mge-derived-cortical-interneuron-hierarchy

[AvolaAmg]

fixes #2428

[Caroline-99]

#gogoeditdiff

[dosumis]

Updated to use inferred classification #gogoeditdiff

[dosumis]

@AvolaAmg - it would be good to add refs supporting MGE origin, + some note on evidence in comment. This will make it easier for future editors to understand and work with, as well as being potentially useful to users.

[dosumis]

Also wondering what the status is on moving some of these to T-types - particularly SST CHODL to move out from under SST.

[Caroline-99]

#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/2024-09-24/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/2024-09-24/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus) http://purl.obolibrary.org/obo/CL_4023030

Removed

• L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus) SubClassOf sst GABAergic cortical interneuron

Added

• L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus) SubClassOf cerebral cortex GABAergic interneuron

L4 sst Martinotti interneuron (Mmus) http://purl.obolibrary.org/obo/CL_4023031

Removed

• L4 sst Martinotti interneuron (Mmus) SubClassOf sst GABAergic cortical interneuron

Added

• L4 sst Martinotti interneuron (Mmus) SubClassOf cerebral cortex GABAergic interneuron

L5 non-Martinotti sst GABAergic interneuron (Mmus) http://purl.obolibrary.org/obo/CL_4023028

Removed

• L5 non-Martinotti sst GABAergic interneuron (Mmus) SubClassOf sst GABAergic cortical interneuron

Added

• L5 non-Martinotti sst GABAergic interneuron (Mmus) SubClassOf cerebral cortex GABAergic interneuron

L5 sst T-Martinotti interneuron (Mmus) http://purl.obolibrary.org/obo/CL_4023027

Removed

• L5 sst T-Martinotti interneuron (Mmus) SubClassOf sst GABAergic cortical interneuron

Added

• L5 sst T-Martinotti interneuron (Mmus) SubClassOf cerebral cortex GABAergic interneuron

L5/6 non-Martinotti sst GABAergic interneuron (Mmus) http://purl.obolibrary.org/obo/CL_4023118

Removed

• L5/6 non-Martinotti sst GABAergic interneuron (Mmus) SubClassOf sst GABAergic cortical interneuron

Added

• L5/6 non-Martinotti sst GABAergic interneuron (Mmus) SubClassOf cerebral cortex GABAergic interneuron

L6 th sst GABAergic interneuron (Mmus) http://purl.obolibrary.org/obo/CL_4023075

Removed

• L6 th sst GABAergic interneuron (Mmus) SubClassOf sst GABAergic cortical interneuron

Added

• L6 th sst GABAergic interneuron (Mmus) SubClassOf cerebral cortex GABAergic interneuron

oxytocin receptor sst GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023122

Removed

• oxytocin receptor sst GABAergic cortical interneuron SubClassOf sst GABAergic cortical interneuron

Added

• oxytocin receptor sst GABAergic cortical interneuron SubClassOf cerebral cortex GABAergic interneuron

pvalb GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023018

Removed

• pvalb GABAergic cortical interneuron SubClassOf cerebral cortex GABAergic interneuron

Added

• pvalb GABAergic cortical interneuron SubClassOf medial ganglionic eminence derived GABAergic cortical interneuron

sst GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023017

Removed

• sst GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27477017"

• sst GABAergic cortical interneuron SubClassOf cerebral cortex GABAergic interneuron

Added

• sst GABAergic cortical interneuron definition "A GABAergic neuron that develops from medial ganglionic eminence and is located in the cerebral cortex. The interneuron expresses somatostatin (sst) and secretes gamma-aminobutyric acid."

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27477017"

• sst GABAergic cortical interneuron SubClassOf medial ganglionic eminence derived GABAergic cortical 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

chandelier pvalb GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023036

Added

• chandelier pvalb GABAergic cortical interneuron SubClassOf pvalb GABAergic cortical interneuron

medial ganglionic eminence derived GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023069

Added

• medial ganglionic eminence derived GABAergic cortical interneuron SubClassOf medial ganglionic eminence derived interneuron

pvalb GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023018

Removed

• pvalb GABAergic cortical interneuron EquivalentTo interneuron and (has soma location some cerebral cortex) and (capable of some gamma-aminobutyric acid secretion, neurotransmission) and (expresses some parvalbumin alpha)

Added

• pvalb GABAergic cortical interneuron EquivalentTo medial ganglionic eminence derived GABAergic cortical interneuron and (has soma location some cerebral cortex) and (capable of some gamma-aminobutyric acid secretion, neurotransmission) and (expresses some parvalbumin alpha)

• pvalb GABAergic cortical interneuron SubClassOf develops from some medial ganglionic eminence

sst GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023017

Removed

• sst GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27477017"

• sst GABAergic cortical interneuron EquivalentTo interneuron and (has soma location some cerebral cortex) and (capable of some gamma-aminobutyric acid secretion, neurotransmission) and (expresses some somatostatin)

Added

• sst GABAergic cortical interneuron definition "A GABAergic neuron that develops from medial ganglionic eminence and is located in the cerebral cortex. The interneuron expresses somatostatin (sst) and secretes gamma-aminobutyric acid."

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27477017"

• sst GABAergic cortical interneuron EquivalentTo medial ganglionic eminence derived GABAergic cortical interneuron and (has soma location some cerebral cortex) and (capable of some gamma-aminobutyric acid secretion, neurotransmission) and (expresses some somatostatin)

• sst GABAergic cortical interneuron SubClassOf develops from some medial ganglionic eminence

sst chodl GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023121

Added

• sst chodl GABAergic cortical interneuron SubClassOf medial ganglionic eminence derived GABAergic cortical interneuron

• sst chodl GABAergic cortical interneuron SubClassOf develops from some medial ganglionic eminence

[Caroline-99]

@AvolaAmg The classification looks good. The only suggestion I have is to align the textual defs with the logical ones (if you want). ie. sst GABAergic cortical interneuron: A GABAergic neuron that develops from medial ganglionic eminence and is located in the cerebral cortex. The interneuron expresses somatostatin (sst) and secretes gamma-aminobutyric acid.

[AvolaAmg]

@Caroline-99 thank you Caroline! all done, see next commit!

[AvolaAmg]

#gogoeditdiff