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Fixes #2602 NTR granulosa cells and remake class hierarchy (#2608)
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* Fixes #2602 NTR granulosa cells and remake class hierarchy

Fixes #2602 NTR granulosa cells and remake class hierarchy

* Address review comments

---------

Co-authored-by: CEastwood <[email protected]>
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@aleixpuigb @Caroline-99
aleixpuigb and Caroline-99 authored Sep 25, 2024
1 parent f6cc188 commit 03dc3a0
Showing 1 changed file with 41 additions and 8 deletions.
49 changes: 41 additions & 8 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3035,6 +3035,8 @@ Declaration(Class(obo:CL_4033064))
Declaration(Class(obo:CL_4033065))
Declaration(Class(obo:CL_4033066))
Declaration(Class(obo:CL_4033067))
Declaration(Class(obo:CL_4033083))
Declaration(Class(obo:CL_4033084))
Declaration(Class(obo:CL_4040000))
Declaration(Class(obo:CL_4040001))
Declaration(Class(obo:CL_4040002))
Expand Down Expand Up @@ -3145,8 +3147,9 @@ Declaration(Class(obo:PR_000007479))
Declaration(Class(obo:PR_000007489))
Declaration(Class(obo:PR_000007785))
Declaration(Class(obo:PR_000009981))
Declaration(Class(obo:PR_000013047))
Declaration(Class(obo:PR_000010529))
Declaration(Class(obo:PR_000013047))
Declaration(Class(obo:PR_000013433))
Declaration(Class(obo:PR_000013502))
Declaration(Class(obo:PR_000014419))
Declaration(Class(obo:PR_000014898))
Expand Down Expand Up @@ -7713,7 +7716,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000501 "granulosa cell of o
AnnotationAssertion(rdfs:label obo:CL_0000501 "granulosa cell")
SubClassOf(obo:CL_0000501 obo:CL_0000174)
SubClassOf(obo:CL_0000501 obo:CL_0002174)
SubClassOf(obo:CL_0000501 ObjectSomeValuesFrom(obo:RO_0002207 obo:CL_4033066))
SubClassOf(obo:CL_0000501 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4033066))

# Class: obo:CL_0000502 (type D enteroendocrine cell)

Expand Down Expand Up @@ -9631,8 +9634,8 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000711 "BTO:0002236")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000711 "MESH:D054885")
AnnotationAssertion(rdfs:label obo:CL_0000711 "cumulus cell")
SubClassOf(obo:CL_0000711 obo:CL_0000154)
SubClassOf(obo:CL_0000711 obo:CL_0002174)
SubClassOf(obo:CL_0000711 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000501))
SubClassOf(obo:CL_0000711 obo:CL_0000501)
SubClassOf(obo:CL_0000711 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4033084))

# Class: obo:CL_0000712 (stratum granulosum cell)

Expand Down Expand Up @@ -15530,6 +15533,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002174 "FMA:70589")
AnnotationAssertion(rdfs:label obo:CL_0002174 "follicular cell of ovary")
SubClassOf(obo:CL_0002174 obo:CL_0000500)
SubClassOf(obo:CL_0002174 obo:CL_0002078)
SubClassOf(obo:CL_0002174 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001305))

# Class: obo:CL_0002175 (primary follicular cell of ovary)

Expand Down Expand Up @@ -32053,21 +32057,50 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32759216") Annotation(ob
AnnotationAssertion(rdfs:label obo:CL_4033066 "pre-granulosa cell")
SubClassOf(obo:CL_4033066 obo:CL_0000630)
SubClassOf(obo:CL_4033066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000992))
SubClassOf(obo:CL_4033066 ObjectSomeValuesFrom(obo:RO_0002210 obo:CL_0000501))
SubClassOf(obo:CL_4033066 ObjectSomeValuesFrom(obo:RO_0002210 obo:CL_4033083))

