NTR: parasympathetic cholinergic nerve

obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology

http://obophenotype.github.io/uberon/

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NTR: parasympathetic cholinergic nerve #2104

Closed paolaroncaglia closed 3 years ago

paolaroncaglia commented 3 years ago

@emquardokus (cc @dosumis, please see question below)

Preferred term label: parasympathetic cholinergic nerve

Definition (free text, please give PubMed ID) A parasympathetic nerve that releases acetylcholine. PMID:24676230

Parent term (use https://www.ebi.ac.uk/ols/ontologies/uberon) 'parasympathetic nerve' overlaps some 'cholinergic neuron'? (This would be similar to how 'cholinergic enteric nerve' is modelled) present in taxon Homo sapiens

For reference, this request stems from https://github.com/obophenotype/cell-ontology/issues/1279.

dosumis commented 3 years ago

CC @tgbugs

tgbugs commented 3 years ago

This prompted me to look again at how these cases were handled, and I think that the right thing to do here is to update the modelling so that we wind up with parasypathetic cholinergic neuron projection bundle, because I think that there are very few cases of nerves that are purely cholinergic (though some branches might be). We have been working to develop clearer definitions for nerves, nerve branches, fiber bundles, etc., but they aren't quite ready.

dosumis commented 3 years ago

because I think that there are very few cases of nerves that are purely cholinergic (though some branches might be)

That's what I suspected. Is SPARC purely using Uberon? Would be good to coordinate.

dosumis commented 3 years ago

I guess if we have precedent here, fixing the modelling here needn't delay adding the term.

paolaroncaglia commented 3 years ago

@dosumis @tgbugs Thanks for your feedback.

[x] I'll add the term with "old style" axioms for now, but with a 'see also' annotation property pointing to this ticket.
[x] I'll also open a placeholder ticket "Consider coordinating with SPARC to revise modeling of autonomic nervous system?", tagging @tgbugs , referencing the recent SPARC paper. I'll assign to @dosumis to start with, for discussion and coordination.

paolaroncaglia commented 3 years ago

@emquardokus @dosumis The new term is UBERON:8410062 parasympathetic cholinergic nerve. I updated the spreadsheet.

emquardokus commented 3 years ago

All the SPARC work I've seen is using FMA. We have a whole table for peripheral nervous system in collaboration with SPARC.

dosumis commented 3 years ago

All the SPARC work I've seen is using FMA. We have a whole table for peripheral nervous system in collaboration with SPARC.

@tgbugs - would be good to have a call on this. I suspect there are similar issues to the ones we're facing with incorporating vasculature terms and connectivity from Griffin Weber's work.