From 701d17153f3e66409a6e4ae19d65d19dbe65d85b Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Wed, 22 Jul 2026 16:05:30 -0700 Subject: [PATCH] NEXT_TASKS: log pending enrichment of single-edge DIET/syntrophy records MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Record a pending causal thread: six 2-node records carry one hand-authored donor→acceptor downstream edge but have not had an Edison causal-graph pass — DIET trio 000031/032/033 and syntrophies 000068/069/070. A full run could add mechanistic nodes/edges (conductive pili / OmcS-OmcZ cytochromes, conductive-material mediation, formate-vs-H2 routes, feedback edges). Also notes the stray untracked *.yaml.bak backups in kb/communities/ (gitignored; target the .yaml files). Co-Authored-By: Claude Opus 4.8 (1M context) --- NEXT_TASKS.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/NEXT_TASKS.md b/NEXT_TASKS.md index b5d665c6..66379c3a 100644 --- a/NEXT_TASKS.md +++ b/NEXT_TASKS.md @@ -360,6 +360,20 @@ errors, e.g. sulfite → CHEBI:16731 *(E)-cinnamaldehyde* instead of CHEBI:17359 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). +**PENDING — enrich the single-edge records via a full causal-graph run.** Six 2-node +records already carry one hand-authored `downstream` edge (donor→acceptor) from original +curation but have not had an Edison causal-graph pass: the DIET trio +`Geobacter_Clostridium_DIET` (000031, PMID:28287150), +`Geobacter_Methanosaeta_DIET` (000032, doi:10.1039/C3EE42189A), +`Geobacter_Methanosarcina_DIET` (000033, PMID:24837373); and the syntrophies +`Syntrophobacter_Methanobacterium_Syntrophy` (000068), `Syntrophobacter_Methanospirillum_Syntrophy` +(000069), `Syntrophomonas_Methanospirillum_Syntrophy` (000070). A full run could add +mechanistic nodes/edges (e.g. conductive pili / OmcS-OmcZ cytochromes, conductive-material +mediation, formate-vs-H2 routes, reverse/feedback edges) beyond the single existing edge. +Run `just research-community-causal CommunityMech:0000NN` per record, then curate +conservatively as usual. NB: stray untracked `*.yaml.bak` backups exist alongside these in +`kb/communities/` (gitignored, not in the repo) — target the `.yaml` files. + **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 **fixed in the runner** (#245): `load_api_key()` now treats the repo `.env` FILE as the