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JABelfiore
requested review from
AvolaAmg and
Caroline-99
and removed request for
AvolaAmg
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -simple file):Ontology comparisonLeft
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Ontology importsOntology annotationslaminin enterocyte of colon
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationslaminin enterocyte of colon
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This PR is still in progress - Need new references to support the definition + consider renaming to laminin colonocytes |
src/ontology/cl-edit.owl
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| # Class: obo:CL_4047021 (laminin enterocyte of colon) | ||
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| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:14585148") Annotation(oboInOwl:hasDbXref "PMID:35101094") obo:IAO_0000115 obo:CL_4047021 "An enterocyte located in the epithelium of the large intestine. This cell expresses and interacts with specific laminin isoforms, particularly laminin-332 (composed of α3, β3, and γ2 chains) and laminin-511 (composed of α5, β1, and γ1 chains). Laminin enterocytes of the colon are attached to the basement membrane via hemidesmosomes containing α6β4 integrin, which binds to laminins. This cell exhibits differential expression of laminin chains along the crypt-surface axis") |
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These references are not relevant - new references are needed to support the definition.
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@JABelfiore - https://pubmed.ncbi.nlm.nih.gov/35101094/ - still needs updating.
I couldn't get hold of the other paper - but it is quite old - way before the single cell transciptomics era. Might be useful for cross-referencing location of lamins that are markers for these cell types
From GCA:
VG: not sure if we'll see these in the integrated dataset, but we repeatedly see this cluster of colonocytes that express these laminin genes, particularly LAMA3. Unfortunately, we haven't validate them yet by ISH or IF
Sounds like this is a transcriptomically distinct subset of colonocytes. Might be worth asking VG for reference.
src/ontology/cl-edit.owl
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| AnnotationAssertion(terms:contributor obo:CL_4047021 <https://orcid.org/0009-0005-7919-4905>) | ||
| AnnotationAssertion(terms:date obo:CL_4047021 "2024-09-24T14:36:31Z"^^xsd:dateTime) | ||
| AnnotationAssertion(rdfs:label obo:CL_4047021 "laminin enterocyte of colon"@en) | ||
| EquivalentClasses(obo:CL_4047021 ObjectIntersectionOf(obo:CL_1000347 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0013740))) |
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This defines the cell type as
"Any colonocyte that is part of the crypt or Lieberkuhn" probably too strong. If so, use SubClassOf
src/ontology/cl-edit.owl
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| # Class: obo:CL_4047021 (laminin enterocyte of colon) | ||
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| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:14585148") Annotation(oboInOwl:hasDbXref "PMID:35101094") obo:IAO_0000115 obo:CL_4047021 "An enterocyte located in the epithelium of the large intestine. This cell expresses and interacts with specific laminin isoforms, particularly laminin-332 (composed of α3, β3, and γ2 chains) and laminin-511 (composed of α5, β1, and γ1 chains). Laminin enterocytes of the colon are attached to the basement membrane via hemidesmosomes containing α6β4 integrin, which binds to laminins. This cell exhibits differential expression of laminin chains along the crypt-surface axis") |
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@JABelfiore - https://pubmed.ncbi.nlm.nih.gov/35101094/ - still needs updating.
I couldn't get hold of the other paper - but it is quite old - way before the single cell transciptomics era. Might be useful for cross-referencing location of lamins that are markers for these cell types
From GCA:
VG: not sure if we'll see these in the integrated dataset, but we repeatedly see this cluster of colonocytes that express these laminin genes, particularly LAMA3. Unfortunately, we haven't validate them yet by ISH or IF
Sounds like this is a transcriptomically distinct subset of colonocytes. Might be worth asking VG for reference.
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Please fix PMIDs first as this will help discussion. |
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Updated name and subclass to suggested. Replaced PMID with PMID on laminin isoforms. however still needs another reference mentioning laminin colonocytes or laminin enterocyte of colon by name. I couldn't find these in literature, spoke to GCA and they also don't have current papers on this. Action: Icebox ticket and create list of new cells not in literature for GCA to create a publication on |
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This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so. |
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@JABelfiore Can you please inform us:
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