Addresses #2180 NTR mammary luminal epithelial cells #2187
Conversation
Addresses #2180 NTR mammary luminal epithelial cells
|
#gogoeditdiff |
Fix annotation property
|
Your branch is 8 commit/s behind, please update your branch. |
|
#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -simple file):Ontology comparisonLeft
Right
Ontology importsOntology annotationsCL_4033057
|
Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
Right
Ontology importsOntology annotationsCL_4033057
|
src/ontology/cl-edit.owl
Outdated
| @@ -31685,6 +31688,50 @@ 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.") | |||
There was a problem hiding this comment.
- "lactocyte" is not defined in the ontology.
- "EPCAM" <-- should this be "EpCAM"?
- " ... and in mice, it can be... " <-- comma should be removed
- "TSPAN8" <-- should this be "Tspan8"?
|
|
||
| # 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. 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).") |
There was a problem hiding this comment.
See comments on other text def as some apply here as well.
| 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. |
There was a problem hiding this comment.
Typically comments do not include multiple paragraphs. Unsure if this will cause downstream formatting issues.
There was a problem hiding this comment.
Merged all in one paragraph
| 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)) |
There was a problem hiding this comment.
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.
| SubClassOf(obo:CL_4033057 obo:CL_0002326) | ||
| SubClassOf(obo:CL_4033057 obo:CL_0011115) | ||
|
|
||
| # Class: obo:CL_4033058 (luminal hormone sensing cell) |
| 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 "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasBroadSynonym obo:CL_4033058 "ER-positive luminal hormone-sensor cell") | ||
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone sensing cell") |
There was a problem hiding this comment.
Consider if this should be considered a parent class rather than a broad synonym.
There was a problem hiding this comment.
As in the dbxref is used as a synonym, I would prefer to maintain it as a broad synonym.
| 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 "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasBroadSynonym obo:CL_4033058 "ER-positive luminal hormone-sensor cell") |
There was a problem hiding this comment.
Consider if this is a narrow or exact synonym.
There was a problem hiding this comment.
Following the ER comment above, it should be an exact synonym.
There was a problem hiding this comment.
Defer content review to requester; otherwise, see inline comments.
Unsure how to evaluate dbxrefs as comment states there are no references for them yet, but these classes have dbxrefs added. Did not find term in all references after cursory review.
|
Thank you for the review. I have applied the changes requested. About the name the authors of the dbxrefs were present during the breast jam atlas and decided the names. There was a bioinformatic analysis that showed that cells found in the respective scRNA-seq and had different names were indeed the same cell type, and they proceeded to find the most adequate name. Since this is not published yet, my ORCID can be used as a dbxref. |
|
#gogoeditdiff |
|
"luminal hormone sensing cell" potentially sounds broader than the definition - I'm sure there are hormone sensing cells in the lumen's of many organs. Consider making clear that this is breast/mammary gland specific from name. |
Ok, both labels can be broader than what is intended, therefore I will add "of mammary gland" in both. |
Addresses #2180 NTR mammary luminal epithelial cells
Context: these cell types were requested during the breast atlas jamboree. The names were decided then, and therefore there are no references for them yet (a manuscript is coming soon).