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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
Creative Commons Attribution 4.0 International
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[NTR] spiny VIP neuron #2355

Closed AvolaAmg closed 1 week ago

AvolaAmg commented 2 months ago

Please check that the term does not already exist by using the ontology search tool OLS: https://www.ebi.ac.uk/ols4/ontologies/cl

cell label: spiny VIP neuron

Text definition: A vip GABAergic cortical interneuron with a soma located in L1-3 of the neocortex in Mmus. This neuron has a multipolar morphology with spiny dendrites concentrating on L1 of the cortex and has a burst firing electrophysiological signature with highly dynamic dendritic spines.

Database_cross_reference: PMID:35418660

Has a related synonym: superficial VIP-positive spiny neuron Database_cross_reference: PMID:35418660

Has a related synonym: multipolar VIP neuron Database_cross_reference: PMID:35418660

anatomical structure: neocortex

parent term: vip GABAergic cortical interneuron

@aleixpuigb A new term to review.

AvolaAmg commented 2 months ago

@JABelfiore @Caroline-99 @aleixpuigb to review

aleixpuigb commented 1 week ago

Thank you for the term request, @AvolaAmg

Has a related synonym: superficial VIP-positive spiny neuron

I think it can be an exact synonym, since superficial is referring to location L1 and L2/3: image

Text definition: A vip GABAergic cortical interneuron with a soma located in L1-3 of the neocortex in Mmus. This neuron has a multipolar morphology with spiny dendrites concentrating on L1 of the cortex and has a burst firing electrophysiological signature with highly dynamic dendritic spines.

Definition looks good. What is the standard nomenclature for VIP? I see it often capitalized, but the CL term vip GABAergic cortical interneuron is not. Should it be amended? If not, this term might also have to be spiny vip neuron, but I prefer the first option and capitalize in the definition.

AvolaAmg commented 1 week ago

Hi @aleixpuigb thanks for your review. The paper I cite as a reference uses the capitalised version. I would prefer it capitalised as well if that is okay as VIP stands for vasoactive intestinal peptide and so it is an acronym. Apart from that I will turn this ticket into a PR.

aleixpuigb commented 1 week ago

Great, then you can relabel vip GABAergic cortical interneuron to VIP GABAergic cortical interneuron in this ticket.

aleixpuigb commented 1 week ago

These are the terms that has vip in lower case in label, symbol, definition or synonym: image

AvolaAmg commented 1 week ago

happy to capitalise all of them