From a058d753fdab2553201b6f3de671921d54453ef8 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 11 Aug 2026 17:09:33 -0700 Subject: [PATCH 1/2] Detect one node_id carrying several node_types across records (#356) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Every other check in this file is scoped to one graph. This defect is not: two RECORDS disagree about what a node is, and neither is wrong read alone — which is exactly why nothing caught it. Adds node_type_index() and an INCONSISTENT_NODE_TYPE finding, baselined at 294 occurrences across 63 node_ids. THE ISSUE UNDERSTATES THE SCALE BY ~7x. It reports proton_motive_force typed four ways across 9 records. Measured, it is 35: STATE 18 BIOLOGICAL_PROCESS 13 CHEMICAL 2 CAPACITY 2 and 63 node_ids disagree with themselves corpus-wide, membrane_potential also at four types. It stopped being cosmetic when #355 minted `powers` (METPO:2007900) gated to subject_types = BIOLOGICAL_PROCESS|STATE. Two byte-identical assertions now behave differently purely by subject typing — carboxydotrophic.yaml's proton_motive_force (STATE) grounds, phototrophic.yaml's (CAPACITY) is blocked_by_node_type. Typing decides groundings now. REPORTED PER OCCURRENCE, not on a presumed-wrong minority: nothing here knows which type is right. proton_motive_force splits 18 STATE / 13 BIOLOGICAL_PROCESS, and the gradient genuinely IS a state while generating it IS a process — the majority is an observation, not a verdict. Per-occurrence rows also mean a family clears together the moment it is normalised. The detail leads with node_id, so `_key` discriminates by node within a graph. Deliberately NOT led with the type set: a family part-way through a burn-down would re-key on every step and un-suppress rows nobody has reached yet, which is FRAGMENTED_GRAPH's documented failure from the other direction. Pinned by a test. NOT EVERY HIT IS A DEFECT, and the baseline is where that gets decided. `terminal electron acceptor` is deliberately both CHEMICAL and MOLECULAR_FUNCTION — node_grounding.tsv carries a row for each, saying one METPO class covers both senses and the MOLECULAR_FUNCTION typing "surfaces the role-of interpretation". Same two-senses shape as `reduces` (#330/#333). Where a family really does mean two things the fix is TWO node_ids, not one type; written into the playbook as a decision table. Detection only — no trait data changed. The burn-down is the next step, and the playbook carries #352's lesson for it: the test is not "is this type defensible in isolation" but "is it compatible with what the record and its predicates already assert". 534 tests pass (4 new) - ruff clean. Co-Authored-By: Claude Opus 5 --- conf/causal_graph_audit_baseline.tsv | 294 ++++++++++++++++++ docs/CURATION_PLAYBOOK.md | 44 +++ ...2026-08-12T000912Z-claude-code-779670.yaml | 43 +++ reports/causal_graph_audit.tsv | 294 ++++++++++++++++++ scripts/audit_causal_graphs.py | 81 +++++ tests/test_audit_causal_graphs.py | 82 +++++ 6 files changed, 838 insertions(+) create mode 100644 history/infrastructure/inconsistent-node-type/2026-08-12T000912Z-claude-code-779670.yaml diff --git a/conf/causal_graph_audit_baseline.tsv b/conf/causal_graph_audit_baseline.tsv index 156f7496..cc02fac4 100644 --- a/conf/causal_graph_audit_baseline.tsv +++ b/conf/causal_graph_audit_baseline.tsv @@ -1,11 +1,13 @@ file graph_id defect severity detail data/traits/ecology/animal_pathogen.yaml animal_pathogen_metazoan_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='low_iron_environment' label='low-iron host environment' type=ENVIRONMENTAL_FACTOR — in an island with no path to animal_pathogen_trait data/traits/ecology/animal_pathogen.yaml animal_pathogen_metazoan_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='siderophore_biosynthesis' label='siderophore biosynthesis gene expression' type=BIOLOGICAL_PROCESS — in an island with no path to animal_pathogen_trait +data/traits/ecology/animal_pathogen.yaml animal_pathogen_metazoan_adaptation INCONSISTENT_NODE_TYPE WARN node_id='immune_evasion' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/ecology/animal_pathogen.yaml animal_pathogen_metazoan_adaptation FRAGMENTED_GRAPH WARN components=2 of 17 node(s) (sizes: 15, 2) — one record, several unrelated mechanisms data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community UNREACHABLE_FROM_TRAIT WARN node_id='planktonic_cell' label='planktonic cell' type=STATE — in an island with no path to biofilm_formation_trait data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community UNREACHABLE_FROM_TRAIT WARN node_id='amenable_surface' label='amenable surface' type=ENVIRONMENTAL_FACTOR — in an island with no path to biofilm_formation_trait data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community UNREACHABLE_FROM_TRAIT WARN node_id='nitric_oxide' label='nitric oxide' type=CHEMICAL — in an island with no path to biofilm_formation_trait data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community UNREACHABLE_FROM_TRAIT WARN node_id='biofilm_dispersal' label='biofilm dispersal' type=BIOLOGICAL_PROCESS — in an island with no path to biofilm_formation_trait +data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community INCONSISTENT_NODE_TYPE WARN node_id='eps_matrix' type=CHEMICAL here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 9, 2, 2) — one record, several unrelated mechanisms data/traits/ecology/biosafety_level.yaml