Community scouting + GTDB grounding + computational-provenance; 29 new community records by realmarcin · Pull Request #180 · CultureBotAI/CommunityMech

realmarcin · 2026-07-02T22:42:15Z

Summary

Adds a literature-scouting → curation pipeline, GTDB grounding of taxa (from the local kg-microbe NCBI↔GTDB mapping), a computational-provenance schema structure, and 29 new evidence-backed community records produced by that pipeline.

Note: this branch also carries the earlier commit 4447ea4 (METPO ROBOT-template cultivation proposal), which predates this work. Happy to split it into its own PR if preferred.

Schema (regenerated datamodel)

ComputationalProvenance on EvidenceItem — queryable tool/version/model/medium provenance for model-derived (COMPUTATIONAL) evidence (+ ComputationalPredictionTypeEnum).
GtdbClassification on TaxonDescriptor — gtdb_id/taxon/lineage/ncbi_source_id/majority_fraction/is_reclassified/mapping_source. gtdb_id is a pattern-checked string, not an OAK-bound term, so id↔label validation ignores it.

Skills & scripts

scout-communities (scripts/scout_communities.py, scout_loop.py) — Europe PMC discovery of newly published communities, deduped vs kb/communities/, community-signal scoring, loop-until-dry sweep.
ground-taxa-gtdb (scripts/gtdb_ground.py) — rank-aware GTDB grounding: species → s__ (id then name fallback), genus/family/order → g__/f__/o__ by genome-weighted majority (≥50%), else AMBIGUOUS. --apply writes blocks via add-only text edits. Sources data/raw/NCBI2GTDB.tsv.gz from a local kg-microbe checkout.

Records — 29 new (`CommunityMech:000272`, `000274`–`000302`)

From a scout sweep: 40 score≥4 leads → triaged to 30 curatable communities → minus 1 exact-paper dup → plus 3 leads whose DOIs were recovered via CrossRef. Each grounds taxa in NCBITaxon (OAK) + GTDB + ENVO with verbatim evidence snippets and abstract-supported interactions. GTDB reclassifications captured (e.g. A. deltae→A. leguminum, Enterococcus→Enterococcus_B, C. aceticum→Clostridium_W aceticum). Spans bioremediation, syntrophy/electrosynthesis, lignocellulose, and gut/diet consortia. 000273 intentionally skipped (dup).

Two ANME-SRB records (000134↔000276) cross-referenced via CROSS_REFERENCE curation events as consolidation candidates.

Validation

validate-all (all records), validate-terms-all, per-record validate + validate-terms, and the 227-test suite all pass. No duplicate papers across the KB or within the batch.

Known follow-ups

000274 and 000285 are thin (members named only as functional groups); their source papers are closed-access (Unpaywall confirms no OA), so enrichment needs full-text access.
Genus/family GTDB grounding uses a ≥50% genome-majority cutoff; borderline cases (e.g. Bacillus at 0.51 across 102 GTDB genera) are flagged in mapping_source.

