ANME-SRB seep consortium: curate causal graph (DIET conduit + S-inhibition)#230
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…ition) Curates the Edison causal-graph run into the already-grounded ANME-SRB Marine Methane Seep Consortium (CommunityMech:000134). The two core syntrophy interactions (sulfate-coupled AOM; ANME→SRB DIET) were already present and grounded, so the clean value-add is: - DIET interaction: add the hypothesized conductive-pili / multiheme (S-layer) cytochrome conduit as the proposed principal mechanism of sulfate-dependent AOM (mBio, PMID:33975943), incl. a HYPOTHESIZED downstream edge to the sulfate-coupled AOM interaction. - Two chemical-inhibition environmental_factors (the graph's "-" branch, which has no taxon-taxon interaction_type home): sulfite (1.0 mM) and zero-valent sulfur (polythionate/polysulfide) inhibit ANME AOM (Front. Microbiol., PMID:30559729). Edison mislabeled sulfite as CHEBI:16731 ((E)-cinnamaldehyde); corrected to CHEBI:17359 in prose. Also fixes scripts/cache_fulltext.py to append OA full text to the cache file the reference validator actually reads (PMID_<id>.md when present, else legacy .txt) — previously it always wrote .txt, so full-text snippets for PMIDs that had a .md abstract cache never validated. This clears 5 pre-existing growth_media snippet failures for PMID:37747940. Validates: linkml-validate, id-label (--labels), validate-references. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Jul 21, 2026
… 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>
This was referenced Jul 22, 2026
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Curates the Edison causal-graph run into the already-grounded
ANME-SRB Marine Methane Seep Consortium (
CommunityMech:000134).The two core syntrophy interactions — sulfate-coupled AOM, and ANME→SRB
DIET → SRB sulfate reduction — were already present and fully grounded
(NCBITaxon/GO/CHEBI + PMID evidence). The causal run's genuine value-add:
DIET mechanism
conduit as the proposed principal mechanism of sulfate-dependent AOM
(mBio, PMID:33975943): description enrichment, a new evidence item, and a
HYPOTHESIZEDdownstreamedge to the Sulfate-Coupled AOM interaction.Chemical-inhibition branch (the graph's "−" edges)
These have no taxon↔taxon
interaction_typehome, so they're modeled asenvironmental_factors(chemical perturbations), from Front. Microbiol.PMID:30559729:
Helper fix (
scripts/cache_fulltext.py)Appends OA full text to the cache file the reference validator actually
reads —
PMID_<id>.mdwhen present, else legacy.txt. Previously italways wrote
.txt, so full-text snippets for any PMID that had a.mdabstract cache never validated. This clears 5 pre-existing
growth_mediasnippet failures for PMID:37747940 (OA full text now appended to its
.md).Validates locally:
linkml-validate, id-label (--labels),just validate-references— all pass.🤖 Generated with Claude Code