Add oRGC1 (CL_9900001) retinal ganglion cell orthotype term

[Copilot]

• Verify parent term CL_0000740 (retinal ganglion cell) exists
• Fetch and review referenced publications (PMID:37066415, PMID:31784286)
• Determine appropriate CL ID for new term (using CL_9900001 for new term request)
• Add new term oRGC1 with:
  • ID: CL_9900001
  • Label: oRGC1
  • Definition with inline PMID references and in-text citations
  • SubClassOf relationship to CL_0000740
  • Contributor annotation (ORCID: 0000-0002-5507-2103)
  • Standard metadata (namespace, id annotation)
  • Date annotation for tracking
• Validate ontology syntax with robot convert
• Run robot reason to check consistency
• Address code review feedback
• Preserve in-text references in definition per reviewer request

Original prompt

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This section details on the original issue you should resolve

<issue_title>[NTR] Create new term for oRGC1</issue_title>
<issue_description>Please check that the term does not already exist by using the ontology search tool OLS:
https://www.ebi.ac.uk/ols4/ontologies/cl

Preferred term label
oRGC1

Synonyms (add reference(s), please)

Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX)
A conserved retinal ganglion cell orthotype whose transcriptomic profile groups together OFF midget RGCs from primate foveal and peripheral retina with their molecularly homologous mouse alpha RGC subtype (OFF‑sustained alpha-RGC, C42) (Hahn et al., 2023; Tran et al., 2019).

Reference:
PMID:37066415
PMID:31784286

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols4/ontologies/cl)
CL_0000740

Anatomical structure where the cell type is found (check Uberon for anatomical structures: https://www.ebi.ac.uk/ols4/ontologies/uberon)

Your ORCID
https://orcid.org/0000-0002-5507-2103

Additional notes or concerns

</issue_description>

<agent_instructions>Please create a new CL term with the information provided</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes [NTR] Create new term for oRGC1 #3513

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[RiveraAndrea83]

@copilot please preserve in text references in the definition

[Copilot]

@copilot please preserve in text references in the definition

Added in-text references to the definition: "(Hahn et al., 2023; Tran et al., 2019)" as requested (commit d912ec9).

[Caroline-99]

#gogoeditdiff

[github-actions]

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/2026-01-29/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/2026-01-29/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

oRGC1 http://purl.obolibrary.org/obo/CL_9900001

Added

• Class: oRGC1

• oRGC1 contributor 0000-0002-5507-2103

• oRGC1 date "2025-12-08T11:40:49Z"^^dateTime

• oRGC1 id "CL:9900001"

• oRGC1 IAO_0000115 "A conserved retinal ganglion cell orthotype whose transcriptomic profile groups together OFF midget RGCs from primate foveal and peripheral retina with their molecularly homologous mouse alpha RGC subtype (OFF-sustained alpha-RGC, C42) (Hahn et al., 2023; Tran et al., 2019)."

  • hasDbXref "PMID:37066415"

  • hasDbXref "PMID:31784286"

• oRGC1 label "oRGC1"

• oRGC1 SubClassOf retinal ganglion cell

[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

oRGC1 http://purl.obolibrary.org/obo/CL_9900001

Added

• Class: oRGC1

• oRGC1 contributor 0000-0002-5507-2103

• oRGC1 date "2025-12-08T11:40:49Z"^^dateTime

• oRGC1 id "CL:9900001"

• oRGC1 definition "A conserved retinal ganglion cell orthotype whose transcriptomic profile groups together OFF midget RGCs from primate foveal and peripheral retina with their molecularly homologous mouse alpha RGC subtype (OFF-sustained alpha-RGC, C42) (Hahn et al., 2023; Tran et al., 2019)."

  • has cross-reference "PMID:31784286"

  • has cross-reference "PMID:37066415"

• oRGC1 label "oRGC1"

• oRGC1 SubClassOf retinal ganglion cell

[RiveraAndrea83]

#gogoeditdiff

[Caroline-99]

#gogoeditdiff

[Caroline-99]

#gogoeditdiff

[RiveraAndrea83]

#gogoeditdiff