Add CL_9900001 (oRGC5) term for retinal ganglion cell orthotype

[Copilot]

Plan for creating oRGC5 term (CL_9900001)

• Understand the repository structure and how terms are defined
• Locate the parent term (CL_0000740 - retinal ganglion cell)
• Review similar terms (OFF parasol ganglion cell - CL_4033051) for pattern
• Create new term CL_9900001 with:
  • Declaration: Declaration(Class(obo:CL_9900001))
  • Label: oRGC5
  • Definition with inline PMID references: "(Hahn et al., 2023, PMID:37066415; Tran et al., 2019, PMID:31784286)"
  • SubClassOf relationship to CL_0000740 (retinal ganglion cell)
  • Creator annotation (GitHub Copilot)
  • Contributor ORCID annotation (https://orcid.org/0000-0002-5507-2103)
  • Date annotation (2025-12-08T11:46:13Z)
• Validate the ontology syntax with robot convert
• Validate reasoning with robot reason
• Run code review and address feedback
  • Fixed non-standard en dash character to standard hyphen
• Run security checks (no code vulnerabilities found)
• Address PR comment: Added PMID references inline within definition text

Summary

Successfully created new Cell Ontology term CL_9900001 (oRGC5) with complete inline references. The definition now includes both author citations and PMID identifiers in the text, following ontology best practices.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>[NTR] Create term for oRGC5</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
oRGC5

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 parasol RGCs from primate foveal and peripheral retina with their molecularly homologous mouse α RGC subtype (OFF‑transient α RGC, C45) (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 term for oRGC5 #3517

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[RiveraAndrea83]

@copilot please reinstate in text references in the definition

[Copilot]

@copilot please reinstate in text references in the definition

Added PMID references inline in the definition text: "(Hahn et al., 2023, PMID:37066415; Tran et al., 2019, PMID:31784286)." - commit 785109d

[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

oRGC5 http://purl.obolibrary.org/obo/CL_9900001

Added

• Class: oRGC5

• oRGC5 contributor 0000-0002-5507-2103

• oRGC5 creator "GitHub Copilot"

• oRGC5 date "2025-12-08T11:46:13Z"^^dateTime

• oRGC5 IAO_0000115 "A conserved retinal ganglion cell orthotype whose transcriptomic profile groups together OFF parasol RGCs from primate foveal and peripheral retina with their molecularly homologous mouse α RGC subtype (OFF-transient α RGC, C45) (Hahn et al., 2023, PMID:37066415; Tran et al., 2019, PMID:31784286)."

  • hasDbXref "PMID:37066415"

  • hasDbXref "PMID:31784286"

• oRGC5 label "oRGC5"

• oRGC5 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

oRGC5 http://purl.obolibrary.org/obo/CL_9900001

Added

• Class: oRGC5

• oRGC5 contributor 0000-0002-5507-2103

• oRGC5 creator "GitHub Copilot"

• oRGC5 date "2025-12-08T11:46:13Z"^^dateTime

• oRGC5 definition "A conserved retinal ganglion cell orthotype whose transcriptomic profile groups together OFF parasol RGCs from primate foveal and peripheral retina with their molecularly homologous mouse α RGC subtype (OFF-transient α RGC, C45) (Hahn et al., 2023, PMID:37066415; Tran et al., 2019, PMID:31784286)."

  • database_cross_reference "PMID:37066415"

  • database_cross_reference "PMID:31784286"

• oRGC5 label "oRGC5"

• oRGC5 SubClassOf retinal ganglion cell

[Caroline-99]

#gogoeditdiff

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.