[NTR] Add Oriens-Lacunosum Moleculare neuron (CL_9900001) by Copilot · Pull Request #3603 · obophenotype/cell-ontology

Copilot · 2026-04-10T10:47:51Z

New term request for the OLM interneuron, a well-characterized hippocampal CA1 cell type with a distinctive morphology (soma in stratum oriens, axon exclusively in stratum lacunosum-moleculare) and strong molecular markers (Sst, Grm1, Chrna2).

New term: `CL_9900001`

Label: Oriens-Lacunosum Moleculare neuron
Synonyms: OLM neuron (exact), OLM (related/abbreviation)
Parent: hippocampal interneuron (CL_1001569)
Soma location: CA1 stratum oriens (UBERON_0014552) via RO_0002100
Capability: capable of GABA secretion (GO_0061534) via RO_0002215
References: PMID:20421280, PMID:29487503, PMID:33361464, PMID:10804195, PMID:31420995, PMID:23042082
ID range: temporary (CL_99xxxxx, idrange:81)

Adds new term request from issue #3602: - Term ID: CL_9900001 (temporary ID, idrange:81) - Label: Oriens-Lacunosum Moleculare neuron - Synonyms: OLM neuron (exact), OLM (related/abbreviation) - Definition with 6 PMID references - Parent: hippocampal interneuron (CL_1001569) - has_soma_location CA1 stratum oriens (UBERON_0014552) - capable_of GABA secretion (GO_0061534) - term_tracker_item: issue #3602 Signed-off-by: GitHub Copilot Agent-Logs-Url: https://github.com/obophenotype/cell-ontology/sessions/39dceee3-3f1f-463d-ab4a-53c274c9f960 Co-authored-by: RiveraAndrea83 <205639972+RiveraAndrea83@users.noreply.github.com>

…lare-neuron

dosumis · 2026-04-20T10:46:48Z

#gogoeditdiff

github-actions · 2026-04-20T10:53:18Z

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

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2026-04-20/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2026-04-20/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

Oriens-Lacunosum Moleculare neuron `http://purl.obolibrary.org/obo/CL_9900001`

Added

Class: Oriens-Lacunosum Moleculare neuron
Oriens-Lacunosum Moleculare neuron IAO_0000233 "[NTR] Oriens-Lacunosum Moleculare neuron #3602"
Oriens-Lacunosum Moleculare neuron creator "GitHub Copilot"
Oriens-Lacunosum Moleculare neuron date "2026-04-10T10:48:46Z"^^dateTime
Oriens-Lacunosum Moleculare neuron IAO_0000115 "A GABAergic interneuron of the hippocampal CA1 region whose horizontally oriented soma is located in the stratum oriens at the stratum oriens–alveus border, with spiny dendrites confined to stratum oriens; the axon ascends vertically to arborize exclusively in stratum lacunosum-moleculare, innervating the apical tufts of pyramidal neurons. Electrophysiologically, these cells display regular-to-adapting spiking with a prominent hyperpolarization-activated cation current (Ih) and theta-frequency resonance. In rodents, canonical markers include somatostatin (Sst) and metabotropic glutamate receptor 1 (Grm1/mGluR1); the alpha-2 nicotinic acetylcholine receptor subunit (Chrna2) is a highly specific marker in mouse."
- hasDbXref "PMID:29487503"
- hasDbXref "PMID:31420995"
- hasDbXref "PMID:10804195"
- hasDbXref "PMID:20421280"
- hasDbXref "PMID:33361464"
- hasDbXref "PMID:23042082"
Oriens-Lacunosum Moleculare neuron hasExactSynonym "OLM neuron"
- hasDbXref "PMID:20421280"
Oriens-Lacunosum Moleculare neuron hasRelatedSynonym "OLM"
- hasDbXref "PMID:20421280"
- hasSynonymType OMO_0003000
Oriens-Lacunosum Moleculare neuron label "Oriens-Lacunosum Moleculare neuron"
Oriens-Lacunosum Moleculare neuron SubClassOf cerebral cortex GABAergic interneuron
Oriens-Lacunosum Moleculare neuron SubClassOf hippocampal interneuron
Oriens-Lacunosum Moleculare neuron SubClassOf RO_0002100 some UBERON_0014552