biosafety_level_hazard_classification UNREACHABLE_FROM_TRAIT WARN node_id='lack_of_countermeasures' label='lack of effective treatment or vaccine' type=QUALITY — in an island with no path to biosafety_level_trait/bsl1/bsl2/bsl3/bsl4/bsl5 data/traits/ecology/biosafety_level.yaml biosafety_level_hazard_classification UNREACHABLE_FROM_TRAIT WARN node_id='bsl4_containment' label='BSL-4 containment requirement' type=EXPERIMENTAL_FACTOR — in an island with no path to biosafety_level_trait/bsl1/bsl2/bsl3/bsl4/bsl5 @@ -26,6 +28,7 @@ data/traits/ecology/endosymbiosis.yaml endosymbiosis_intracellular_genome_reduct data/traits/ecology/endosymbiosis.yaml endosymbiosis_intracellular_genome_reduction FRAGMENTED_GRAPH WARN components=3 of 10 node(s) (sizes: 6, 2, 2) — one record, several unrelated mechanisms data/traits/ecology/free_living.yaml free_living_environmental_habitat UNREACHABLE_FROM_TRAIT WARN node_id='trehalose_biosynthesis' label='trehalose biosynthesis/transport' type=PATHWAY — in an island with no path to free_living_trait data/traits/ecology/free_living.yaml free_living_environmental_habitat UNREACHABLE_FROM_TRAIT WARN node_id='environmental_stress_tolerance' label='stress tolerance in fluctuating environments' type=BIOLOGICAL_PROCESS — in an island with no path to free_living_trait +data/traits/ecology/free_living.yaml free_living_environmental_habitat INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/ecology/free_living.yaml free_living_environmental_habitat FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 7, 2) — one record, several unrelated mechanisms data/traits/ecology/gut_associated.yaml gut_associated_microbiota_metabolism UNREACHABLE_FROM_TRAIT WARN node_id='peristalsis' label='intestinal peristalsis' type=ENVIRONMENTAL_FACTOR — in an island with no path to gut_associated_trait data/traits/ecology/gut_associated.yaml gut_associated_microbiota_metabolism UNREACHABLE_FROM_TRAIT WARN node_id='duodenal_retention' label='colonization/retention in duodenum' type=BIOLOGICAL_PROCESS — in an island with no path to gut_associated_trait @@ -37,6 +40,7 @@ data/traits/ecology/habitat_association.yaml habitat_association_biogeographic_s data/traits/ecology/habitat_association.yaml habitat_association_biogeographic_structure UNREACHABLE_FROM_TRAIT WARN node_id='ecological_drift' label='ecological drift in community assembly' type=BIOLOGICAL_PROCESS — in an island with no path to habitat_association_trait data/traits/ecology/habitat_association.yaml habitat_association_biogeographic_structure UNREACHABLE_FROM_TRAIT WARN node_id='dispersal_limitation' label='dispersal limitation in community assembly' type=BIOLOGICAL_PROCESS — in an island with no path to habitat_association_trait data/traits/ecology/habitat_association.yaml habitat_association_biogeographic_structure FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 6, 4) — one record, several unrelated mechanisms +data/traits/ecology/host_associated.yaml host_associated_microbiome INCONSISTENT_NODE_TYPE WARN node_id='root_exudates' type=ENVIRONMENTAL_FACTOR here — also CHEMICAL×1 elsewhere in the corpus data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit UNREACHABLE_FROM_TRAIT WARN node_id='cross_feeding_architecture' label='co-auxotrophy / cross-feeding architecture' type=BIOLOGICAL_PROCESS — in an island with no path to mutualism_trait data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit UNREACHABLE_FROM_TRAIT WARN node_id='obligate_mutualism_syntrophy' label='obligate mutualism (syntrophy)' type=STATE — in an island with no path to mutualism_trait data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit UNREACHABLE_FROM_TRAIT WARN node_id='metabolite_secretion_profile' label='metabolite secretion profile' type=CHEMICAL — in an island with no path to mutualism_trait @@ -44,6 +48,7 @@ data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit UNREACHABLE_FROM data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit FRAGMENTED_GRAPH WARN components=3 of 10 node(s) (sizes: 6, 2, 2) — one record, several unrelated mechanisms data/traits/ecology/pathogenic_to_host.yaml pathogenic_to_host_virulence_factor_program UNREACHABLE_FROM_TRAIT WARN node_id='biofilm_matrix' label='biofilm extracellular matrix' type=CELLULAR_LOCALIZATION — in an island with no path to pathogenic_to_host_trait data/traits/ecology/pathogenic_to_host.yaml pathogenic_to_host_virulence_factor_program UNREACHABLE_FROM_TRAIT WARN node_id='antibiotic_tolerance' label='antibiotic tolerance' type=BIOLOGICAL_PROCESS — in an island with no path to pathogenic_to_host_trait +data/traits/ecology/pathogenic_to_host.yaml pathogenic_to_host_virulence_factor_program INCONSISTENT_NODE_TYPE WARN node_id='immune_evasion' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/ecology/pathogenic_to_host.yaml pathogenic_to_host_virulence_factor_program FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 12, 2) — one record, several unrelated mechanisms data/traits/ecology/plant_pathogen.yaml plant_pathogen_t3ss_effector_program UNREACHABLE_FROM_TRAIT WARN node_id='quorum_sensing' label='quorum sensing' type=BIOLOGICAL_PROCESS — in an island with no path to plant_pathogen_trait data/traits/ecology/plant_pathogen.yaml plant_pathogen_t3ss_effector_program UNREACHABLE_FROM_TRAIT WARN node_id='biofilm_formation' label='biofilm formation' type=BIOLOGICAL_PROCESS — in an island with no path to plant_pathogen_trait @@ -60,6 +65,7 @@ data/traits/ecology/predatory_bacterium.yaml predatory_bacterium_prey_killing FR data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate UNREACHABLE_FROM_TRAIT WARN node_id='bacterial_chemotaxis' label='bacterial chemotaxis' type=BIOLOGICAL_PROCESS — in an island with no path to rhizosphere_trait data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate UNREACHABLE_FROM_TRAIT WARN node_id='mcp_chemoreceptor' label='methyl-accepting chemotaxis protein (MCP)' type=GENE_OR_PROTEIN — in an island with no path to rhizosphere_trait data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate UNREACHABLE_FROM_TRAIT WARN node_id='root_colonization' label='root colonization' type=BIOLOGICAL_PROCESS — in an island with no path to rhizosphere_trait +data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate INCONSISTENT_NODE_TYPE WARN node_id='root_exudates' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 6, 3) — one record, several unrelated mechanisms data/traits/ecology/saprotrophy.yaml saprotrophy_decomposition_cycling UNREACHABLE_FROM_TRAIT WARN node_id='extracellular_exoenzymes' label='extracellular exoenzymes' type=GENE_OR_PROTEIN — in an island with no path to saprotrophy_trait data/traits/ecology/saprotrophy.yaml saprotrophy_decomposition_cycling UNREACHABLE_FROM_TRAIT WARN node_id='soluble_organic_compounds' label='soluble organic compounds' type=CHEMICAL — in an island with no path to saprotrophy_trait @@ -91,37 +97,54 @@ data/traits/ecology/symbiosis.yaml symbiosis_host_interaction UNREACHABLE_FROM_T data/traits/ecology/symbiosis.yaml symbiosis_host_interaction UNREACHABLE_FROM_TRAIT WARN node_id='o_antigen' label='O-antigen' type=CHEMICAL — in an island with no path to symbiosis_trait data/traits/ecology/symbiosis.yaml symbiosis_host_interaction UNREACHABLE_FROM_TRAIT WARN node_id='immune_evasion' label='immune evasion' type=BIOLOGICAL_PROCESS — in an island with no path to symbiosis_trait data/traits/ecology/symbiosis.yaml symbiosis_host_interaction UNREACHABLE_FROM_TRAIT WARN node_id='adhesins' label='adhesins' type=GENE_OR_PROTEIN — in an island with no path to symbiosis_trait +data/traits/ecology/symbiosis.yaml symbiosis_host_interaction INCONSISTENT_NODE_TYPE WARN node_id='immune_evasion' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/ecology/symbiosis.yaml symbiosis_host_interaction FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 7, 6) — one record, several unrelated mechanisms data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='hopanoid_and_membrane_proteins' label='hopanoid lipids and membrane proteins (Omp40, PspA)' type=CELLULAR_LOCALIZATION — in an island with no path to acidophilic_trait data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='proton_exclusion' label='proton exclusion' type=BIOLOGICAL_PROCESS — in an island with no path to acidophilic_trait data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='bipolar_tetraether_lipids' label='bipolar tetraether lipids (GDNT/GDGT)' type=CHEMICAL — in an island with no path to acidophilic_trait data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='low_passive_proton_permeability' label='low passive proton permeability' type=QUALITY — in an island with no path to acidophilic_trait +data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='reversed_membrane_potential' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 9, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/acidotolerant.yaml acidotolerant_acid_stress_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=PATHWAY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus +data/traits/environment/aerobic.yaml aerobic_trait_mechanism INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/aerobic.yaml aerobic_trait_mechanism INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=MOLECULAR_FUNCTION here — also CHEMICAL×3 elsewhere in the corpus +data/traits/environment/aerobic.yaml aerobic_trait_mechanism INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide' label='hydrogen peroxide' type=CHEMICAL — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide_detoxification' label='hydrogen peroxide detoxification' type=BIOLOGICAL_PROCESS — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='catalase' label='catalase' type=GENE_OR_PROTEIN — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='rubrerythrin' label='rubrerythrin' type=GENE_OR_PROTEIN — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='nadh_peroxidase' label='NADH peroxidase' type=GENE_OR_PROTEIN — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='nadph_peroxidase' label='NADPH peroxidase' type=GENE_OR_PROTEIN — in an island with no path to aerotolerant_trait +data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense INCONSISTENT_NODE_TYPE WARN node_id='superoxide_dismutase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 5, 4, 2) — one record, several unrelated mechanisms data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='alkaline_external_ph' label='alkaline external pH' type=ENVIRONMENTAL_FACTOR — in an island with no path to alkalotolerant_trait data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='electrogenic_na_h_antiport' label='electrogenic Na+/H+ antiport' type=MOLECULAR_FUNCTION — in an island with no path to alkalotolerant_trait +data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cation_proton_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='electrogenic_na_h_antiport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms