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Merge pull request #2024 from obophenotype/1975-NTR-urothelial_cell_t…
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Addresses #1975 [NTR] urothelial cell types
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bvarner-ebi committed Jun 19, 2023
2 parents c67fce5 + e3fed49 commit 926771b
Showing 1 changed file with 29 additions and 4 deletions.
33 changes: 29 additions & 4 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -2928,6 +2928,8 @@ Declaration(Class(obo:CL_4030047))
Declaration(Class(obo:CL_4030048))
Declaration(Class(obo:CL_4030049))
Declaration(Class(obo:CL_4030050))
Declaration(Class(obo:CL_4030051))
Declaration(Class(obo:CL_4030052))
Declaration(Class(obo:CL_4032000))
Declaration(Class(obo:CL_4032001))
Declaration(Class(obo:CL_4033000))
Expand Down Expand Up @@ -3157,7 +3159,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition")

AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to")

# Annotation Property: obo:IAO_0000700 (has ontology root term)
# Annotation Property: obo:IAO_0000700 (preferred_root)

AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root")

Expand Down Expand Up @@ -3926,8 +3928,8 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation(
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "BTO:0000452")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "CALOHA:TS-0362")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "FMA:63877")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "VHOG:0001482")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "NCIT:C12482")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "VHOG:0001482")
AnnotationAssertion(rdfs:comment obo:CL_0000057 "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.")
AnnotationAssertion(rdfs:label obo:CL_0000057 "fibroblast")
SubClassOf(obo:CL_0000057 obo:CL_0002320)
Expand Down Expand Up @@ -8403,9 +8405,9 @@ AnnotationAssertion(owl:deprecated obo:CL_0000585 "true"^^xsd:boolean)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D005854") obo:IAO_0000115 obo:CL_0000586 "The reproductive cell in multicellular organisms.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "BTO:0000535")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "NCIT:C12597")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "VHOG:0001534")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "WBbt:0006796")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "NCIT:C12597")
AnnotationAssertion(rdfs:label obo:CL_0000586 "germ cell")
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000586 obo:CL_0000039)
SubClassOf(obo:CL_0000586 ObjectSomeValuesFrom(obo:RO_0002216 obo:GO_0009566))
Expand Down Expand Up @@ -27711,9 +27713,9 @@ SubClassOf(obo:CL_1001451 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000004

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MP:0008462") Annotation(oboInOwl:hasDbXref "doi:10.1073/pnas.242428599") obo:IAO_0000115 obo:CL_1001474 "An inhibitory, GABAergic projection neuron in the striatum that integrates glutamatergic signals arising from the cerebral cortex and thalamus.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1001474 "BTO:0004778")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0021773") oboInOwl:hasExactSynonym obo:CL_1001474 "striatal medium spiny neuron")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1073/pnas.242428599") oboInOwl:hasExactSynonym obo:CL_1001474 "gamma-aminobutyric acid (GABA)ergic spiny projection neuron")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1073/pnas.242428599") oboInOwl:hasExactSynonym obo:CL_1001474 "gamma-aminobutyric acid ergic spiny projection neuron")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0021773") oboInOwl:hasExactSynonym obo:CL_1001474 "striatal medium spiny neuron")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "BTO:0004778") oboInOwl:hasRelatedSynonym obo:CL_1001474 "medium-sized densely spiny neuron")
AnnotationAssertion(rdfs:label obo:CL_1001474 "medium spiny neuron")
SubClassOf(obo:CL_1001474 obo:CL_0000540)
Expand Down Expand Up @@ -31081,6 +31083,29 @@ SubClassOf(obo:CL_4030050 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005382
SubClassOf(obo:CL_4030050 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000001175))
SubClassOf(obo:CL_4030050 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000001177))

# Class: obo:CL_4030051 (intermediate cell of urothelium)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41385-022-00565-0") obo:IAO_0000115 obo:CL_4030051 "A urothelial cell that is part of the regenerative layer(s) of cells directly superficial to basal cells in urothelium. The layer of intermediate cells in the urothelium ranges from one to several layers thick depending on the species with intermediate cells attached to adjacent cell layers and one another via desmosomes.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030051 "https://orcid.org/0000-0003-3065-9183")
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4030051 "2023-06-16T07:53:43Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_4030051 "FMA:84155")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1007/978-3-030-14366-4_8") oboInOwl:hasExactSynonym obo:CL_4030051 "
urothelial intermediate cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41385-022-00565-0") rdfs:comment obo:CL_4030051 "It has been noted in at least some mammalian species that the urothelial intermediate cell type is similar to basal cells by expressing CK17 and (unlike umbrella cells) p63 but is positive for uroplakins (UPK) and negative for CK5. Urothelial intermediate cells have also been noted to be larger in diameter than urothelial basal cells.")
AnnotationAssertion(rdfs:label obo:CL_4030051 "intermediate cell of urothelium")
SubClassOf(obo:CL_4030051 obo:CL_0000731)

# Class: obo:CL_4030052 (umbrella cell of urothelium)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41385-022-00565-0") obo:IAO_0000115 obo:CL_4030052 "A urothelial cell that is terminally differentiated and part of the urothelial apical surface that forms the high-resistance barrier of urothelium. Umbrella cells have been described as the largest of urothelial cell types, highly polarized, and, in some species, multinucleated. In the relaxed state, these cells form a dome-shaped structure at the apical pole and can also cover multiple underlying intermediate cells, leading to the name umbrella cells. In contrast, these cells flatten when the bladder is filled.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030052 "https://orcid.org/0000-0003-3065-9183")
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4030052 "2023-06-16T07:59:43Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_4030052 "FMA:84149")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41385-022-00565-0") oboInOwl:hasExactSynonym obo:CL_4030052 "facet cell of urothelium")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41385-022-00565-0") oboInOwl:hasExactSynonym obo:CL_4030052 "superficial cell of urothelium")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41385-022-00565-0") rdfs:comment obo:CL_4030052 "Umbrella cells are attached to sub-superficial cell layers via desmosomes, while tight junctions localized between superficial cells aid in forming a high-resistance barrier function. Another distinguishing feature of an umbrella cell type is the presence of subapical discoidal/fusiform-shaped vesicles contributing to the plasticity in urothelial cell surface area through a regulated process of endocytosis/exocytosis. It has been noted in at least some mammalian species that the urothelial umbrella cell type expresses UPK1A, UPK1B, UPK2 and UPK3A. Unlike intermediate and basal cells of the urothelium, CK17 is reported to be completely absent and p63 not expressed in umbrella cells.")
AnnotationAssertion(rdfs:label obo:CL_4030052 "umbrella cell of urothelium")
SubClassOf(obo:CL_4030052 obo:CL_0000731)

# Class: obo:CL_4032000 (club-like cell of the urethral epithelium)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30566875") Annotation(oboInOwl:hasDbXref "PMID:32497356") obo:IAO_0000115 obo:CL_4032000 "An epithelial cell of the urethra that has an expression profile similar to lung club cells. Club-like cells of the urethra epithelium are similar to lung club cells in their expression of SCGB1A1 and in their enrichment of immunomodulatory programs.")
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