Backfill related_ingredients via full-text re-fetch (Kombucha, Lotus, OMM12) (#30)#154
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… OMM12) (#30) Applies the (b) re-fetch technique with FULL TEXT (not just abstracts): pulled Europe PMC OA fullTextXML for stub-cache-limited / abstract-poor files, folded the body into the canonical PMID_<id>.md caches, then backfilled. 14 new CHEBI-grounded ingredients: - Kombucha (PMID_26061774.md enriched): +4 (glucose, acetic acid, lactic acid, lactose) on top of the existing sucrose/cellulose - Lotus_LjSC3 (PMID_34312531.md created from full text): 9 — the paper's defined artificial-root-exudate medium (glucose, fructose, sucrose, succinic acid, sodium lactate, citric acid, serine, alanine, glutamic acid) - OMM12 (PMID_29051233.md + PMID_31998276.md enriched): 1 (complex carbohydrates; bile acid/mucin correctly rejected — only in cited-ref titles / host machinery) Caches updated in-repo so snippets remain verifiable/reproducible (validator reads .md primary). Not recoverable via Europe PMC OA (404 / not OA): Cheese_Rind, Maize_Root, Infant_Gut_Phage, hCom2. Altered_Schaedler full text fetched but genuinely names no metabolites — confirmed un-backfillable. Verified: 16/16 labels canonical, 16/16 snippets exact substrings of the enriched caches, all 3 pass linkml-validate, `just validate-products` exits 0. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Applies the (b) re-fetch technique with full text: for stub-cache-limited and abstract-poor files, pulled Europe PMC OA
fullTextXML, folded the body into the canonicalPMID_<id>.mdcaches (so snippets stay verifiable), then backfilled. 14 new CHEBI-grounded ingredients across 3 files.Full-text fetch outcomes
Verification
linkml-validateall 3 → exit 0just validate-products(blocking gate) → exit 0 (5461 OK_CANONICAL)Adoption: 207 → 209 / 265 (Lotus + OMM12 newly populated; Kombucha enriched).
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