Merge branch 'master' into 2582-ntr-early-enterocyte-of-colon

src/ontology/cl-edit.owl

@@ -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))
@@ -3066,6 +3068,7 @@ Declaration(Class(obo:CL_4042021))
 Declaration(Class(obo:CL_4042022))
 Declaration(Class(obo:CL_4042023))
 Declaration(Class(obo:CL_4042024))
+Declaration(Class(obo:CL_4042025))
 Declaration(Class(obo:CL_4042026))
 Declaration(Class(obo:CL_4042027))
 Declaration(Class(obo:CL_4047006))
@@ -3084,6 +3087,7 @@ Declaration(Class(obo:CL_4052006))
 Declaration(Class(obo:CL_4052007))
 Declaration(Class(obo:CL_4052008))
 Declaration(Class(obo:CL_4052009))
+Declaration(Class(obo:CL_4052010))
 Declaration(Class(obo:CL_4052048))
 Declaration(Class(obo:CL_4052049))
 Declaration(Class(obo:CP_0000000))
@@ -3146,8 +3150,9 @@ 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))
@@ -3207,6 +3212,7 @@ Declaration(Class(obo:UBERON_0009852))
 Declaration(Class(obo:UBERON_0010397))
 Declaration(Class(obo:UBERON_0011184))
 Declaration(Class(obo:UBERON_0011949))
+Declaration(Class(obo:UBERON_0012186))
 Declaration(Class(obo:UBERON_0012398))
 Declaration(Class(obo:UBERON_0012399))
 Declaration(Class(obo:UBERON_0012419))
@@ -5518,14 +5524,14 @@ SubClassOf(obo:CL_0000209 obo:CL_0002076)
 
 # Class: obo:CL_0000210 (photoreceptor cell)
 
-AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D010786") obo:IAO_0000115 obo:CL_0000210 "A cell specialized to detect and transduce light.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D010786") obo:IAO_0000115 obo:CL_0000210 "A cell specialized in detecting light stimuli that are involved in visual perception.")
 AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000210 "BTO:0001060")
 AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000210 "CALOHA:TS-0868")
 AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000210 "FMA:86740")
 AnnotationAssertion(rdfs:label obo:CL_0000210 "photoreceptor cell")
 AnnotationAssertion(foaf:depiction obo:CL_0000210 "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg"^^xsd:anyURI)
-EquivalentClasses(obo:CL_0000210 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050962)))
-SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000210 obo:CL_0000006)
+EquivalentClasses(obo:CL_0000210 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050908)))
+SubClassOf(obo:CL_0000210 obo:CL_0008028)
 
 # Class: obo:CL_0000211 (electrically active cell)
 
@@ -7714,7 +7720,7 @@ 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)
 
@@ -9632,8 +9638,8 @@ 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)
 
@@ -15531,6 +15537,7 @@ 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)
 
@@ -32054,21 +32061,50 @@ 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)
 
@@ -32429,6 +32465,16 @@ AnnotationAssertion(rdfs:label obo:CL_4042024 "striatal PTHLH MOXD1 expressing i
 SubClassOf(obo:CL_4042024 obo:CL_4042023)
 SubClassOf(obo:CL_4042024 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000010529))
 
+# Class: obo:CL_4042025 (substantia nigra dopaminergic neuron)
+
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32826893") Annotation(oboInOwl:hasDbXref "PMID:35308118") obo:IAO_0000115 obo:CL_4042025 "A midbrain dopaminergic neuron that has its soma located in a substantia nigra. This dopaminergic neuron type is highly metabolically active and it is involved in the regulation of movement, cognition, motivation and reward. Neurodegeneration of this dopaminergic neuronal type causes loss in fine motor control in Parkinson's Disease.")
+AnnotationAssertion(terms:contributor obo:CL_4042025 <https://orcid.org/0000-0002-0098-8958>)
+AnnotationAssertion(terms:date obo:CL_4042025 "2024-09-16T13:09:29Z"^^xsd:dateTime)
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35308118") oboInOwl:hasNarrowSynonym obo:CL_4042025 "SNpc dopaminergic neuron")
+AnnotationAssertion(rdfs:label obo:CL_4042025 "substantia nigra dopaminergic neuron"@en)
+SubClassOf(obo:CL_4042025 obo:CL_0002614)
+SubClassOf(obo:CL_4042025 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061527))
+
 # Class: obo:CL_4042026 (GABAergic interneuron of the anterior substantia nigra pars reticulata)
 
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36148148") obo:IAO_0000115 obo:CL_4042026 "A GABAergic interneuron that has its soma in the anterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterized by the expression of Six3 and Foxp1 and it develops from Nkx6-2 expressing neuronal progenitors in the ventrolateral midbrain-diencephalon region.")
@@ -32625,6 +32671,18 @@ AnnotationAssertion(rdfs:label obo:CL_4052009 "crypt-top fibroblast")
 SubClassOf(obo:CL_4052009 obo:CL_4052007)
 SubClassOf(obo:CL_4052009 ObjectSomeValuesFrom(obo:RO_0002220 obo:UBERON_0013740))
 
+# Class: obo:CL_4052010 (pre-theca cell)
+
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20628033") Annotation(oboInOwl:hasDbXref "PMID:31320652") Annotation(oboInOwl:hasDbXref "PMID:36205477") obo:IAO_0000115 obo:CL_4052010 "A stromal cell that serves as a precursor to the theca cell layers in the ovary growing follicles. This cell is present in the early stages of follicular growth, particularly in smaller follicles. Unlike mature theca cell, a pre-theca cell is initially non-steroidogenic and lacks luteinizing hormone receptors.")
+AnnotationAssertion(terms:contributor obo:CL_4052010 <https://orcid.org/0009-0000-8480-9277>)
+AnnotationAssertion(terms:date obo:CL_4052010 "2024-09-25T11:15:57Z"^^xsd:dateTime)
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36205477") oboInOwl:hasExactSynonym obo:CL_4052010 "early theca cell")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31320652") oboInOwl:hasExactSynonym obo:CL_4052010 "progenitor theca cell")
+AnnotationAssertion(rdfs:label obo:CL_4052010 "pre-theca cell")
+SubClassOf(obo:CL_4052010 obo:CL_0000499)
+SubClassOf(obo:CL_4052010 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0012186))
+SubClassOf(obo:CL_4052010 ObjectSomeValuesFrom(obo:RO_0002203 obo:CL_0000503))
+
 # Class: obo:CL_4052048 (intercalated cell of salivary gland)
 
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.")