add subtypes of medium spiny neurons #1752
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Here's a diff of how these changes impact the classified ontology (on -simple file):Ontology comparisonLeft
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Ontology importsOntology annotationsCL_4023026
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsCL_4023026
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Agree if only distinction is gene expression. In PCL should have taxon constraint. Ideally would have a bag of markers too. Is is possible to curate this from paper? |
I can put a rodent taxon constraint, and there are markers, but its a pretty big bag so representing all of them might be unwieldy. However, the major concern with that the reason we are adding the term (or at least the reason why its on our radar) is that a cell in adult human brain is annotated as eSPN, so we still need a grouping term regardless. |
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opened ticket for eccentric medium spiny neuron in PCL and removed it from here, ready for review |
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See inline comments.
A quick online search reveals several papers describing direct and indirect pathway spiny neurones, so may want to consult and reference those instead of wikipedia.
To also consider: describing these cell types as D1+ MSNs or D2+ MSNs may actually get to what is really differentiating these cell type phenotypes instead of relying solely on location.
Traditionally yes, but with new transcriptomics stuff, eccentric MSN kindda messes that up. I think it is accurate to have them as exact synonyms and to add that into definitions. |
| AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023026 <https://orcid.org/0000-0001-7258-9596>) | ||
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34727523"^^xsd:string) Annotation(oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/cl#abbreviation>) oboInOwl:hasExactSynonym obo:CL_4023026 "D2-MSN") | ||
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30096299"^^xsd:string) Annotation(oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/cl#abbreviation>) oboInOwl:hasExactSynonym obo:CL_4023026 "dSPN"^^xsd:string) | ||
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34727523"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4023026 "dopamine 2 medium spiny neuron") |
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This is a synonym for indirect pathway MSN.
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Actually do not see this synonym in the dbxref.
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its spelling out the short form that they used - my thinking being that some people might search using full name and all
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Since this synonym (in a spelled out form) does not appear in the reference, consider removing it and/or the dbxref. If a user searches "dopamine 1 medium spiny neuron", the class will still appear in Protégé without this synonym present.
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agree, ill remove the dbxref. I'd still rather keep the synonym in as I think it is useful.
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34727523"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4023026 "dopamine 1 medium spiny neuron") | ||
| AnnotationAssertion(rdfs:label obo:CL_4023026 "direct pathway medium spiny neuron") | ||
| SubClassOf(obo:CL_4023026 obo:CL_1001474) | ||
| SubClassOf(obo:CL_4023026 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000001175)) |
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May be an upstream modelling issue, but is there evidence D1A receptors are expressed (versus any D1 receptor)? Uberon shows D1 receptor and D1A receptors as exact synonyms... unsure if that is accurate.
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It is accurate according to PR ontology definition (translation of DRD1) where it is imported from - DRD1 encodes for dopamine 1 receptors. I think the modelling is right as it groups D1-like together (which includes DRD5). Took me a second look when I was adding that too and I studied dopamine receptors for my PhD >.< 2 years and everything is forgotten lol
#gogoeditdiff
fixes #1744
Not too sure about eSPN -> might belong in PCL instead, thoughts @dosumis?