Backfill related_ingredients via NCBI BioC full-text re-fetch (hCom2, Cheese_Rind) (#30)#158
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… Cheese_Rind) (#30) Option-1 follow-up: the 4 papers that Europe PMC OA couldn't serve were retried via the NCBI BioC PMC API (bionlp/RESTful/pmcoa.cgi/BioC_json). 2 of 4 recovered; folded their full text into the canonical PMID_<id>.md caches and backfilled. 16 new CHEBI-grounded ingredients (hand-authored — the subagent API was unstable; same strict protocol, all snippets verbatim from the enriched caches): - hCom2_Complex_Gut_Microbiome (PMID_36070752.md created from full text): 10 — arginine deiminase pathway (arginine→ornithine + CO2 + ammonium) + community amino-acid utilization set (methionine, histidine, isoleucine, valine, tyrosine) + bile acid. Reagent-catalog hits (Sigma acetate/formate) and a reference-title "butyrate" correctly excluded. - Cheese_Rind (PMID_25036636.md enriched): 6 — branched-chain AA degradation (valine, leucine, isoleucine), cysteine/methionine metabolism, and methanethiol (the volatile sulfur aroma product). Still unrecoverable (not in BioC PMC either): Maize_Root (PMC5373366), Infant_Gut_Phage (PMC11156429). Verified: 16/16 labels canonical, 16/16 snippets exact substrings, both pass linkml-validate, `just validate-products` (blocking gate) exits 0. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Option 1 of the plan: retry the 4 papers that Europe PMC OA returned 404 for, via the NCBI BioC PMC API. 2 of 4 recovered full text; folded into the canonical
PMID_<id>.mdcaches and backfilled. 16 new CHEBI-grounded ingredients.Discipline held under hand-authoring (subagent API was unstable): excluded Sigma reagent-catalog hits (acetate/formate as "Sodium acetate Sigma…"), a bibliography "butyrate" reference title, and generic class terms.
Still unrecoverable (not in BioC PMC either): Maize_Root (PMC5373366), Infant_Gut_Phage (PMC11156429).
Verification
linkml-validateboth → exit 0just validate-products(blocking gate) → exit 0 (5497 OK_CANONICAL)Adoption: 215 → 217 / 265 (hCom2 + Cheese_Rind newly populated).
🤖 Generated with Claude Code