Add oRGC4 term (CL_9900001)

[Copilot]

• Understand the repository structure and term format
• Create new term CL_9900001 for oRGC4
• Add term declaration
• Add label annotation
• Add definition with PMIDs (37066415, 31784286)
• Add parent relationship (SubClassOf CL_0000740)
• Add standard metadata (id, namespace)
• Add contributor ORCID (0000-0002-5507-2103)
• Add creator metadata
• Validate syntax with robot convert
• Fix en dash character in definition
• Add in-text references to definition
• Run code review
• Run security checks

Original prompt

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This section details on the original issue you should resolve

<issue_title>[NTR] Create new term for oRGC4</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
oRGC4

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 midget RGCs from primate foveal and peripheral retina with their molecularly homologous mouse alpha RGC subtype (ON‑sustained α RGC, C43)(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 oRGC4 #3515

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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. See commit 52c3834.

[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

oRGC4 http://purl.obolibrary.org/obo/CL_9900001

Added

• Class: oRGC4

• oRGC4 contributor 0000-0002-5507-2103

• oRGC4 creator "GitHub Copilot"

• oRGC4 id "CL:9900001"

• oRGC4 IAO_0000115 "A conserved retinal ganglion cell orthotype whose transcriptomic profile groups together ON midget RGCs from primate foveal and peripheral retina with their molecularly homologous mouse alpha RGC subtype (ON-sustained α RGC, C43) (Hahn et al., 2023; Tran et al., 2019)."

  • hasDbXref "PMID:37066415"

  • hasDbXref "PMID:31784286"

• oRGC4 label "oRGC4"

• oRGC4 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

oRGC4 http://purl.obolibrary.org/obo/CL_9900001

Added

• Class: oRGC4

• oRGC4 contributor 0000-0002-5507-2103

• oRGC4 creator "GitHub Copilot"

• oRGC4 id "CL:9900001"

• oRGC4 definition "A conserved retinal ganglion cell orthotype whose transcriptomic profile groups together ON midget RGCs from primate foveal and peripheral retina with their molecularly homologous mouse alpha RGC subtype (ON-sustained α RGC, C43) (Hahn et al., 2023; Tran et al., 2019)."

  • database_cross_reference "PMID:37066415"

  • database_cross_reference "PMID:31784286"

• oRGC4 label "oRGC4"

• oRGC4 SubClassOf retinal ganglion cell

[Caroline-99]

#gogoeditdiff