Fix PALLADIUM CHEBI enum: CHEBI:33373 (promethium) → CHEBI:33363 (palladium)#206
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Fix PALLADIUM CHEBI enum: CHEBI:33373 (promethium) → CHEBI:33363 (palladium)#206realmarcin wants to merge 1 commit into
realmarcin wants to merge 1 commit into
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MetalElementEnum.PALLADIUM was grounded to CHEBI:33373, which is actually
"promethium atom" — one of a run of sequential CHEBI ids shared with the
lanthanides, a copy-paste/off-by-one grounding error. The correct term is
CHEBI:33363 ("palladium"), confirmed via OAK.
- schema/communitymech.yaml: PALLADIUM meaning -> CHEBI:33363
- datamodel/communitymech.py: regenerated (just gen-python)
- metal_extraction.py: fix parallel METAL_CHEBI_MAP key
Community YAMLs already cited CHEBI:33363 in their term.{id,label} pairs, so
no data records needed changing. validate-all clean; 197 tests pass.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Problem
MetalElementEnum.PALLADIUMin the LinkML schema was grounded toCHEBI:33373, which is actually promethium atom — not palladium. The id sits in a run of sequential CHEBI ids shared with the lanthanides (NEODYMIUM33372, TERBIUM33374, GADOLINIUM33375…), a classic copy-paste / off-by-one grounding error. The correct term isCHEBI:33363("palladium"), confirmed via OAK.Fix
src/communitymech/schema/communitymech.yaml—PALLADIUMmeaning: CHEBI:33373→CHEBI:33363src/communitymech/datamodel/communitymech.py— regenerated (just gen-python)src/communitymech/metal_extraction.py— corrected the parallelMETAL_CHEBI_MAPkeyThe curated community YAMLs already cited the correct
CHEBI:33363in theirterm.{id,label}pairs, so no data records needed editing — the bug was confined to the schema's authoritative enum grounding.Verification
just validate-all— clean (exit 0)just test— 197 passed🤖 Generated with Claude Code