Re-ground acetate to CHEBI:30089 (KB convention) — quad-culture review fix#228
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Review of the #226 curation decisions against KB-wide convention: acetate should be CHEBI:30089 "acetate" (the anion), used in 69 records / 112 instances, not CHEBI:15366 "acetic acid" (only 7 records). This record's grounding (both the new Rc->Mc interaction metabolite and the pre-existing related_ingredients entry) was the outlier; re-ground both to CHEBI:30089 for KB + internal consistency (also the physiologically apt species at neutral pH). The other five #226 modeling decisions were confirmed best by convention/schema and are unchanged: keep COMMUNITY_LEVEL + PAIRWISE (6 records mix scopes); SYNTROPHY for interspecies H2 transfer (textbook; 130x in KB); directed COMPETITION with source_taxon (KB convention); sulfate cascade as downstream (56 records use it); KNOWLEDGE_GAP (a missing causal/evidentiary link, not a community-debated hypothesis). Verified: linkml-validate clean, id-label passed (CHEBI:30089 canonical), validate-references passes. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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… threads) (#231) - discussions slot marked DONE (PR #226) under the DisMech section; datasets migration + QC dashboard flagged still-pending. - New "Causal-graph curation" section: deep-research causal-edge mode + cache_fulltext path fix; done on quad-culture/Dehalococcoides/ANME-SRB (#226/#228/#229/#230); 58/300 records carry downstream edges. - New "Space-regolith community curation" section: 5/16 candidates curated (000303-000307), remaining ~8 listed with PMIDs + priority. Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Context
You asked me to research each of the 6 curation decisions from #226 and pick the
better option. 5 of 6 stand; only the acetate grounding changes. Verdicts, each
grounded in KB-wide convention + schema/ontology:
downstreamdownstreamused in 56 records for causal chainsThis PR
Re-grounds acetate → CHEBI:30089 "acetate" (the anion) in both places it appears
in
Cellulose_Methane_Quad_Culture_SynCom— the new Rc→Mc interaction metabolite andthe pre-existing
related_ingredientsentry — matching the KB's dominant convention(30089 in 69 records / 112 instances vs 15366 in 7) and keeping the record internally
consistent. The anion is also the physiologically apt species at neutral pH.
Verification
linkml-validate— cleanvalidate-references— passes (full text cached in Cache OA full text for reference-snippet validation (reusable) #227)🤖 Generated with Claude Code