# Class: obo:CL_4033067 (mural granulosa cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27815559") Annotation(oboInOwl:hasDbXref "PMID:33970370") Annotation(oboInOwl:hasDbXref "PMID:34198768") obo:IAO_0000115 obo:CL_4033067 "A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH).")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27815559") Annotation(oboInOwl:hasDbXref "PMID:33970370") Annotation(oboInOwl:hasDbXref "PMID:34198768") obo:IAO_0000115 obo:CL_4033067 "A follicular cell of ovary that differentiates from a cuboidal granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH).")
AnnotationAssertion(terms:contributor obo:CL_4033067 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:contributor obo:CL_4033067 <https://orcid.org/0000-0001-7655-4833>)
AnnotationAssertion(terms:date obo:CL_4033067 "2024-06-07T12:15:13Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_4033067 "EFO:0005289")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1530/REP-16-0500") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033067 "MGC")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34198768") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033067 "mural GC")
AnnotationAssertion(rdfs:label obo:CL_4033067 "mural granulosa cell")
SubClassOf(obo:CL_4033067 obo:CL_0002174)
SubClassOf(obo:CL_4033067 obo:CL_0000501)
SubClassOf(obo:CL_4033067 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000992))
SubClassOf(obo:CL_4033067 ObjectSomeValuesFrom(obo:RO_0002207 obo:CL_0000501))
SubClassOf(obo:CL_4033067 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4033084))

# Class: obo:CL_4033083 (squamous granulosa cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:28892263") obo:IAO_0000115 obo:CL_4033083 "A granulosa cell that has a squamous morphology and form a single layer around the oocyte in primordial follicles. This cell develops directly into a cuboidal granulosa cell during the primordial-to-primary follicle transition.")
AnnotationAssertion(terms:contributor obo:CL_4033083 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:date obo:CL_4033083 "2024-09-24T13:13:24Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22402964") oboInOwl:hasExactSynonym obo:CL_4033083 "flattened granulosa cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33914868") oboInOwl:hasRelatedSynonym obo:CL_4033083 "pre-granulosa cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33914868") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033083 "squamous GC")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") rdfs:comment obo:CL_4033083 "Often in literature squamous granulosa cell and pre-granulosa cell are used as synonyms. However, this term only makes reference to the quiescent granulosa cells that surround the primordial ovarian follicle, while a pre-granulosa cell proliferates to form the primordial follicle (and thus cells become the squamous granulosa cells).")
AnnotationAssertion(rdfs:label obo:CL_4033083 "squamous granulosa cell")
SubClassOf(obo:CL_4033083 obo:CL_0000501)
SubClassOf(obo:CL_4033083 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003981))
SubClassOf(obo:CL_4033083 ObjectSomeValuesFrom(obo:RO_0002207 obo:CL_4033066))
SubClassOf(obo:CL_4033083 ObjectSomeValuesFrom(obo:RO_0002210 obo:CL_4033084))

# Class: obo:CL_4033084 (cuboidal granulosa cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:28892263") obo:IAO_0000115 obo:CL_4033084 "A granulosa cell that has a cuboidal morphology and develops from squamous granulosa cell during the transition between primordial follicle to primary follicle. Cuboidal granulosa cells proliferate to form a second layer within secondary follicles.")
AnnotationAssertion(terms:contributor obo:CL_4033084 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:date obo:CL_4033084 "2024-09-24T13:14:57Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19001500") oboInOwl:hasExactSynonym obo:CL_4033084 "columnar granulosa cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31849844") oboInOwl:hasExactSynonym obo:CL_4033084 "cuboidal epithelial granulosa cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19001500") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033084 "columnar GC")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33914868") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033084 "cuboidal GC")
AnnotationAssertion(rdfs:label obo:CL_4033084 "cuboidal granulosa cell")
SubClassOf(obo:CL_4033084 obo:CL_0000501)
SubClassOf(obo:CL_4033084 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001305))
SubClassOf(obo:CL_4033084 ObjectSomeValuesFrom(obo:RO_0002207 obo:CL_4033083))

# Class: obo:CL_4040000 (glial restricted tripotential precursor cell)

Expand Down

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