obophenotype
Add oRGC1 (CL_9900001) retinal ganglion cell orthotype term
- [x] Verify parent term CL_0000740 (retinal ganglion cell) exists
- [x] Fetch and review referenced publications (PMID:37066415, PMID:31784286)
- [x] Determine appropriate CL ID for new term (using CL_9900001 for new term request)
- [x] 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
- [x] Validate ontology syntax with robot convert
- [x] Run robot reason to check consistency
- [x] Address code review feedback
- [x] Preserve in-text references in definition per reviewer request
Original prompt
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 obophenotype/cell-ontology#3513
✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.
@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).
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/2026-02-18/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/2026-02-18/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
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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)."
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oRGC1 SubClassOf retinal ganglion cell
![github-actions[bot] avatar](https://avatars.githubusercontent.com/in/15368?v=4 "Published by a pub.dev verified publisher"){kind=small}
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 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)."
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has cross-reference "PMID:31784286"
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has cross-reference "PMID:37066415"
-
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oRGC1 SubClassOf retinal ganglion cell