data/traits/environment/alkaphilic.yaml alkaliphilic_na_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to alkaphilic_trait data/traits/environment/alkaphilic.yaml alkaliphilic_na_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='proton' label='proton' type=CHEMICAL — in an island with no path to alkaphilic_trait data/traits/environment/alkaphilic.yaml alkaliphilic_na_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_proton_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to alkaphilic_trait data/traits/environment/alkaphilic.yaml alkaliphilic_na_cycle_homeostasis FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 8, 3) — one record, several unrelated mechanisms +data/traits/environment/anaerobic.yaml anaerobic_trait_oxygen_exclusion INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/delta_phenotype_with_numerical_limits.yaml delta_phenotype_breadth_descriptor INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='trehalose' label='trehalose' type=CHEMICAL — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='plasma_membrane' label='plasma membrane' type=CELLULAR_LOCALIZATION — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='vitrification' label='vitrification / glass formation' type=BIOLOGICAL_PROCESS — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='chaperone_activity' label='heat shock protein / chaperone activity' type=MOLECULAR_FUNCTION — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='protein_aggregation' label='protein aggregation' type=BIOLOGICAL_PROCESS — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='desiccation_idps' label='desiccation-related intrinsically disordered proteins' type=GENE_OR_PROTEIN — in an island with no path to desiccation_tolerant_trait +data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 7, 4, 2) — one record, several unrelated mechanisms data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='mechanosensitive_channels' label='mechanosensitive channels (Msc)' type=GENE_OR_PROTEIN — in an island with no path to euryhaline_trait data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='osmotic_downshock' label='osmotic downshock' type=BIOLOGICAL_PROCESS — in an island with no path to euryhaline_trait data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to euryhaline_trait data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_sodium' label='cytoplasmic sodium ions' type=CHEMICAL — in an island with no path to euryhaline_trait +data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_transport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance FRAGMENTED_GRAPH WARN components=3 of 17 node(s) (sizes: 13, 2, 2) — one record, several unrelated mechanisms data/traits/environment/extreme_hyperthermophilic.yaml extreme_hyperthermophilic_archaeal_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='reverse_gyrase' label='reverse gyrase' type=GENE_OR_PROTEIN — in an island with no path to extreme_hyperthermophilic_trait data/traits/environment/extreme_hyperthermophilic.yaml extreme_hyperthermophilic_archaeal_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='dna_positive_supercoiling' label='DNA positive supercoiling' type=BIOLOGICAL_PROCESS — in an island with no path to extreme_hyperthermophilic_trait @@ -130,12 +153,22 @@ data/traits/environment/extreme_hyperthermophilic.yaml extreme_hyperthermophilic data/traits/environment/extreme_hyperthermophilic.yaml extreme_hyperthermophilic_archaeal_adaptation FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 7, 4) — one record, several unrelated mechanisms data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to extremely_halophilic_trait data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome UNREACHABLE_FROM_TRAIT WARN node_id='sodium_efflux' label='sodium efflux' type=BIOLOGICAL_PROCESS — in an island with no path to extremely_halophilic_trait +data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms +data/traits/environment/facultative_oxygen_preference.yaml facultative_oxygen_preference_switching INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/facultative_oxygen_preference.yaml facultative_oxygen_preference_switching INCONSISTENT_NODE_TYPE WARN node_id='anaerobic_metabolism_genes' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='exopolysaccharides' label='extracellular polymeric substances (EPS)' type=CHEMICAL — in an island with no path to facultative_psychrophilic_trait data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='freeze_thaw_cycles' label='freeze-thaw cycles' type=ENVIRONMENTAL_FACTOR — in an island with no path to facultative_psychrophilic_trait +data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance INCONSISTENT_NODE_TYPE WARN node_id='fatty_acid_desaturase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='hopanoid_biosynthesis' label='hopanoid biosynthetic process' type=BIOLOGICAL_PROCESS — in an island with no path to facultatively_acidophilic_trait data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='membrane_proton_permeability' label='membrane proton permeability' type=QUALITY — in an island with no path to facultatively_acidophilic_trait +data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='inside_positive_membrane_potential' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='membrane_proton_permeability' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='glutamate_decarboxylase_system' type=GENE_OR_PROTEIN