Add oRGC2 retinal ganglion cell orthotype term (CL_9900000)

[Copilot]

Plan for creating oRGC2 term (New Term Request)

• Understand the issue requirements
• Review existing retinal ganglion cell terms for format
• Identify appropriate temporary ID: CL_9900000
• Add the new term to cl-edit.owl with all required annotations
• Validate the changes with robot convert
• Run robot reason to check logical consistency
• Address code review feedback
• Run security checks
• Address PR comment: Reinstate in-text references in definition
• Address PR comment: Remove hasOBONamespace annotation

Summary

Successfully created new term CL_9900000 for oRGC2 with:

• Label: oRGC2
• Parent: CL_0000740 (retinal ganglion cell)
• Definition with in-text references (Hahn et al., 2023; Tran et al., 2019) and PMID annotations (PMID:31784286, PMID:37066415)
• Contributor ORCID annotation
• ID annotation
• All validations passed

Original prompt

---

This section details on the original issue you should resolve

<issue_title>[NTR] Create term for oRGC2</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
oRGC2

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 ON parasol RGCs from primate foveal and peripheral retina with their molecularly homologous mouse α RGC subtype (ON‑transient α RGC, C41) (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>

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

• Fixes [NTR] Create term for oRGC2 #3519

---

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

[RiveraAndrea83]

@copilot please reinstate in text references in the definition

[Copilot]

@copilot please reinstate in text references in the definition

Done. Added in-text references back to the definition in commit ee3c106.

[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/2025-12-17/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/2025-12-17/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

oRGC2 http://purl.obolibrary.org/obo/CL_9900000

Added

• Class: oRGC2

• oRGC2 contributor 0000-0002-5507-2103

• oRGC2 id "CL:9900000"

• oRGC2 IAO_0000115 "A conserved retinal ganglion cell orthotype whose transcriptomic profile groups together ON parasol RGCs from primate foveal and peripheral retina with their molecularly homologous mouse α RGC subtype (ON-transient α RGC, C41) (Hahn et al., 2023; Tran et al., 2019)."

  • hasDbXref "PMID:37066415"

  • hasDbXref "PMID:31784286"

• oRGC2 label "oRGC2"

• oRGC2 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

oRGC2 http://purl.obolibrary.org/obo/CL_9900000

Added

• Class: oRGC2

• oRGC2 contributor 0000-0002-5507-2103

• oRGC2 id "CL:9900000"

• oRGC2 definition "A conserved retinal ganglion cell orthotype whose transcriptomic profile groups together ON parasol RGCs from primate foveal and peripheral retina with their molecularly homologous mouse α RGC subtype (ON-transient α RGC, C41) (Hahn et al., 2023; Tran et al., 2019)."

  • database_cross_reference "PMID:37066415"

  • database_cross_reference "PMID:31784286"

• oRGC2 label "oRGC2"

• oRGC2 SubClassOf retinal ganglion cell

[RiveraAndrea83]

@copilot please remove this AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_9900000 "cell")

[Copilot]

@copilot please remove this AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_9900000 "cell")

Done. Removed the hasOBONamespace annotation in commit 9aacaf9.

[Caroline-99]

#gogoeditdiff