New Term Request TAC3-positive medium spiny neurons

[AvolaAmg]

Fixes #2301

[AvolaAmg]

#gogoeditdiff

[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/2024-03-04/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/2024-03-04/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 has exact synonym "D1Sh TAC3 archetype"

  • database_cross_reference "PMID:34727523"

• CL_4042001 definition "A nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron that expresses TAC3. This medium spiny neuron has an enriched expression of the genes MPPED1, HPCAL1, MEIS3.
"

  • database_cross_reference "PMID:34727523"

• CL_4042001 label "TAC3-positive medium spiny neuron"@en

• CL_4042001 has exact synonym "TAC3-positive MSN"

  • database_cross_reference "PMID:34727523"

• CL_4042001 contributor "https://orcid.org/0000-0002-0098-8958"

• CL_4042001 has_broad_synonym "nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron"

• CL_4042001 has exact synonym "TAC3-positive D1Sh-MSN"

  • database_cross_reference "PMID:34727523"

• Class: CL_4042001

• CL_4042001 SubClassOf nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron

[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 has exact synonym "D1Sh TAC3 archetype"

  • database_cross_reference "PMID:34727523"

• CL_4042001 definition "A nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron that expresses TAC3. This medium spiny neuron has an enriched expression of the genes MPPED1, HPCAL1, MEIS3.
"

  • database_cross_reference "PMID:34727523"

• CL_4042001 label "TAC3-positive medium spiny neuron"@en

• CL_4042001 has exact synonym "TAC3-positive MSN"

  • database_cross_reference "PMID:34727523"

• CL_4042001 contributor "https://orcid.org/0000-0002-0098-8958"

• CL_4042001 has_broad_synonym "nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron"

• CL_4042001 has exact synonym "TAC3-positive D1Sh-MSN"

  • database_cross_reference "PMID:34727523"

• Class: CL_4042001

• CL_4042001 SubClassOf nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron

[dosumis]

Is there some consensus on a short name for these neurons yet?

[AvolaAmg]

No there is not. Should I check with people from the BRAIN data standards slack?

[aleixpuigb]

Thank you for this new term. Please, consider the suggested changes.

[scheuerm]

What does enriched expression mean? Are these cells also found in other brain regions? Are these genes also expressed in equivalent cell types in other species?

[AvolaAmg]

What does enriched expression mean? Are these cells also found in other brain regions? Are these genes also expressed in equivalent cell types in other species?

@scheuerm

Thanks for you comment

In PMID:34727523

Differential gene analysis of the D1Sh TAC3 archetype revealed selectively enriched genes in this archetype, including MPPED1, HPCAL1, and MEIS3. This result demonstrates within-subtype variations with potentially functional roles.

I hope this helps to clarify. With enriched expression, it is intended an increased expression of these specific genes in the D1Sh TAC3 archetype (cell type identified through archetype analysis) after performing Differential gene expression analysis. In particular the D1Sh TAC3 archetype was found between the two set of samples they acquired in this dataset. Afterwards, they performed a Dirichlet Simplex Nest (DSN) analysis to identify the distribution of gene expression cross cell archetypes. The molecular markers MPPED1, HPCAL1, MEIS3 were found by performing gene’s Pearson correlation with each archetype of interest.

The TAC3+ Medium spiny neurons are described in PMID:34727523. So far it seems to be the only paper that describes this cell type, therefore there is no additional information in the literature that the molecular signature of these neurons is found 1) in other brain regions and 2) in other species.

[aleixpuigb]

Please, see inline comments.