🤖 Generated with Claude Code

Lifts the cultivation hardware/mode slice added in PR #171 into a new METPO proposal cohort: CultivationModeEnum (10 leaves), CultivationSystemEnum (13 minted leaves + BIOREACTOR_UNSPECIFIED mapped to existing OBI:0001046), under a new "microbial community cultivation setup" domain class, plus 3 cultivation object properties. - Classes: METPO:1008100-1008132 (above the v1 high-water mark 1008013; no overlap) - Predicates: METPO:2008100-2008102 (above 2008002) - Subset: metpo_communitymech_2026_06 - Term metadata reused from vocab/cultivation_terms.yaml Verified: ROBOT column counts (11/12), full enum coverage, parent integrity, no duplicate or v1-overlapping IDs. METPO submission is downstream/external. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…schema Discovery + grounding + provenance tooling, with one pilot record exercising all three. Skills & scripts: - scout-communities: Europe PMC discovery of newly published communities, deduped vs kb/communities (cited PMID/DOI + name overlap), community-signal scoring, and a loop-until-dry multi-angle sweep (scripts/scout_communities.py, scout_loop.py). - ground-taxa-gtdb: GTDB grounding from the local kg-microbe NCBI2GTDB mapping; resolves NCBITaxon id/name/community to GTDB CURIE+lineage+confidence, flags reclassifications (scripts/gtdb_ground.py). Schema (regenerated datamodel): - ComputationalProvenance on EvidenceItem: queryable tool/version/model/medium provenance for model-derived (COMPUTATIONAL) evidence + ComputationalPredictionTypeEnum. - GtdbClassification on TaxonDescriptor: gtdb_id/taxon/lineage/ncbi_source_id/ majority_fraction/is_reclassified/mapping_source (gtdb_id is a pattern-checked string, not an OAK-bound Term, so id-label validation ignores it). Pilot record CommunityMech:000272 (SynCom Y, A. deltae + B. velezensis biofilm co-culture): NCBITaxon + GTDB grounding on both taxa (A. deltae -> GTDB Agrobacterium leguminum, reclassified), cross-feeding interactions with computational_provenance (CarveMe / COBRA Toolbox v3.0 / FBA, LBGM, SRA genomes). Validated: linkml-validate + validate-terms on the record, validate-all (286 records), 197 tests pass. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…ty handling The kg-microbe NCBI2GTDB table is keyed on strain/genome-level NCBI ids, so species-level ids (e.g. Shewanella oneidensis NCBITaxon:70863) miss on exact-id lookup even though the species is in GTDB. Fall back to NCBI-species-name matching; when GTDB splits one NCBI species into several (e.g. Bacillus cereus -> Bacillus_A cereus/anthracis/thuringiensis...), report AMBIGUOUS and emit no forced grounding rather than guessing. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Batch-minted from the scout-communities discovery sweep: 40 score>=4 leads triaged to 30 curatable communities (6 reviews, 4 too-vague, 1 methods paper dropped), minus 1 exact-paper duplicate of the pilot and 3 leads with no citable source. Each record was drafted by an isolated agent against a shared spec and grounds taxa in NCBITaxon (OAK canonical labels) + GTDB (local kg-microbe NCBI2GTDB mapping) + ENVO, with abstract-verbatim evidence snippets and abstract-supported ecological interactions. GTDB reclassifications are captured where they occur (e.g. Agrobacterium deltae -> Agrobacterium leguminum; Clostridium aceticum -> Clostridium_W aceticum). 11/26 carry species-level GTDB grounding; the rest have genus-rank, eukaryotic, or GTDB-ambiguous taxa (genus-level grounding is a pending follow-up). Spans bioremediation, syntrophy/electrosynthesis, lignocellulose, and gut/diet consortia. IDs 000273/000278/000292/000302 intentionally skipped (dup + 3 no-source leads). Validated: validate-all (all records), per-record validate + validate-terms, 227-test suite. No duplicate papers across the KB or within the batch. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Ground taxa at the rank of the input, not species-only: - Species (binomial) -> GTDB:s__ via NCBI id then species-name fallback; GTDB species split -> AMBIGUOUS. - Genus/family/order/... (single-name label) -> GTDB:g__/f__/o__: aggregate the GTDB rank column over all genomes under the NCBI taxon and ground to the GTDB taxon holding a >=50% genome majority, else AMBIGUOUS. mapping_source records the rank and the number of GTDB taxa under the NCBI taxon (e.g. NCBI genus Bacillus -> g__Bacillus at 0.51, 102 GTDB genera; Shewanella/Bifidobacterium ~1.0). Corrects the earlier misconception that genus rank is "not in GTDB" — GTDB is a full hierarchy; the tool just hadn't grounded above species. New --apply mode writes gtdb_classification into a community file via add-only text edits (no YAML round-trip, so plain-scalar wrapping and everything else is byte-for-byte unchanged; skips taxa already grounded and AMBIGUOUS ones). Backfilled 24 genus-level blocks across 12 batch records (274-301). GTDB is bacteria/archaea only, so eukaryotic members still never ground. Validated: per-record validate + validate-terms on all changed files, 227 tests. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…sortia Task 4 (no-source leads): the 3 leads dropped earlier for lacking a citable id were not false positives — all real 2025 SynCom papers indexed in Europe PMC only via the AGR source (no PMID). Recovered their DOIs via CrossRef and curated them into the reserved gap ids: - CommunityMech:000278 SynCom BsBv cigar-tobacco leaf fermentation (B. safensis + B. velezensis) — doi:10.1016/j.indcrop.2025.122621 - CommunityMech:000292 Pseudomonas + Rahnella Artemisia argyi phytoremediation SynCom — doi:10.1016/j.indcrop.2025.122518 - CommunityMech:000302 MetG2 rhizobacteria SynCom for sugarcane stress resilience — doi:10.1016/j.rhisph.2025.101142 Each grounds taxa in NCBITaxon + GTDB (genus/species as named) + ENVO with verbatim DOI-abstract evidence. Task 3 (dedup/curation): added CROSS_REFERENCE curation events linking CommunityMech:000134 (canonical natural ANME-SRB seep consortium) and CommunityMech:000276 (redox-conduction/DIET study of the same syntrophy) as candidates for future consolidation. Task 2 (thin stubs 000274, 000285): deep-research enrichment attempted; both source papers are paywalled with no OA full text and no accessible source names their members, so no taxa were added (no fabrication). Left as-is. Validated: per-record validate + validate-terms on all changed files. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

