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Addresses #2180 NTR mammary luminal epithelial cells #2187

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merged 12 commits into from
Oct 17, 2023
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Addresses #2180 NTR mammary luminal epithelial cells #2187

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a414537
Addresses #2180 NTR mammary luminal epithelial cells
aleixpuigb Oct 16, 2023
dce1251
Fix annotation property
aleixpuigb Oct 16, 2023
8fa830d
Merge branch 'master' into 2180_NTR_mammary_epithelial_cell
aleixpuigb Oct 16, 2023
3fc3ba8
Unify comments
aleixpuigb Oct 16, 2023
e50cc8b
ORCID was a string
aleixpuigb Oct 16, 2023
0ee7d6e
Fix change synonym type
aleixpuigb Oct 16, 2023
033c99a
Import estrogen receptor and add axioms
aleixpuigb Oct 16, 2023
73f57cd
Merge branch 'master' into 2180_NTR_mammary_epithelial_cell
aleixpuigb Oct 16, 2023
69a27e4
Addresses edits requested by reviewer
aleixpuigb Oct 17, 2023
f735ec3
Merge branch 'master' into 2180_NTR_mammary_epithelial_cell
aleixpuigb Oct 17, 2023
045eeae
Add " of mammary gland" to the labels
aleixpuigb Oct 17, 2023
9c75379
Merge branch 'master' into 2180_NTR_mammary_epithelial_cell
aleixpuigb Oct 17, 2023
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45 changes: 45 additions & 0 deletions src/ontology/cl-edit.owl
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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 @@ -31698,6 +31701,48 @@ 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)

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")
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hormone sensing --> hormone-sensing

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")
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See comments on other text def as some apply here as well.

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")
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Consider if this is a narrow or exact synonym.

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Following the ER comment above, it should be an exact synonym.

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LP")
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Consider if this should be considered a parent class rather than a broad synonym.

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As in the dbxref is used as a synonym, I would prefer to maintain it as a broad synonym.

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")
SubClassOf(obo:CL_4033057 obo:CL_0002326)
SubClassOf(obo:CL_4033057 obo:CL_0011115)

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

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).")
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Typically comments do not include multiple paragraphs. Unsure if this will cause downstream formatting issues.

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Merged all in one paragraph

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")
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Don't see this reflected in text def.

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Asking to SME about if all LHS cells have estrogen receptors:

LHS cells are typically ESR1/ERa-high (they do NOT express ERb), especially in younger women and mice, when hormone levels are high. In older women, ER levels can drop off in at least some cells, but it is a pretty robust marker generally speaking. In our experience, FOXA1 (a master TF of this lineage and pioneer factor for ER) may be slightly more reliable than ER.

As I see it, even if the levels are lower at certain points, if it is a robust marker it should be included. I will add it to the textual definition.

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")
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.")
Expand Down
3 changes: 2 additions & 1 deletion src/ontology/imports/pr_terms.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -36,4 +36,5 @@ PR:P49582
PR:P60041
PR:Q9D387
PR:Q9Z0F7
PR:000001666
PR:000001666
PR:000007204