diff --git a/NEXT_TASKS.md b/NEXT_TASKS.md index 02c808a7c..432314073 100644 --- a/NEXT_TASKS.md +++ b/NEXT_TASKS.md @@ -5,7 +5,7 @@ update this file as work is started/finished — move done items out, add new deferrals here. Keep the cross-Mech items in sync with the sibling repos' `NEXT_TASKS.md` (CultureMech / MIM / TraitMech). -Last reconciled: 2026-07-19. +Last reconciled: 2026-07-20. ## 0. Element enum CHEBI groundings are wrong + ungated (found 2026-07-18) @@ -283,13 +283,57 @@ Coordinated cross-Mech adoption of DisMech's domain-general features. Full plan, locked decisions, and DisMech schema references live in culturebotai-claw#7 (the shared, pinned LinkML module is authored once and vendored across all four Mechs). This repo's slice: -- Knowledge gaps — add a `discussions` slot (broad `Discussion` supertype; `kind` - incl. KNOWLEDGE_GAP / OPEN_QUESTION / CONTROVERSY / CURATION_TODO) to - `MicrobialCommunity`, imported from the shared module; bind `attaches_to` - anchors to `ecological_interactions#…`. Wire a `knowledge-gap-scan` recipe over - the existing Edison harness. -- Datasets — migrate the existing `AssociatedDataset` (DatasetRepositoryEnum) to - the canonical shared `Dataset` (data-preserving; reconcile repository/accession - into the canonical enum, which also carries omics `data_type`). -- QC dashboard — adopt the generalized dashboard from Phase 3 (CommunityMech - currently has only the `qc` recipe, no rendered dashboard). +- Knowledge gaps — **DONE (2026-07-20, PR #226).** Added the `discussions` slot + (broad `Discussion` supertype; `kind` incl. KNOWLEDGE_GAP / OPEN_QUESTION / + CONTROVERSY / CURATION_TODO) to `MicrobialCommunity`, imported from the shared + module, with `attaches_to` anchors bound to `ecological_interactions#…`. First + real use: a KNOWLEDGE_GAP block in `Cellulose_Methane_Quad_Culture_SynCom`. + **Still pending:** a standing `knowledge-gap-scan` recipe over the Edison harness + (the causal-graph mode below is the closest existing capability). +- Datasets — **STILL PENDING.** Migrate the existing `AssociatedDataset` + (DatasetRepositoryEnum) to the canonical shared `Dataset` (data-preserving; + reconcile repository/accession into the canonical enum, which also carries omics + `data_type`). +- QC dashboard — **STILL PENDING.** Adopt the generalized dashboard from Phase 3 + (CommunityMech currently has only the `qc` recipe, no rendered dashboard). + +## Causal-graph curation over ecological_interactions (in progress) + +New capability built this session: the `deep-research-community` skill gained a +**causal-edge mode** (scoped to one community at a time) that runs an Edison +PaperQA3 causal-graph template and returns node/edge/DOT artifacts under +`research/communities/-*-causal-artifacts/` (gitignored). Curated records +get directed `downstream` edges on their `ecological_interactions` (and, where the +causal branch has no taxon↔taxon `interaction_type` home, `environmental_factors` +for chemical perturbations). Supporting work: `templates/community_causal_graph_research.md` +(PR #225), `scripts/cache_fulltext.py` for OA full-text snippet validation (PR #227; +**cache-path fix PR #230** — append to the file the reference validator reads, +`PMID_.md` when present else legacy `.txt`). + +**Done so far:** `Cellulose_Methane_Quad_Culture_SynCom` (#226; + acetate→CHEBI:30089 +in #228), `Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy` (#229), +`ANME_SRB_Marine_Methane_Seep_Consortium` (#230). **58/300 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). + +## Space-regolith community curation (in progress — branch `feat/space-regolith-records`) + +Scout report `reports/scout_space_regolith.md` lists **16 defined-community +candidates**. **5 curated** (CommunityMech:000303–000307): BioRock basalt biomining +(#1; folds in vanadium #6 PMID:33868198 + cell-conc #7 PMID:33154740 as evidence), +lettuce PGPB SynCom (#2), P-solubilizers for *N. benthamiana* (#3), Anabaena/MGS-1 +anaerobic-digestion methanogen consortium (#4), BioAsteroid ISS chondrite biomining +(#5; #16 is its preprint — cite the published npj Microgravity version). + +**Remaining candidates to curate** (~8 distinct new records; prioritize defined +multi-microbe communities): #10 cyanobacteria panel (PMID:35865930), #11 Mars-meteorite +4-organism panel (PMID:38665180), #9 AMF+PGPB tomato multi-kingdom (PMID:41597718), +#8 moss-derived microbiome (EPMC AGRICOLA IND609292674), #15 sealed mini-ecosystems +(PMID:39487149), #12 legume–rhizobia mutualism (PMID:34879082), #13 microbial-fertilizer +consortia (PMID:41829787; composition partly undefined — lower priority), #14 AMF chickpea +(PMID:41786794; loosely defined — lower priority). Match the existing regolith records' +house style: `ecological_state: ENGINEERED`, `community_origin: SYNTHETIC`, +`environment_term` → ENVO:01001405 "laboratory environment" with `modeled_environment` +→ ENVO:01000747 "regolith"; every member/interaction evidence snippet fuzzy-matches a +cached abstract/OA full text. See [[space-regolith-scouting-gap]].