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Merge pull request #2187 from obophenotype/2180_NTR_mammary_epithelia…
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…l_cell

Addresses #2180 NTR mammary luminal epithelial cells
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@aleixpuigb
aleixpuigb authored Oct 17, 2023
2 parents 20bc1f1 + 9c75379 commit 79a59d1
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45 changes: 45 additions & 0 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3004,6 +3004,8 @@ Declaration(Class(obo:CL_4033053))
Declaration(Class(obo:CL_4033054))
Declaration(Class(obo:CL_4033055))
Declaration(Class(obo:CL_4033056))
Declaration(Class(obo:CL_4033057))
Declaration(Class(obo:CL_4033058))
Declaration(Class(obo:CL_4033059))
Declaration(Class(obo:CL_4033060))
Declaration(Class(obo:CL_4040000))
Expand Down Expand Up @@ -3055,6 +3057,7 @@ Declaration(Class(obo:PR_000002123))
Declaration(Class(obo:PR_000003264))
Declaration(Class(obo:PR_000005444))
Declaration(Class(obo:PR_000005460))
Declaration(Class(obo:PR_000007204))
Declaration(Class(obo:PR_000007785))
Declaration(Class(obo:PR_000009981))
Declaration(Class(obo:PR_000013502))
Expand Down Expand Up @@ -31699,6 +31702,48 @@ AnnotationAssertion(rdfs:label obo:CL_4033056 "onychocyte")
SubClassOf(obo:CL_4033056 obo:CL_0000312)
SubClassOf(obo:CL_4033056 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008198))

# Class: obo:CL_4033057 (luminal adaptive secretory precursor cell of mammary gland)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:35617956") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033057 "A luminal epithelial cell of the mammary gland that can proliferate and has the potential to differentiate into a lactocyte during pregnancy. In humans, a luminal adaptive secretory precursor cell can be identified by high levels of the markers EpCAM and CD49f, and in mice it can be identified by low levels of CD29 and high levels of CD14, Kit, CD61, and Tspan8.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033057 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033057 <https://orcid.org/0000-0003-4969-670X>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033057 "2023-10-13T13:02:55Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35617956") oboInOwl:hasBroadSynonym obo:CL_4033057 "alveolar cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") oboInOwl:hasBroadSynonym obo:CL_4033057 "alveolar progenitor")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") oboInOwl:hasBroadSynonym obo:CL_4033057 "luminal progenitor")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20346151") oboInOwl:hasBroadSynonym obo:CL_4033057 "luminal progenitor cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") oboInOwl:hasBroadSynonym obo:CL_4033057 "luminal secretory cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasExactSynonym obo:CL_4033057 "ER-negative luminal alveolar progenitor")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "AP")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35617956") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "AV")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LASP")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LP")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LumSec")
AnnotationAssertion(rdfs:label obo:CL_4033057 "luminal adaptive secretory precursor cell of mammary gland")
SubClassOf(obo:CL_4033057 obo:CL_0002326)
SubClassOf(obo:CL_4033057 obo:CL_0011115)

# Class: obo:CL_4033058 (luminal hormone-sensing cell of mammary gland)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033058 "A luminal epithelial cell of the mammary gland that transduces endocrine cues to orchestrate proliferation, architectural remodeling, and differentiation of other cells in the mammary gland via paracrine signaling. This cell expresses high levels of estrogen receptors. In humans, a luminal hormone-sensing cell can be identified by high levels of EpCAM and low levels of CD49f, and in mice it can be identified by low levels of CD29 and high levels of Foxa1, CD133, and Sca1 (Ly6a).")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033058 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033058 <https://orcid.org/0000-0003-4969-670X>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033058 "2023-10-16T08:30:25Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone sensing cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone-sensing mammary epithelial cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") oboInOwl:hasBroadSynonym obo:CL_4033058 "luminal hormone-responsive cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20346151") oboInOwl:hasBroadSynonym obo:CL_4033058 "luminal mature cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasExactSynonym obo:CL_4033058 "ER-positive luminal hormone-sensor cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS-MEC")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LHS")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LumHR")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin. In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation. During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad.")
AnnotationAssertion(rdfs:label obo:CL_4033058 "luminal hormone-sensing cell of mammary gland")
SubClassOf(obo:CL_4033058 obo:CL_0000512)
SubClassOf(obo:CL_4033058 obo:CL_0002326)
SubClassOf(obo:CL_4033058 ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000007204))

# Class: obo:CL_4033059 (lactocyte type 1)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasDbXref "PMID:35377806") obo:IAO_0000115 obo:CL_4033059 "A lactocyte that highly expresses genes associated with transcription, immune cell function, and cellular stress. A lactocyte type 1 also expresses genes involved in milk component biosynthesis (e.g., LALBA and CSNs), albeit at lower levels than a lactocyte type 2.")
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3 changes: 2 additions & 1 deletion src/ontology/imports/pr_terms.txt
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Expand Up @@ -36,4 +36,5 @@ PR:P49582
PR:P60041
PR:Q9D387
PR:Q9Z0F7
PR:000001666
PR:000001666
PR:000007204

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