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NEXT_TASKS: record ORNL trophic-model causal curation (#249) #250

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realmarcin merged 1 commit into from
Jul 22, 2026
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NEXT_TASKS: record ORNL trophic-model causal curation (#249) #250

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13 changes: 8 additions & 5 deletions NEXT_TASKS.md
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Expand Up @@ -345,11 +345,14 @@ in #228), `Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy` (#229),
syntrophic loop 1→2→3→1 + negative product-inhibition edge from the Edison graph on
PMID:30038609), `Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture` (#246;
CommunityMech:000268, reversible magnetite-"battery" loop 2⇄3 + both half-reactions →
battery, PMID:25814583). ~60/304 records now carry `downstream` causal edges. **Next:**
continue on high-value syntrophies (e.g. `ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model`
000176, 4 nodes/0 downstream); always use the RECORD's canonical taxon ids (Edison
groundings have had errors, e.g. sulfite → CHEBI:16731 *(E)-cinnamaldehyde* instead of
CHEBI:17359).
battery, PMID:25814583), `ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model` (#249;
CommunityMech:000176 — conservative: full text unretrievable, so 2 directly-implied
donor→partner edges + a KNOWLEDGE_GAP discussion, modeled-limitation node left isolated).
~61/304 records now carry `downstream` causal edges. **Next:** continue on high-value
syntrophies; always use the RECORD's canonical taxon ids (Edison groundings have had
errors, e.g. sulfite → CHEBI:16731 *(E)-cinnamaldehyde* instead of CHEBI:17359). NB: when
the primary full text isn't retrievable, keep edges to abstract-supported/directly-implied
claims and file the rest as a KNOWLEDGE_GAP (000176 is the worked example).

**Edison auth (resolved 2026-07-21):** the key was refreshed in `.env`
(`EDISON_API_KEY`) and authenticates (HTTP 200). The stale-key shadowing footgun is
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