047051 <https://orcid.org/0009-0005-7919-4905>)
+AnnotationAssertion(terms:date obo:CL_4047051 "2024-07-25T13:05:50Z"^^xsd:dateTime)
+AnnotationAssertion(rdfs:label obo:CL_4047051 "small intestine BEST4+ enterocyte")
+EquivalentClasses(obo:CL_4047051 ObjectIntersectionOf(obo:CL_0000584 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001902) ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q8NFU0)))
+
+# Class: obo:CL_4047052 (BEST4+ colonocyte)
+
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047052 "An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels.  These cells have a distinct transcriptomic profile compared to other enterocytes and are scattered through the colon epithelium.")
+AnnotationAssertion(terms:contributor obo:CL_4047052 <https://orcid.org/0009-0005-7919-4905>)
+AnnotationAssertion(terms:date obo:CL_4047052 "2024-07-25T13:21:19Z"^^xsd:dateTime)
+AnnotationAssertion(rdfs:label obo:CL_4047052 "BEST4+ colonocyte")
+EquivalentClasses(obo:CL_4047052 ObjectIntersectionOf(obo:CL_1000347 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q8NFU0)))
+
 # Class: obo:CL_4052001 (multiciliated ependymal cell)
 
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25045600") Annotation(oboInOwl:hasDbXref "PMID:28067220") Annotation(oboInOwl:hasDbXref "PMID:37008045") obo:IAO_0000115 obo:CL_4052001 "An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis.")