Record id-label residual triage: validate-terms-all blocked upstream#159
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…134 follow-up) Triaged all 34 curator-accepted residuals against the current OAK snapshot. Finding: each residual id resolves to an UNRELATED entity in the current ChEBI/ENVO/NCBITaxon build, and broad `runoak search` finds no repoint target for the intended label — the compound/environment is genuinely absent from the ontology and the placeholder id is semantically wrong (e.g. CHEBI:33104 "chromium(III) hydroxide" → hydridoarsenic; ENVO:00000274 "soda lake" → continental rise). Only near-match: sodium metasilicate → CHEBI:60720 sodium silicate (generalization; not applied). Conclusion: enabling `validate-terms-all` as a blocking gate is genuinely upstream-blocked — minting ChEBI/ENVO/GO/NCBITaxon terms is an external OBO process. Recorded the real fix path (term requests + GO repoints) and the data-quality caveat (these groundings carry the wrong id in the KGX export) in NEXT_TASKS.md item 1. No code/data change. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Option 2 of the plan ("mint/clean the 34 residuals so validate-terms-all can go blocking") — triage result.
Re-checked all 34 curator-accepted
exceptionsresiduals against the current OAK snapshot. The finding is sharper than the old "needs minting" reasons suggest: every residual id resolves to an unrelated entity in the current ChEBI/ENVO/NCBITaxon build, and broadrunoak searchfinds no repoint target for the intended label — the compound/environment is genuinely absent from the ontology, and the placeholder id is semantically wrong.Examples:
CHEBI:33104"chromium(III) hydroxide" → hydridoarsenic(2.) (triplet)CHEBI:34818"humic acid" → Leucomycin A8CHEBI:89981"yeast extract" → LPS with O-antigenENVO:00000274"soda lake" → continental riseNCBITaxon:3050471"Stenotrophomonas goyi" → unclassified DissulfuribacterOnly near-repoint: sodium metasilicate (
CHEBI:86154) →CHEBI:60720"sodium silicate" (a generalization that changes the label; not applied).Conclusion
validate-terms-allcannot be made a blocking gate now — minting ChEBI/ENVO/GO/NCBITaxon terms is an external OBO process I can't perform. Documented inNEXT_TASKS.mditem 1: the real fix path (term requests for ~9 CHEBI + 3 ENVO + 2 NCBITaxon; GO obsolete repoints), and the data-quality caveat that these groundings carry the wrong id in the KGX export (worth tracking separately).Doc-only; no code/data change.
validate-productsstays green via theexceptionsallow-list.🤖 Generated with Claude Code