here — also PATHWAY×2 elsewhere in the corpus +data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='intracellular_ph' type=QUALITY here — also STATE×1 elsewhere in the corpus data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis FRAGMENTED_GRAPH WARN components=2 of 15 node(s) (sizes: 13, 2) — one record, several unrelated mechanisms data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='molecular_oxygen' label='molecular oxygen' type=CHEMICAL — in an island with no path to facultative_aerobic_trait data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='aerobic_respiration' label='aerobic respiration' type=BIOLOGICAL_PROCESS — in an island with no path to facultative_aerobic_trait @@ -146,6 +179,8 @@ data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_fle data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='anaerobic_metabolism_genes' label='anaerobic metabolism genes' type=GENE_OR_PROTEIN — in an island with no path to facultative_aerobic_trait data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='aerobic_metabolism_genes' label='aerobic metabolism genes' type=GENE_OR_PROTEIN — in an island with no path to facultative_aerobic_trait data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='cytochrome_bd_oxidase' label='cytochrome bd oxidase' type=GENE_OR_PROTEIN — in an island with no path to facultative_aerobic_trait +data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth INCONSISTENT_NODE_TYPE WARN node_id='anaerobic_metabolism_genes' type=GENE_OR_PROTEIN here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to facultatively_alkaphilic_trait data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='proton' label='proton' type=CHEMICAL — in an island with no path to facultatively_alkaphilic_trait @@ -154,22 +189,38 @@ data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_s data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='f1fo_atp_synthase' label='F1Fo-ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to facultatively_alkaphilic_trait data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='atp_production_alkaline' label='ATP production at alkaline pH' type=BIOLOGICAL_PROCESS — in an island with no path to facultatively_alkaphilic_trait data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 5, 4, 2) — one record, several unrelated mechanisms +data/traits/environment/facultatively_anaerobic.yaml facultative_anaerobe_oxygen_switch INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='proton_pumping_atpase_respiration' label='F0F1-ATPase / proton-pumping respiratory chain activity' type=MOLECULAR_FUNCTION — in an island with no path to growth_range_phenotype_trait/nacl_range/ph_range/temperature_range data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='prevent_cytoplasm_acidification' label='prevention of cytoplasmic acidification' type=BIOLOGICAL_PROCESS — in an island with no path to growth_range_phenotype_trait/nacl_range/ph_range/temperature_range data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='hypertonic_salinity_increase' label='hypertonic salinity increase' type=ENVIRONMENTAL_FACTOR — in an island with no path to growth_range_phenotype_trait/nacl_range/ph_range/temperature_range data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='cell_shrinkage_low_turgor' label='cell shrinkage and lowered turgor' type=STATE — in an island with no path to growth_range_phenotype_trait/nacl_range/ph_range/temperature_range +data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='cation_proton_antiporter' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×3 elsewhere in the corpus +data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='cytoplasm_acidification' type=STATE here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='aa_decarboxylase_antiporter' type=MOLECULAR_FUNCTION here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 11, 2, 2) — one record, several unrelated mechanisms data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='choline_oxidation_pathway' label='choline oxidation pathway' type=PATHWAY — in an island with no path to haloalkaliphilic_trait data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='glycine_betaine' label='glycine betaine' type=CHEMICAL — in an island with no path to haloalkaliphilic_trait +data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/environment/halophilic.yaml halophilic_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to halophilic_trait data/traits/environment/halophilic.yaml halophilic_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to halophilic_trait data/traits/environment/halophilic.yaml halophilic_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='k_uniport' label='K+ uniport system' type=GENE_OR_PROTEIN — in an island with no path to halophilic_trait data/traits/environment/halophilic.yaml halophilic_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='potassium_ion' label='potassium ion' type=CHEMICAL — in an island with no path to halophilic_trait +data/traits/environment/halophilic.yaml halophilic_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/halophilic.yaml halophilic_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/halophilic.yaml halophilic_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='acidified_proteome' type=STATE here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/halophilic.yaml