From 8105bd81598c9df620b3a976e261be09f8e90564 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 21 Jul 2026 22:39:08 -0700 Subject: [PATCH] NEXT_TASKS: record ORNL trophic-model causal curation (#249, ~61/304) Add CommunityMech:000176 to the causal "done" list and note the conservative pattern for records whose primary full text can't be retrieved (abstract- supported edges only + a KNOWLEDGE_GAP discussion; 000176 is the worked example). Co-Authored-By: Claude Opus 4.8 (1M context) --- NEXT_TASKS.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/NEXT_TASKS.md b/NEXT_TASKS.md index a133869c..f45d5419 100644 --- a/NEXT_TASKS.md +++ b/NEXT_TASKS.md @@ -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