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Pull request overview

This PR expands CommunityMech’s curation workflow and schema to support (1) automated literature scouting for new microbial communities, (2) GTDB grounding alongside existing NCBITaxon grounding, and (3) structured computational provenance for model-derived evidence—then adds a batch of new community records and cached reference artifacts produced by that pipeline.

Changes:

Extend the LinkML schema with ComputationalProvenance (plus ComputationalPredictionTypeEnum) and GtdbClassification for queryable computational evidence + GTDB grounding.
Add Europe PMC scouting scripts (scout_communities.py, scout_loop.py) and corresponding just recipes + Claude skill docs.
Add a METPO cultivation cohort proposal and many new/updated KB community records + reference-cache artifacts.

Reviewed changes

Copilot reviewed 54 out of 54 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
src/communitymech/schema/communitymech.yaml	Adds schema structures for computational provenance on evidence items and GTDB grounding on taxon descriptors.
scripts/scout_loop.py	Adds a “loop-until-dry” runner that repeatedly scouts Europe PMC across multiple query angles with global deduping and consolidated output.
scripts/scout_communities.py	Adds the core Europe PMC scouting + scoring + deduping implementation and optional stub emission.
references_cache/PMID_42125264.md	Adds cached abstract-only reference content for a newly curated PMID used by new community records.
references_cache/epmc_chem_PMC8072228.txt	Adds extracted chemical-term cache content associated with a referenced PMC article.
references_cache/epmc_chem_PMC5373366.txt	Adds extracted chemical-term cache content associated with a referenced PMC article.
references_cache/epmc_chem_PMC4984294.txt	Adds extracted chemical-term cache content associated with a referenced PMC article.
references_cache/epmc_chem_PMC4510191.txt	Adds extracted chemical-term cache content associated with a referenced PMC article.
references_cache/epmc_chem_PMC242454.txt	Adds extracted chemical-term cache content associated with a referenced PMC article.
references_cache/epmc_chem_PMC1287685.txt	Adds extracted chemical-term cache content associated with a referenced PMC article.
proposals/metpo_communitymech_cultivation_v1/proposal.md	Adds narrative proposal for lifting cultivation setup/mode/system terms into METPO.
proposals/metpo_communitymech_cultivation_v1/metpo_proposal_properties_robot.tsv	Adds ROBOT template rows for proposed cultivation-related object properties.
proposals/metpo_communitymech_cultivation_v1/metpo_proposal_classes_robot.tsv	Adds ROBOT template rows for proposed cultivation-related classes.
kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml	Adds a new curated community record (composting SynCom; includes GTDB grounding where available).
kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml	Adds a new curated community record; exercises `computational_provenance` for model-predicted cross-feeding evidence.
kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml	Adds a new curated community record (rhizosphere SynCom; GTDB genus-level grounding).
kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml	Adds a new curated community record (plant host + phylum-level microbial grounding).
kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml	Adds a new curated community record (SynCom–microalga coupling system).
kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml	Adds a new curated community record (two-member Bacillus SynCom for fermentation).
kb/communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.yaml	Adds a new curated community record (Fe0-driven electro-syntrophy denitrifying pair).
kb/communities/Shewanella_oneidensis_Rhodopseudomonas_palustris_Electrosyntrophic_Coculture.yaml	Adds a new curated community record (engineered electro-syntrophic co-culture).
kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml	Adds a new curated community record (biochar-bridged engineered bioremediation consortium).
kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml	Adds a new curated community record (TPA-fed coculture with competition mechanisms).
kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml	Adds a new curated community record (5-strain antibiotic-degrading consortium; GTDB grounding for subset).
kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml	Adds a new curated community record (endophytic biocontrol SynCom; GTDB grounding where available).
kb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml	Adds a new curated community record (lithosyntrophy phosphite-oxidizing syntrophic pair).
kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml	Adds a new curated community record (microalga–yeast mutualistic co-culture).
kb/communities/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J.yaml	Adds a new curated community record (multi-stage AD SynComs; functional-group level).
kb/communities/Infant_Gut_Prebiotic_Response_SynCom.yaml	Adds a new curated community record (infant-gut SynCom; prebiotic-driven interaction rewiring).
kb/communities/Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium.yaml	Adds a new curated community record (PE degradation division of labor; GTDB grounding where available).
kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml	Adds a new curated community record (defined MES consortia; multiple IET modes).
kb/communities/Electrostimulated_Mixotrophic_VFA_Producing_Enrichment_Consortium.yaml	Adds a new curated community record (electrostimulated enrichment; GTDB reclassification captured).
kb/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.yaml	Adds a new curated community record (infant-gut mutualistic cross-feeding pair).
kb/communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.yaml	Adds a new curated community record (sequential inoculation + reinforcement member).
kb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml	Adds a new curated community record (DIET-based simplified methanogenic consortia).
kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml	Adds a new curated community record (dechlorination consortium; syntrophic H2 supply concept).
kb/communities/Crucian_Carp_Gut_Disease_Resistance_SynCom.yaml	Adds a new curated community record (fish gut SynCom; pathogen suppression).
kb/communities/Corynebacterium_glutamicum_Shewanella_oneidensis_Succinic_Acid_Coculture.yaml	Adds a new curated community record (engineered co-culture for succinate).
kb/communities/Composting_SynCom_Lignocellulose_Degradation_Humus.yaml	Adds a new curated community record (SynCom-driven enrichment of native degraders).
kb/communities/Butyrivibrio_Selenomonas_Ruminococcus_Lignocellulolytic_Rumen_Consortium.yaml	Adds a new curated community record (rumen consortium; model-predicted compatibility validated in vitro).
kb/communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.yaml	Adds a new curated community record (gnotobiotic BSFL gut SynCom).
kb/communities/ANME_SRB_Marine_Methane_Seep_Consortium.yaml	Updates an existing record with a cross-reference curation event for consolidation tracking.
kb/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.yaml	Adds a new curated record (ANME/SRB syntrophy; redox conduction / DIET mechanism focus).
justfile	Adds `just` recipes for `scout-communities` and `ground-taxa-gtdb`.
.claude/skills/scout-communities/skill.md	Adds skill documentation for Europe PMC scouting workflow and outputs.
.claude/skills/ground-taxa-gtdb/skill.md	Adds skill documentation for rank-aware GTDB grounding using the local kg-microbe mapping.

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+    "crossfeeding",
+    "syntrophy",
+    "syntrophic",
+    "mutualis",


+        description: >-
+          Canonical GTDB CURIE (spaces in the taxon name become underscores),
+          e.g. GTDB:s__Bacillus_velezensis or GTDB:g__Agrobacterium.
+        pattern: "^GTDB:[cdfgops]__.+"


+    snippet: 'Paraclostridium (p Pseudomonas (p A. hydrophila (p < 0.05) by activating intestinal
+      immune responses and reinforcing the gut barrier.'