halophilic_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/halophilic.yaml halophilic_osmoadaptation FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 11, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/halophily_preference.yaml halophily_preference_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_transport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/halophily_preference.yaml halophily_preference_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/halophily_preference.yaml halophily_preference_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='acidified_proteome' type=QUALITY here — also STATE×1 elsewhere in the corpus +data/traits/environment/halotolerant.yaml halotolerant_salt_stress_response INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_transport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/halotolerant.yaml halotolerant_salt_stress_response INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability UNREACHABLE_FROM_TRAIT WARN node_id='cdpg' label='cyclic 2,3-diphosphoglycerate (cDPG)' type=CHEMICAL — in an island with no path to hyperthermophilic_trait data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability UNREACHABLE_FROM_TRAIT WARN node_id='archaeal_proteins' label='archaeal proteins' type=GENE_OR_PROTEIN — in an island with no path to hyperthermophilic_trait data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability UNREACHABLE_FROM_TRAIT WARN node_id='dna_oxidative_damage' label='DNA oxidative damage by hydroxyl radicals' type=BIOLOGICAL_PROCESS — in an island with no path to hyperthermophilic_trait +data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability INCONSISTENT_NODE_TYPE WARN node_id='membrane_lipid_composition' type=CELLULAR_LOCALIZATION here — also BIOLOGICAL_PROCESS×1, QUALITY×1 elsewhere in the corpus data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 10, 3) — one record, several unrelated mechanisms data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to mesophilic_trait data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='homoviscous_lipid_composition' label='homoviscous lipid composition' type=CELLULAR_LOCALIZATION — in an island with no path to mesophilic_trait @@ -182,6 +233,7 @@ data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREAC data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='rpoh_sigma32' label='sigma-32 (RpoH)' type=GENE_OR_PROTEIN — in an island with no path to mesophilic_trait data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='heat_shock_genes' label='heat shock genes' type=GENE_OR_PROTEIN — in an island with no path to mesophilic_trait data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='dnak' label='DnaK chaperone' type=GENE_OR_PROTEIN — in an island with no path to mesophilic_trait +data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation FRAGMENTED_GRAPH WARN components=5 of 15 node(s) (sizes: 4, 4, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/metal_tolerant.yaml metal_tolerance_efflux_detoxification UNREACHABLE_FROM_TRAIT WARN node_id='arsenate' label='arsenate As(V)' type=CHEMICAL — in an island with no path to metal_tolerant_trait/arsenic_tolerance data/traits/environment/metal_tolerant.yaml metal_tolerance_efflux_detoxification UNREACHABLE_FROM_TRAIT WARN node_id='arsenite' label='arsenite As(III)' type=CHEMICAL — in an island with no path to metal_tolerant_trait/arsenic_tolerance @@ -194,6 +246,7 @@ data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respirati data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='superoxide_dismutase_sodb' label='superoxide dismutase (SodB)' type=GENE_OR_PROTEIN — in an island with no path to microaerophilic_trait data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='reactive_oxygen_species' label='reactive oxygen species' type=CHEMICAL — in an island with no path to microaerophilic_trait data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='ahpc' label='alkyl hydroperoxide reductase (AhpC)' type=GENE_OR_PROTEIN — in an island with no path to microaerophilic_trait +data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 7, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/microaerotolerant.yaml microaerotolerant_low_oxygen_defense UNREACHABLE_FROM_TRAIT WARN node_id='superoxide' label='superoxide' type=CHEMICAL — in an island with no path to microaerotolerant_trait data/traits/environment/microaerotolerant.yaml microaerotolerant_low_oxygen_defense UNREACHABLE_FROM_TRAIT WARN node_id='superoxide_reductase' label='superoxide reductase' type=GENE_OR_PROTEIN — in an island with no path to microaerotolerant_trait @@ -211,6 +264,7 @@ data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth UNREACHABL data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth UNREACHABLE_FROM_TRAIT WARN node_id='high_maximal_nacl_tolerance' label='high maximal NaCl tolerance' type=QUALITY — in an island with no path to nacl_delta_trait data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth UNREACHABLE_FROM_TRAIT WARN node_id='mechanosensitive_channels' label='mechanosensitive channels (MscL/MscS)' type=GENE_OR_PROTEIN — in an island with no path to nacl_delta_trait data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth UNREACHABLE_FROM_TRAIT WARN node_id='hypoosmotic_shock' label='hypoosmotic shock' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_delta_trait +data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 5, 4, 2, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline UNREACHABLE_FROM_TRAIT WARN node_id='high_external_salinity' label='high external salinity' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_delta_high_trait/nacl_delta data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible-solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_high_trait/nacl_delta @@ -224,6 +278,7 @@ data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline UNREACHABLE_FROM_TRAIT WARN node_id='hypersaline_environment' label='hypersaline environment' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_delta_high_trait/nacl_delta data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline UNREACHABLE_FROM_TRAIT WARN node_id='halophilic_osmoadaptation' label='halophilic osmoadaptation strategies' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_high_trait/nacl_delta data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline FRAGMENTED_GRAPH WARN components=6 of 14 node(s) (sizes: 3, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/nacl_delta_low.yaml nacl_delta_low_stenohaline INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='osmotic_upshift' label='osmotic upshift' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_delta_mid1_trait/nacl_delta data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='k_import' label='potassium import' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_mid1_trait/nacl_delta data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_mid1_trait/nacl_delta @@ -232,6 +287,7 @@ data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNRE data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='ectoine' label='ectoine' type=CHEMICAL — in an island with no path to nacl_delta_mid1_trait/nacl_delta data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='c_di_amp' label='cyclic di-AMP' type=CHEMICAL — in an island with no path to nacl_delta_mid1_trait/nacl_delta data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='organic_osmolyte_influx_biosynthesis' label='compatible organic osmolyte influx and biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_mid1_trait/nacl_delta +data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 8, 3) — one record, several unrelated mechanisms data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cyclic_di_amp' label='cyclic di-AMP' type=CHEMICAL — in an island with no path to nacl_delta_mid2_trait/nacl_delta data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='potassium_uptake_systems' label='potassium uptake systems' type=GENE_OR_PROTEIN — in an island with no path to nacl_delta_mid2_trait/nacl_delta @@ -243,6 +299,8 @@ data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREA data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='eps_matrix' label='exopolysaccharide matrix' type=CELLULAR_LOCALIZATION — in an island with no path to nacl_delta_mid2_trait/nacl_delta data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to nacl_delta_mid2_trait/nacl_delta data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='water_retention' label='water retention / reduced pericellular Na+ toxicity' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_mid2_trait/nacl_delta +data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_transport' type=BIOLOGICAL_PROCESS here — also MOLECULAR_FUNCTION×3 elsewhere in the corpus +data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth INCONSISTENT_NODE_TYPE WARN node_id='eps_matrix' type=CELLULAR_LOCALIZATION here — also CHEMICAL×1 elsewhere in the corpus data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 3, 3, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='salt_in_strategy' label='salt-in strategy' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_optimum_trait data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_k_accumulation' label='intracellular K+ accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_optimum_trait @@ -252,9 +310,14 @@ data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation U data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='lower_energetic_cost' label='lower energetic cost than de novo synthesis' type=QUALITY — in an island with no path to nacl_optimum_trait data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='na_antiport_activity' label='Na+/H+ antiport activity' type=MOLECULAR_FUNCTION — in an island with no path to nacl_optimum_trait data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_na_homeostasis' label='cytoplasmic Na+ homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_optimum_trait +data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_uptake' type=BIOLOGICAL_PROCESS here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation FRAGMENTED_GRAPH WARN components=5 of 16 node(s) (sizes: 8, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile UNREACHABLE_FROM_TRAIT WARN node_id='acidic_aa_content' label='increased acidic amino-acid content' type=QUALITY — in an island with no path to nacl_optimum_high_trait/nacl_optimum data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile UNREACHABLE_FROM_TRAIT WARN node_id='protein_solubility_high_salt' label='protein solubility in high salt' type=QUALITY — in an island with no path to nacl_optimum_high_trait/nacl_optimum +data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_optimum_low.yaml