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BEST4 enterocyte and subtypes #2465

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merged 15 commits into from
Sep 14, 2024
Merged

BEST4 enterocyte and subtypes #2465

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dd70a41
class hierarchy revision
JABelfiore Jul 25, 2024
ec0bb2e
Fixes #2410
JABelfiore Aug 2, 2024
91ecd54
Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…
dosumis Aug 2, 2024
9d51823
related synonym added
JABelfiore Aug 6, 2024
3e2f3da
Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…
JABelfiore Aug 6, 2024
00c5f36
Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…
Caroline-99 Aug 19, 2024
425230d
CL ID updated
JABelfiore Aug 29, 2024
dcc785e
Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…
JABelfiore Aug 29, 2024
79f889b
Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…
JABelfiore Aug 30, 2024
e44a3cb
Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…
Caroline-99 Sep 2, 2024
ffce836
Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…
Caroline-99 Sep 6, 2024
1a4b12d
Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…
dosumis Sep 13, 2024
e6cf640
Update cl-edit.owl
dosumis Sep 13, 2024
0cb956a
Update cl-edit.owl
dosumis Sep 13, 2024
7c4485c
Update cl-edit.owl
dosumis Sep 13, 2024
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32 changes: 27 additions & 5 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3057,6 +3057,8 @@ Declaration(Class(obo:CL_4042013))
Declaration(Class(obo:CL_4042014))
Declaration(Class(obo:CL_4042015))
Declaration(Class(obo:CL_4042016))
Declaration(Class(obo:CL_4047001))
Declaration(Class(obo:CL_4047002))
Declaration(Class(obo:CP_0000000))
Declaration(Class(obo:CP_0000025))
Declaration(Class(obo:CP_0000027))
Expand Down Expand Up @@ -30811,12 +30813,12 @@ 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+ enterocyte)

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.")
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consider to add the broad synonym
BEST4+ epithelial cell https://www.nature.com/articles/s41586-021-03852-1
BEST4+ cell
and
The related synonym
BEST4-expressing enterocyte (same paper)

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we decided to add as exact

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@JABelfiore Have these terms been added as exact synonyms? I can only see BEST4+ intestinal epithelial cell, human as exact synonym

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+ enterocyte")
SubClassOf(obo:CL_4030026 obo:CL_0000584)
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SubClassOf(obo:CL_4030026 ObjectSomeValuesFrom(obo:RO_0002160 obo:NCBITaxon_9606))
SubClassOf(obo:CL_4030026 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q8NFU0))

Expand Down Expand Up @@ -30948,7 +30950,7 @@ SubClassOf(obo:CL_4030039 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070006))

# Class: obo:CL_4030040 (endometrial ciliated epithelial cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") Annotation(oboInOwl:hasDbXref "doi:10.1016/j.coemr.2024.100503") obo:IAO_0000115 obo:CL_4030040 "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.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") Annotation(oboInOwl:hasDbXref "doi:10.1016/j.coemr.2024.100503") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") obo:IAO_0000115 obo:CL_4030040 "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.")
AnnotationAssertion(terms:date obo:CL_4030040 "2023-02-09T11:25:14Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "ciliated cell of the uterus")
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "uterine ciliated cell")
Expand Down Expand Up @@ -32234,6 +32236,26 @@ SubClassOf(obo:CL_4042016 obo:CL_0000313)
SubClassOf(obo:CL_4042016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005385))
SubClassOf(obo:CL_4042016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011148))

# Class: obo:CL_4047001 (small intestine BEST4+ enterocyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047001 "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels.")
AnnotationAssertion(terms:contributor obo:CL_4047001 <https://orcid.org/0009-0005-7919-4905>)
AnnotationAssertion(terms:date obo:CL_4047001 "2024-07-25T13:05:50Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4047001 "small intestine BEST4+ enterocyte")
SubClassOf(obo:CL_4047001 obo:CL_4030026)
SubClassOf(obo:CL_4047001 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002108))
SubClassOf(obo:CL_4047001 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q8NFU0))

# Class: obo:CL_4047002 (BEST4+ colonocyte)
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AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047002 "An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels.")
AnnotationAssertion(terms:contributor obo:CL_4047002 <https://orcid.org/0009-0005-7919-4905>)
AnnotationAssertion(terms:date obo:CL_4047002 "2024-07-25T13:21:19Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4047002 "BEST4+ colonocyte")
SubClassOf(obo:CL_4047002 obo:CL_4030026)
SubClassOf(obo:CL_4047002 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001155))
SubClassOf(obo:CL_4047002 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q8NFU0))

# Class: obo:CP_0000000 (obsolete CP:0000000)

AnnotationAssertion(obo:IAO_0100001 obo:CP_0000000 obo:CL_0017500)
Expand Down
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