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CL:0020018 'proliferative fibrochondrocyte' duplicates the cyclingCellStates pattern off-pattern #3702
Description
CL:0020018 proliferative fibrochondrocyte (added 2025-11, terms:creator "GitHub Copilot", PMID:31871141) asserts:
SubClassOf(obo:CL_0020018 obo:CL_4072104)
SubClassOf(obo:CL_0020018 ObjectSomeValuesFrom(obo:RO_0000056 obo:GO_0022402))
This is the only occurrence of participates_in some 'cell cycle process' in cl-edit.owl. Every other instance lives in the DOSDP-generated definitions.owl, produced from src/patterns/data/default/cyclingCellStates.tsv (20 rows, pattern from #2354 / #2419).
Biologically this is a "cycling fibrochondrocyte" — down to the word "proliferative", which the pattern generates as the exact synonym of every cycling X:
name: "cycling %s"
generated_synonyms: "proliferating %s"
equivalentTo: "%s and ('participates in' some 'cell cycle process')
and ('has quality' some active)"It lacks the pattern's second conjunct (has quality some PATO:0002354 'active'), so it is not inferred under any cycling term. The result is two independent encodings of proliferative state — one pattern-managed, one not — invisible to each other under reasoning.
Suggested resolution
Either:
- convert it to a row in
cyclingCellStates.tsv(withCL:4072104 fibrochondrocyte, or whichever parent is intended), so it joins the pattern and picks up the cycling hierarchy; or - if it is genuinely meant to be a distinct cell type rather than a cell state, drop the
participates_in some GO:0022402axiom so it stops shadowing the pattern.
Flagging rather than fixing, since which of those applies is a curation call.
@cmungall drove the agent, checked its reasoning, and is accountable for its output.
Generated by Claude Code
Activity
dosumis commentedon Oct 15, 2026
@ai4c-agent please move this to the template table (cyclingCellStates.tsv) as suggested - make sure it gets the PATO quality.
ai4c-agent commentedon Oct 15, 2026
🤖 Working on it...
Follow along: View workflow run
— @ai4c-agent
ai4c-agent commentedon Oct 15, 2026
Done — opened #3798.
Approach: reused the existing ID
CL:0020018incyclingCellStates.tsv(cell =CL:4072104 fibrochondrocyte), and stripped the pattern-managed axioms (rdfs:label,IAO:0000115,SubClassOf CL:4072104,SubClassOf participates_in cell cycle process,terms:date,terms:creator) from the stanza incl-edit.owl. The pattern now generates the labelcycling fibrochondrocyte, theparticipates_in some 'cell cycle process'+has quality some PATO:0002354 'active'equivalent class, the brief definition, andproliferating fibrochondrocyteas an exact synonym — so it joins the cycling hierarchy and picks up the PATO quality.Kept in
cl-edit.owl:ProFCabbreviation, the originalproliferative fibrochondrocytelabel as a related synonym (so the previous name is still searchable), the full lineage/marker description from the paper asrdfs:comment, the contributor ORCID, and aterm_tracker_itemback to this issue.One judgment call to flag: I dropped the two marker-expression
SubClassOfaxioms (expresses FGF7,expresses COL1A1). Combined with the pattern's newEquivalentClasses, they would entail that every cycling fibrochondrocyte expresses those markers, but those are characteristic of the specific cells in PMID:31871141 rather than definitional for cycling fibrochondrocytes in general. The marker info is preserved in therdfs:comment. Happy to put them back (or move them onto a narrower subtype) if that's not the call you'd make.🤖 Generated by @ai4c-agent