BDSO is redefining CL’s "displaced amacrine cell" (CL:4023119)

[gouttegd]

BDSO is currently redefining CL’s 'displaced amacrine cell' with

• a new label: “basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)”;
• a new definition: “A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology.”;
• a new exact synonym: “basket L2/3 PV-like SST (Mus)”;
• a new parent class: 'L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)'
• a new relationship: 'has characteristic' some 'basket cell morphology'.

None of that looks remotely correct.

[dosumis]

This is definitely wrong. Looks like an error in the automated generation pipeline that is adding axioms that should be on a PCL term to an unrelated CL term.

I'll investigate.

[dosumis]

Weirdly - it looks like a manual edit:

https://github.com/obophenotype/brain_data_standards_ontologies/blob/master/src/ontology/bdso-edit.owl#L154

@hkir-dev - Is it safe to assume nothing in cl-edit.owl is automatically generated?

I don't recall why we have manual edits here, but I should be able to work out which PCL term this is meant to apply to.

[hkir-dev]

Yes, the bdso-edit.owl file only have manual edits.

It seems that it was first added with this commit (Moved CL PV-like to PCL).

#234

I think we planned to move this term, but something went wrong with the IDs:

    <!-- http://purl.obolibrary.org/obo/CL_4023078 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_4023078">
        <obo:IAO_0000115>OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology.</obo:IAO_0000115>
        <obo:IAO_0100001>PCL:1000003</obo:IAO_0100001>
        <dc:creator rdf:resource="http://orcid.org/0000-0001-7258-9596"/>
        <oboInOwl:hasExactSynonym>basket L2/3 PV-like SST (Mus)</oboInOwl:hasExactSynonym>
        <rdfs:comment>Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000003 instead.</rdfs:comment>
        <rdfs:label>obsolete basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)</rdfs:label>
        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
    </owl:Class>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_4023078"/>
        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
        <owl:annotatedTarget>OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology.</owl:annotatedTarget>
        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:33184512</oboInOwl:hasDbXref>
    </owl:Axiom>

Probably this is the main issue #132