New Term Request TAC3-Positive interneurons

[AvolaAmg]

Fixes #2300

[anitacaron]

@AvolaAmg, could you please exchange the title and the description?

[dosumis]

#gogoeditdiff

[github-actions]

Your branch is 2 commit/s behind, please update your branch.

[dosumis]

Your branch is 2 commit/s behind, please update your branch.

I have updated.

[dosumis]

#gogoeditdiff

(trying to get diff reports to trigger)

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-03-07/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-03-07/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

CL_4042001 http://purl.obolibrary.org/obo/CL_4042001

Added

• CL_4042001 definition "A GABAergic interneuron that has its soma in the striatum and that has an enriched expression of the gene TAC3."

  • database_cross_reference "PMID:34727523"

• CL_4042001 comment "In Human, Rhesus Macaque, and Marmoset, TAC3-positive interneuron has its soma in the striatum."

  • database_cross_reference "PMID:34727523"

  • database_cross_reference "PMID:32999462"

• CL_4042001 contributor 0000-0002-0098-8958

• CL_4042001 date "2024-03-05T14:29:32Z"^^dateTime

• CL_4042001 has exact synonym "TAC3 interneuron
"

  • database_cross_reference "

PMID:34727523"

• CL_4042001 label "TAC3-positive interneuron"@en

• Class: CL_4042001

• CL_4042001 SubClassOf GABAergic interneuron

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

CL_4042001 http://purl.obolibrary.org/obo/CL_4042001

Added

• CL_4042001 definition "A GABAergic interneuron that has its soma in the striatum and that has an enriched expression of the gene TAC3."

  • database_cross_reference "PMID:34727523"

• CL_4042001 comment "In Human, Rhesus Macaque, and Marmoset, TAC3-positive interneuron has its soma in the striatum."

  • database_cross_reference "PMID:34727523"

  • database_cross_reference "PMID:32999462"

• CL_4042001 contributor 0000-0002-0098-8958

• CL_4042001 date "2024-03-05T14:29:32Z"^^dateTime

• CL_4042001 has exact synonym "TAC3 interneuron
"

  • database_cross_reference "

PMID:34727523"

• CL_4042001 label "TAC3-positive interneuron"@en

• Class: CL_4042001

• CL_4042001 SubClassOf GABAergic interneuron

• CL_4042001 SubClassOf part_of some striatum

[dosumis]

The name sounds super-general (like it applies to any interneuron expressing Tac3) but the axioms are quite specific. Do we really know that all Tac3 expressing interneurons have a soma in the striatum. Isn't it possible that someone will find a Tac3 expressing interneuron elsewhere in the brain?

[AvolaAmg]

@dosumis Thanks for your comment. You are right I did not consider that possibility, I considered the informations in the literature where these cells are described and I used the name that they used in this paper PMID:34727523.
I could either modify the cell label and be more specific about their location, and/or I could do a more in depth literature search to see whether other TAC3 positive interneurons are found elsewhere. Let me know what you think.

[scheuerm]

In the Bakken et al paper (PMID: 34616062), there is a cell type labelled "Inc L3-5 VIP TAC3", which was incorporated into PCL. However, TAC3 is not a very good marker for this cell type and was not selected by NS-Forest (the markers for this cell type were TSHZ2 (Hsap), COL19A1 (Hsap), SOX2-OT (Hsap)). TAC3 was selected as an NS-Forest marker for a number of other interneuron types (see OLS screenshot attached). But I'm not sure if this a logical grouping or not.

[AvolaAmg]

#gogoeditdiff

[aleixpuigb]

Please, see inline comments

[aleixpuigb]

All looks ok!