Backfill Cable Bacteria related_ingredients via re-fetched abstract (#30)#147
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…ct (#30) Part (b) of the backfill effort: re-fetch fuller abstracts for high-value un-backfillable files, then curate. Re-fetched PMID:27058505 (was a stub cache) and folded the full abstract into references_cache/PMID_27058505.md (the validator's primary cache), unlocking the cable-bacteria sulfur/oxygen chemistry. Added 4 CHEBI-grounded ingredients to Cable_Bacteria_Photosynthetic_Biofilm_Sediment: sulfide (CHEBI:15138), dioxygen (CHEBI:15379), sulfate (CHEBI:16189), iron sulfide (CHEBI:75896) — all snippets verbatim from cited+cached references, all labels OAK-canonical. Also re-fetched PMID:38228683 (CeMbio), PMID:34135464 (PMI Variovorax), and PMID:19395564 (Yogurt) but their full abstracts name no metabolite chemistry (behaviour / phenotypic-variation / in-silico HGT papers) — confirmed genuinely un-backfillable, no changes made. Verified: 4/4 labels canonical, 4/4 snippets exact, linkml-validate passes. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Part (b) — re-fetch fuller abstracts for high-value un-backfillable files.
Screened the un-backfilled set for references cached only as stubs/missing, then re-fetched 4 PMIDs via
communitymech.literature:For the one that unlocked, I folded the full abstract into
references_cache/PMID_27058505.md(the validator's primary cache, previously a stub) and added 4 CHEBI-grounded ingredients to the cable-bacteria community: sulfide, dioxygen, sulfate, iron sulfide. The other 3 are confirmed genuinely un-backfillable (re-fetch verified no hidden chemistry); scratch fetches discarded, no changes.Validation
linkml-validate→ exit 0Adoption: 181 → 182 / 265.
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