+    snippet: 'Paraclostridium (p Pseudomonas (p A. hydrophila (p < 0.05) by activating intestinal
+      immune responses and reinforcing the gut barrier.'


New skill deep-researches each community's cited source for cultivation/growth conditions (medium, temperature, pH, atmosphere, incubation, shaking, inoculum, vessel; reactor/mode for engineered systems) and adds evidence-backed growth_media/cultivation_setup blocks, with a strict no-fabrication rule (paywalled/silent sources left unchanged). Pilots: CommunityMech:000272 (OA -> LBGM 30C static, 24-well, TSB preculture), 000294 + 000297 (paywalled -> anaerobic conditions from abstracts). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… sweep) Ran the add-growth-conditions skill across all 154 records that lacked cultivation data. For each, deep-researched the cited source (Europe PMC abstract + OA full-text Methods) and appended evidence-backed conditions: 99 growth_media blocks (medium, temperature, pH, atmosphere, salinity, light, incubation, shaking, inoculum, vessel) and 15 cultivation_setup blocks (reactor/mode, working volume, potential, retention time) for defined reactor/bioelectrochemical/continuous systems. Every added field carries a verbatim source snippet; all edits are strictly append-only. Coverage now 243/295 records. The 52 unchanged were correctly left alone under the no-fabrication rule: paywalled sources with no abstract-level conditions, natural/field communities that were never cultivated, uncultivable endosymbionts, and pure computational (GEM) models. Validated: per-record validate + validate-terms on every edited file; add-only diffs (no existing content altered). Note: the sweep surfaced a pre-existing KB-wide id-label backlog independent of this work — obsolete GO labels (GO:0055114, GO:0019439, GO:0051704, GO:1901575), ENVO label drift (ENVO:00002229, ENVO:00000274, ENVO:01001442), and a CHEBI mislabel (CHEBI:75318 -> canonical "petunidin"); plus a Bayan Obo evidence mis-attribution. Left for a separate id-label-correspondence cleanup pass. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Schema: add the id↔label binding to GeneAnnotation.go_terms (its description already claimed "checked by the term gate" but the binding was missing). Enforcing it on kb/taxa/ needs a CommonTaxon-targeted term-validation pass (follow-up); the community gate is unaffected. Wrong-id fixes (id pointed at an unrelated term; corrected to the id whose canonical label matches the intended term, verified via OAK + live OLS): - CHEBI:86154 -> CHEBI:60720 (sodium silicate) — Coscinodiscus, Pseudonitzschia - CHEBI:38292 -> CHEBI:43515 (dioxouranium(2+)) — Oak_Ridge_FRC - ENVO:00000274 -> ENVO:00002121 (alkaline salt lake / soda lake) — Phormidium - CHEBI:75317 -> CHEBI:187815 (3-hydroxy-dodecanoyl-HSL) — Thermophilic_Pyrite_QS Not fixed here (need curation decisions): - 20 wrong-id rows where the intended label has no term in the target ontology (e.g. lead/zinc sulfide, phyllosphere, anaerobic environment, yeast extract, Stenotrophomonas goyi) — remove the term binding or remap to a parent/related term. - ~140 obsolete-GO rows (GO:0055114 etc., confirmed obsolete vs live GO, no clean replacement) — pending remove/remap/relabel policy decision. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Completes the KB-wide id↔label correspondence cleanup (linkml-term-validator --labels now reports ZERO drift across kb/communities, down from 167). Bucket B — obsolete GO (142 rows, 54 files): each obsolete generic GO term remapped to the nearest valid current term (confirmed obsolete vs live GO API, which offers no official replacement): GO:0055114 oxidation-reduction process -> GO:0016491 oxidoreductase activity GO:0071704 organic substance metabolic -> GO:0008152 metabolic process GO:1901575/GO:0019439 (catabolic) -> GO:0009056 catabolic process GO:0051238 sequestering of metal ion -> GO:0140487 metal ion sequestering activity GO:0051704 multi-organism process -> GO:0044419 interspecies-interaction process GO:0015103 inorganic anion transporter -> GO:0008509 monoatomic anion transmembrane transporter activity Applied via scripts/term_remap.py (text-only, no reflow). Bucket A — 20 wrong-ids whose intended term is absent from the ontology (verified vs live OLS/NCBI): remapped to the nearest existing valid term, e.g. phyllosphere -> ENVO:01001001 plant-associated environment; lead/zinc sulfide -> CHEBI:46718 sulfide salt; Stenotrophomonas goyi -> NCBITaxon:40323 (genus); humic acid -> CHEBI:64709 organic acid; 3-OH-C14-HSL -> CHEBI:55474 N-acyl-L-homoserine lactone. In every case term.{id,label} is the nearest valid ontology grounding while the sibling preferred_term retains the specific intended concept. All edited files pass validate + validate-terms; 227 tests pass. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…tribution - just validate-terms-taxa: id↔label gate for kb/taxa/ CommonTaxon records, enforcing the new GeneAnnotation.go_terms binding (needs --target-class CommonTaxon; both taxa files pass). - Bayan_Obo_REE_Tailings_Consortium: doi:10.1016/j.cej.2024.153492 is confirmed (CrossRef) to be Li et al. 2024 (Chem. Eng. J.) — the correct acid-bioleaching study of the Bayan Obo REE tailings consortium, NOT an "MXene review". Corrected all 5 evidence items from supports: WRONG_STATEMENT -> SUPPORT and rewrote the false MXene-review explanations to attribute the paper correctly. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…ion-proposal

