GTDB-ground all remaining records (24 → 231/295)#185
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… -> 231/295) Ran `gtdb_ground.py --community <file> --apply` (rank-aware: species -> GTDB:s__ via id/name; genus/family -> g__/f__ by genome-majority; ambiguous/eukaryote skipped) over the 271 records that lacked GTDB grounding. Add-only text edits (no reflow); GTDB CURIEs are pattern-checked strings, not OAK-bound, so no id-label drift. The 64 records still ungrounded have only genus-ambiguous, eukaryotic, or unmapped taxa. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Pull request overview
Backfills GTDB grounding metadata across the knowledge-base community YAML records by adding gtdb_classification blocks under each taxonomy entry’s taxon_term, improving cross-database taxon interoperability without altering existing NCBI term grounding.
Changes:
- Added
gtdb_classificationblocks (GTDB CURIE, taxon name, lineage, mapping provenance, and confidence metrics) to many community member taxa. - Captured rank-aware grounding outcomes (species/genus/family/order/phylum/class) with
majority_fractionandis_reclassifiedannotations. - Included mapping provenance via
mapping_sourceacross updated records.
Reviewed changes
Copilot reviewed 207 out of 207 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Wheat_Consortium_C1.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Urine_Nitrification_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Trichoderma_Lactate_Platform.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Tomato_Oxylipin_SynCom3.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/THOR_Rhizosphere_Model_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Syntrophus_Benzoate_Degrader.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Synechococcus_Yarrowia_SPC.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Synechococcus_Ecoli_SPC.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Synechococcus_Bacillus_SPC.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/SPRUCE_Peatland_Methane_Cycling_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Soybean_N_Fixation_sfSynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Soil_Corrinoid_B12_Reservoir_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Soil_BGC_Phylum_Depth_Vegetation_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/SMutans_VParvula_ASC_Biofilm.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Shewanella_Denitrifying_Richness_SynComs.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/SF356_Cellulose_Degrader.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Saccharomyces_Acinetobacter_Lignocellulose_Detox_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Pseudomonas_Pedobacter_Social_Spreading_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Prochlorococcus_Alteromonas_Helper_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Premature_Infant_Gut_Escherichia_Diametric_Ratio_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/PMI_Variovorax_Thermotolerance_Collection.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/PET_Artificial_FourSpecies_Degradation_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Pepper_Phytophthora_SynCom5.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Methylomicrobium_Chlorella_Methane_Sequestration_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Methylocystis_Rhodococcus_Methane_VFA_PHBV_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Methylocaldum_Methyloceanibacter_Methane_Crossfeeding_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Methane_Oxidation_CrVI_Reduction_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/MAMC_M48_Lignocellulose.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Maize_Root_Simplified_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Lotus_LjSC3.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Kombucha_KMC_IMBG1_Fermentation_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/KBase_Synthetic_Bacterial_Community_R2A.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/KBase_ORT_Workflow_Community_Model.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Infant_Gut_Strain_Persistence_Maternal_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Infant_Gut_DNA_Phage_Succession_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Hanford_300_Area_Unconfined_Aquifer_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/GOM_Oil_Degrading_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/GLBRC_Populus_Variovorax_SynCom28.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Geobacter_Methanosarcina_DIET.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Geobacter_Methanosaeta_DIET.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Geobacter_Clostridium_DIET.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/ENIGMA_Denitrifying_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/East_River_Floodplain_Core_Microbiome.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Early_Dental_Biofilm_FiveSpecies.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/DVM_Triculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Defined_Multispecies_Enamel_Caries_Model.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Coniochaeta_Sphingobacterium_Citrobacter_Wheat_Straw_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Thermoanaerobacter_Cellulosic_Bioethanol_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Cellulovorans_Rhodopseudomonas_Cellulose_Biohydrogen_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Caldicellulosiruptor_Minimal_Medium_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Cinnamate_Degradation_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Chlorochromatium_Aggregatum_Phototrophic_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Chlorella_Ecoli_Mixotrophic_Biofuel_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Chlorella_Azospirillum_Synthetic_Mutualism.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Cheese_Rind_InSitu_InVitro_Model_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Cellulomonas_Rhodobacter_Cellulose_Photohydrogen_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Caldicellulosiruptor_TwoSpecies_Hydrogen_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Caldibacillus_Clostridium_Aerotolerant_Cellulose_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Buchnera_Serratia_Cinara_Cedri_Endosymbiont_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Banana_Fusarium_Biocontrol_SynCom12.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/At_RSPHERE_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/ANME_SRB_Marine_Methane_Seep_Consortium.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Anammox_Granule_Metabolic_Interaction_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Anammox_Bioreactor_DNRA_Destabilization_Community.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Acetobacterium_Clostridium_CO2_Electrolysis_Coculture.yaml | Add GTDB classification blocks for member taxa |
| kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml | Add GTDB classification blocks for member taxa |
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This was referenced Jul 5, 2026
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…pages (#203) Deep-research growth-conditions sweep over the 45 records lacking any growth_media/cultivation_setup (via the add-growth-conditions skill + the new sweep runner). One agent per record extracted only source-backed conditions with verbatim evidence snippets; 35 records were correctly left unchanged (uncultured/metagenomic/computational/paywalled — no fabrication). Enriched (10): - ANME_SRB_Marine_Methane_Seep_Consortium (OA full text: anaerobic seawater microcosm, CH4 ± HPG, 4/24/50 C) - Chromium_Sulfur_Reduction_Enrichment (aerobic, pH 8, 30-37 C; dominant strain) - Phylogenetically_Diverse_Denitrifying_SynCom (marine broth 2216 + 20 mM NaNO3, anaerobic, 25 C; OA companion study, attributed) - BioModels_MODEL2209060002_DPigrum_SAureus (in silico SNM3 medium, COMPUTATIONAL) - Aerobic_Denitrification_Disturbance_SynCom, Aerobic_Denitrification_QQ_SynCom, Shewanella_Pseudomonas_Fe0_*, BSFL_Gut_SynCom, SynCom_BsBv_Cigar_*, Thermophilic_Lignocellulose_Composting_* (abstract-level conditions) Dark-mode contrast fix (community.html): preparation_notes, .interaction-flow, .evidence-item, and inline code hardcoded light backgrounds with no text color, rendering invisible (light-on-light) in dark mode — switched to theme variables. Regenerated all 295 community pages (+ browser/index): bakes in the dark-mode fix and syncs page content with already-merged #185 (GTDB), #187 (GO-term cleanup) and #189 (growth media) data that predated the last render. reports/growth_conditions_sweep/INDEX.md: sweep prep/progress report (24 OA full text, 21 abstract-only). Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Summary
Backfills GTDB grounding across the whole KB using the merged
ground-taxa-gtdbtooling (gtdb_ground.py --community <file> --apply), which #180 only applied to the ~30 new records.gtdb_classificationblocks across 207 records → 231/295 records now GTDB-grounded (was 24).GTDB:s__(NCBI id then species-name fallback); genus/family →g__/f__by genome-weighted majority; GTDB-ambiguous splits and eukaryotes correctly skipped.Verification
just validate-all✓ ·pytest✓ · spot-checkedvalidate-terms(0 drift). Sourced from the local kg-microbedata/raw/NCBI2GTDB.tsv.gz.