cell-ontology icon indicating copy to clipboard operation
cell-ontology copied to clipboard

Add basilar papilla auditory hair cell (CL:7770001)

Open Copilot opened this issue 6 months ago • 2 comments

This PR adds a new term for basilar papilla auditory hair cell (CL:7770001) to the Cell Ontology as requested in the New Term Request.

Changes Made

  • Term ID: CL:7770001 (using CL_777xxxx range for new term requests)
  • Label: "basilar papilla auditory hair cell"
  • Synonym: "basilar papilla hair cell" (consistent with cochlea auditory hair cell synonym pattern)
  • Parent: auditory hair cell (CL:0000202)
  • Anatomical location: basilar papilla (UBERON:0013731)

Definition

"An auditory hair cell found in the basilar papilla, the auditory sensory organ of lizards, amphibians, and birds, which is homologous to the Corti in mammals."

The definition is supported by PMID:33761346 and follows the established pattern used for similar cell types in the ontology.

Technical Details

The term follows the cellPartOfAnatomicalEntity design pattern, with the logical definition:

EquivalentClasses(CL:7770001 ObjectIntersectionOf(CL:0000202 ObjectSomeValuesFrom(BFO:0000050 UBERON:0013731)))

This mirrors the structure of cochlea auditory hair cell (CL:4023120) but uses basilar papilla (UBERON:0013731) instead of cochlea (UBERON:0002227) as the anatomical location.

Validation

  • ✅ Ontology syntax validation passes (robot convert)
  • ✅ Reasoning validation passes (robot reason with ELK)
  • ✅ Follows established naming and annotation patterns
  • ✅ Includes proper metadata (contributor ORCID, creation date, issue tracker)

Fixes #3190.


💡 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.

Copilot avatar Aug 19 '25 15:08 Copilot

#gogoeditdiff

dosumis avatar Dec 08 '25 13:12 dosumis

Your branch is 154 commit/s behind, please update your branch.

github-actions[bot] avatar Dec 08 '25 13:12 github-actions[bot]

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.

github-actions[bot] avatar Jan 08 '26 02:01 github-actions[bot]

The PMID reference included with definition confirms occurrence in birds but links are missing for lizards and amphibians.

This should require additional references, ideally.

KrishnaTO avatar Jan 21 '26 19:01 KrishnaTO

I am going to entirely close this as this was neither reviewed, nor did any human do anything here.

matentzn avatar Jan 22 '26 14:01 matentzn