Post-merge-with-main: main's embedding/loader.py uses hashlib.sha1 for a non-crypto cache key, which ruff S324 flags — set usedforsecurity=False. Regenerate datamodel to match the merged schema. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

realmarcin · 2026-07-03T18:39:03Z

Review summary — ready to merge

Large but cohesive change; all gates green after syncing main in.

Scope

Schema: ComputationalProvenance (+ enum) and GtdbClassification structures; GeneAnnotation.go_terms id↔label binding; datamodel regenerated.
Skills/scripts: scout-communities, ground-taxa-gtdb, add-growth-conditions (+ scout_communities.py, scout_loop.py, gtdb_ground.py, term_remap.py, just validate-terms-taxa).
Data: 29 new community records (000272,000274–000302); GTDB grounding (species + genus/family rank-aware); growth conditions on 102 records (243/295 coverage); full id↔label cleanup (167 → 0 drift); Bayan Obo evidence mis-attribution corrected.

Verification (merged with main)

just validate-all ✓ · just validate-terms-all ✓ (0 drift, re-counted) · pytest (227) ✓ · just lint ✓
CI: lint ✓ · validate-strict ✓ · label-correspondence ✓ · validator-pin ✓
All record edits are additive/id-label-only (no content reflow); no duplicate papers.

Follow-ups filed: #181 (wire validate-terms-taxa into CI), #182 (refine best-effort term remaps), #183 (enrich thin/paywalled records), #184 (scout title-dedup for ref-less leads). None blocking.

realmarcin and others added 6 commits June 21, 2026 21:07

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realmarcin and others added 7 commits July 2, 2026 22:47

Merge remote-tracking branch 'origin/main' into claude/metpo-cultivat…

a8aa7a5

…ion-proposal

realmarcin merged commit a192416 into main Jul 3, 2026
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This was referenced Jul 3, 2026

GTDB-ground all remaining records (24 → 231/295) #185

Merged

Follow-ups #181 + #184: taxa term-gate in qc/CI; scout DOI backfill #186

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Community scouting + GTDB grounding + computational-provenance; 29 new community records#180

Community scouting + GTDB grounding + computational-provenance; 29 new community records#180
realmarcin merged 13 commits into
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		snippet: 'Paraclostridium (p Pseudomonas (p A. hydrophila (p < 0.05) by activating intestinal
		immune responses and reinforcing the gut barrier.'

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realmarcin commented Jul 2, 2026

Summary

Schema (regenerated datamodel)

Skills & scripts

Records — 29 new (CommunityMech:000272, 000274–000302)

Validation

Known follow-ups

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Pull request overview

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realmarcin commented Jul 3, 2026

Review summary — ready to merge

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Records — 29 new (`CommunityMech:000272`, `000274`–`000302`)