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obophenotype / brain_data_standards_ontologies

A repository for co-ordinating work on ontologies for the Brain Data Standards Project
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Dealing with X-like in CL and shortening CL labels #118

Closed shawntanzk closed 3 years ago

shawntanzk commented 3 years ago

From @dosumis in relation to CL classes

I'm still uncomfortable with the Pvalb-like classes.

rdfs:label "L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus)" definition "A Sst GABAergic cortical interneuron transcriptomically between the Sst and the Pvalb families with a soma found in L2/3. Some L2/3 PV-like SST cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like SST cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like SST cells have high maximum firing rate variability, with many classified as belonging to the Pvalb subclass on the basis of electrophysiology."

There's not really any way for anyone outside of the BDS project to use these terms for annotation. How will they know when they've found a sufficiently Pvalb-like SST GABAergic to qualify? There's not even an data linked to the term that could be used to project annotations. At least the region specific ones (in BDSO) come with both data and distinguishing markers. The definitions read very much like a case of 'we have a heterogenous cluster in an scRNAseq analysis - here's a summary of various properties of types in it.' In the interests of getting a release out, I'm happy to let them through. But we should make a ticket proposing obsoletion and remove them ASAP.

For CL, I think it will be sufficient to have

L2/3 SST basket neuron L2/3 SST Martinotti neuron

Looking at how easy it was to simplify the names of these (assume all basket and Martonotti are GABAergic), I think we should open a ticket to review long names of recently added neuron types & shorten/simplify where possible.

shawntanzk commented 3 years ago

I've left out the other X-like but added this in cause L2/3 Pvalb-like Sst is actually the name given to it. I think for L2/3 SST basket/Martinotti, we should limit it to the primary motor cortex. Will also look into if there are other L2/3 SST cells with basket/Martinotti morphology, but I think this is unlikely

shawntanzk commented 3 years ago

Related to #19

shawntanzk commented 3 years ago

Related CL ticket: https://github.com/obophenotype/cell-ontology/issues/1138

shawntanzk commented 3 years ago

Decision made on X-like -> change dendrogram file instead (will open a new ticket for this) This will be implemented on all types Labels have been implemented