Relax taxon constraint on UBERON:0001002 (cuticle)#3695
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Relax taxon constraint on UBERON:0001002 (cuticle)#3695ai4c-agent[bot] wants to merge 1 commit intomasterfrom
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Removes the `in_taxon NCBITaxon:6072` (Eumetazoa) constraint from the generic 'cuticle' grouping class. The class is by construction non-homologous (the text definition itself states 'Cuticles are non-homologous, differing in their origin, structure and chemical composition'), so a hard taxon constraint was editorially debatable to begin with. More importantly, the constraint caused downstream taxon constraint violations: GO terms such as 'cuticle development' have logical definitions referencing UBERON:0001002, which propagated the Eumetazoa restriction to plant (Arabidopsis) annotations. This is the least-disruptive fix per @cmungall in #3694, and resolves the violations reported in geneontology/go-ontology#30555 without requiring GO-side changes. The `grouping_class` subset is already present. Updated the comment to explain the rationale and to point users at clade-specific subclasses (e.g. chitin-based cuticle, nematode cuticle), and added a term_tracker_item link to the issue. Improvements to the invertebrate cuticle representation (annelid cuticle, broadening chitin-based cuticle to Panarthropoda, etc.) will be handled in separate PRs as requested. Signed-off-by: @dragon-ai-agent
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Summary
Removes the
in_taxon NCBITaxon:6072(Eumetazoa) constraint from the genericcuticlegrouping class (UBERON:0001002), per @cmungall's main recommendation in #3694.The class is already flagged as a non-homologous grouping (
subset: grouping_class,subset: non_informative) and its own definition acknowledges this: "Cuticles are non-homologous, differing in their origin, structure and chemical composition". The Eumetazoa constraint was therefore an editorial choice rather than a biological assertion, and it caused downstream taxon constraint violations: GO terms likecuticle developmentreference UBERON:0001002 in their logical definitions, propagating the constraint to plant (Arabidopsis) annotations.This is the least-disruptive fix as requested. It does render the generic
cuticleclass quite abstract — clade-specific subclasses (chitin-based cuticle, nematode cuticle, etc.) should be preferred where possible.Changes
relationship: in_taxon NCBITaxon:6072 ! Eumetazoacommentto record the rationale and point users to clade-specific subclassesterm_tracker_itemlinking to incorrect taxon constraints #3694subset: grouping_classwas already present)Resolves
Follow-ups (separate PRs)
Per @cmungall's request, separate PRs will follow improving the invertebrate cuticle representation, e.g.:
annelid cuticle(Lophotrochozoa, collagen-based, non-molted)chitin-based cuticlefrom Arthropoda to Panarthropoda (or addecdysozoan cuticleparent)Test plan
in_taxon Eumetazoa🤖 Generated by @dragon-ai-agent
claude-opus-4-7