UBERON_0014552 `http://purl.obolibrary.org/obo/UBERON_0014552`

Added

Class: UBERON_0014552

github-actions · 2026-04-20T10:53:20Z

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

Oriens-Lacunosum Moleculare neuron `http://purl.obolibrary.org/obo/CL_9900001`

Added

Class: Oriens-Lacunosum Moleculare neuron
Oriens-Lacunosum Moleculare neuron term tracker item "[NTR] Oriens-Lacunosum Moleculare neuron #3602"
Oriens-Lacunosum Moleculare neuron creator "GitHub Copilot"
Oriens-Lacunosum Moleculare neuron date "2026-04-10T10:48:46Z"^^dateTime
Oriens-Lacunosum Moleculare neuron definition "A GABAergic interneuron of the hippocampal CA1 region whose horizontally oriented soma is located in the stratum oriens at the stratum oriens–alveus border, with spiny dendrites confined to stratum oriens; the axon ascends vertically to arborize exclusively in stratum lacunosum-moleculare, innervating the apical tufts of pyramidal neurons. Electrophysiologically, these cells display regular-to-adapting spiking with a prominent hyperpolarization-activated cation current (Ih) and theta-frequency resonance. In rodents, canonical markers include somatostatin (Sst) and metabotropic glutamate receptor 1 (Grm1/mGluR1); the alpha-2 nicotinic acetylcholine receptor subunit (Chrna2) is a highly specific marker in mouse."
- has cross-reference "PMID:23042082"
- has cross-reference "PMID:20421280"
- has cross-reference "PMID:10804195"
- has cross-reference "PMID:33361464"
- has cross-reference "PMID:31420995"
- has cross-reference "PMID:29487503"
Oriens-Lacunosum Moleculare neuron has exact synonym "OLM neuron"
- has cross-reference "PMID:20421280"
Oriens-Lacunosum Moleculare neuron has_related_synonym "OLM"
- has cross-reference "PMID:20421280"
- has_synonym_type abbreviation
Oriens-Lacunosum Moleculare neuron label "Oriens-Lacunosum Moleculare neuron"
Oriens-Lacunosum Moleculare neuron SubClassOf hippocampal interneuron
Oriens-Lacunosum Moleculare neuron SubClassOf has soma location some UBERON_0014552
Oriens-Lacunosum Moleculare neuron SubClassOf capable of some gamma-aminobutyric acid secretion, neurotransmission

Initial plan

9ddd6eb

Copilot AI assigned Copilot and RiveraAndrea83 Apr 10, 2026

Copilot AI linked an issue Apr 10, 2026 that may be closed by this pull request

[NTR] Oriens-Lacunosum Moleculare neuron #3602

Open

Copilot started work on behalf of RiveraAndrea83 April 10, 2026 10:47 View session

Copilot AI changed the title ~~[WIP] Add term Oriens-Lacunosum Moleculare neuron to ontology~~ [NTR] Add Oriens-Lacunosum Moleculare neuron (CL_9900001) Apr 10, 2026

Copilot stopped work on behalf of RiveraAndrea83 due to an error April 10, 2026 10:59
The "Post Install uv" custom setup step from your .github/workflows/copilot-setup-steps.yml file failed.

Copilot AI requested a review from RiveraAndrea83 April 10, 2026 10:59

dosumis marked this pull request as ready for review April 13, 2026 13:23

Merge branch 'master' into copilot/ntr-adding-oriens-lacunosum-molecu…

c373477

…lare-neuron

github-actions Bot mentioned this pull request Apr 21, 2026

cell-ontology report for 2026-04-21 ai4curation/agent-watcher#25

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github-actions Bot mentioned this pull request Apr 28, 2026

cell-ontology report for 2026-04-28 ai4curation/agent-watcher#32

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dosumis approved these changes Apr 30, 2026

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[NTR] Add Oriens-Lacunosum Moleculare neuron (CL_9900001)#3603

[NTR] Add Oriens-Lacunosum Moleculare neuron (CL_9900001)#3603
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Copilot AI commented Apr 10, 2026 •

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dosumis commented Apr 20, 2026

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github-actions Bot commented Apr 20, 2026

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Ontology annotations

Oriens-Lacunosum Moleculare neuron `http://purl.obolibrary.org/obo/CL_9900001`

Added

UBERON_0014552 `http://purl.obolibrary.org/obo/UBERON_0014552`

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github-actions Bot commented Apr 20, 2026

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Oriens-Lacunosum Moleculare neuron `http://purl.obolibrary.org/obo/CL_9900001`

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Copilot AI commented Apr 10, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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New term: CL_9900001

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dosumis commented Apr 20, 2026

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github-actions Bot commented Apr 20, 2026

Ontology comparison

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Ontology annotations

Oriens-Lacunosum Moleculare neuron http://purl.obolibrary.org/obo/CL_9900001

Added

UBERON_0014552 http://purl.obolibrary.org/obo/UBERON_0014552

Added

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github-actions Bot commented Apr 20, 2026

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Ontology annotations

Oriens-Lacunosum Moleculare neuron http://purl.obolibrary.org/obo/CL_9900001

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Copilot AI commented Apr 10, 2026 •

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New term: `CL_9900001`

Oriens-Lacunosum Moleculare neuron `http://purl.obolibrary.org/obo/CL_9900001`

UBERON_0014552 `http://purl.obolibrary.org/obo/UBERON_0014552`

Oriens-Lacunosum Moleculare neuron `http://purl.obolibrary.org/obo/CL_9900001`