nacl_optimum_low_non_halophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cyclic_di_amp' label='cyclic di-AMP' type=CHEMICAL — in an island with no path to nacl_optimum_low_trait/nacl_optimum/non_halophile_optimum_definition/halotolerant_organism data/traits/environment/nacl_optimum_low.yaml nacl_optimum_low_non_halophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='k_uptake_systems' label='K+ uptake systems (Trk/Ktr/Kup/KimA)' type=GENE_OR_PROTEIN — in an island with no path to nacl_optimum_low_trait/nacl_optimum/non_halophile_optimum_definition/halotolerant_organism @@ -263,6 +326,7 @@ data/traits/environment/nacl_optimum_low.yaml nacl_optimum_low_non_halophile_set data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='elevated_nacl' label='elevated external NaCl' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_optimum_mid1_trait/nacl_optimum data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='glycine_betaine' label='glycine betaine' type=CHEMICAL — in an island with no path to nacl_optimum_mid1_trait/nacl_optimum data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='l_proline' label='L-proline' type=CHEMICAL — in an island with no path to nacl_optimum_mid1_trait/nacl_optimum +data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 7, 3) — one record, several unrelated mechanisms data/traits/environment/nacl_range_high.yaml nacl_range_high_extreme_halophile UNREACHABLE_FROM_TRAIT WARN node_id='acidic_amino_acid_enrichment' label='acidic amino acid enrichment (Asp/Glu)' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_high_trait/nacl_range data/traits/environment/nacl_range_high.yaml nacl_range_high_extreme_halophile UNREACHABLE_FROM_TRAIT WARN node_id='protein_function_high_ionic' label='protein function at very high ionic strength' type=MOLECULAR_FUNCTION — in an island with no path to nacl_range_high_trait/nacl_range @@ -278,6 +342,7 @@ data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile UNREACH data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile UNREACHABLE_FROM_TRAIT WARN node_id='opu_solute_importers' label='OpuA/OpuC compatible-solute importers' type=GENE_OR_PROTEIN — in an island with no path to nacl_range_low_trait/nacl_range data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile UNREACHABLE_FROM_TRAIT WARN node_id='choline_uptake' label='choline uptake' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_low_trait/nacl_range data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile UNREACHABLE_FROM_TRAIT WARN node_id='glycine_betaine_synthesis' label='glycine betaine biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_low_trait/nacl_range +data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile INCONSISTENT_NODE_TYPE WARN node_id='hyperosmotic_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile FRAGMENTED_GRAPH WARN components=5 of 12 node(s) (sizes: 3, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_range_mid1.yaml nacl_range_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='potassium_accumulation' label='K+ accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_mid1_trait/nacl_range/slight_halophile/moderate_halophile/halotolerant_and_moderate_halophiles data/traits/environment/nacl_range_mid1.yaml nacl_range_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='osmotic_balance' label='osmotic balance / salt adaptation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_mid1_trait/nacl_range/slight_halophile/moderate_halophile/halotolerant_and_moderate_halophiles @@ -286,6 +351,11 @@ data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis UN data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_proton_influx' label='cytoplasmic proton influx' type=BIOLOGICAL_PROCESS — in an island with no path to neutrophilic_trait data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering_capacity' label='cytoplasmic buffering capacity' type=CAPACITY — in an island with no path to neutrophilic_trait data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_ph' label='intracellular pH' type=STATE — in an island with no path to neutrophilic_trait +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cation_proton_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cytoplasmic_buffering_capacity' type=CAPACITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='intracellular_ph' type=STATE here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='high_osmolarity' label='high osmolarity' type=ENVIRONMENTAL_FACTOR — in an island with no path to non_halophilic_trait data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='water_flux' label='water flux across cytoplasmic membrane' type=BIOLOGICAL_PROCESS — in an island with no path to non_halophilic_trait @@ -297,23 +367,34 @@ data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='rapid_k_uptake' label='rapid potassium uptake' type=BIOLOGICAL_PROCESS — in an island with no path to non_halophilic_trait data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='glutamate' label='L-glutamate' type=CHEMICAL — in an island with no path to non_halophilic_trait data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to non_halophilic_trait +data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_uptake' type=GENE_OR_PROTEIN here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response FRAGMENTED_GRAPH WARN components=3 of 12 node(s) (sizes: 5, 5, 2) — one record, several unrelated mechanisms +data/traits/environment/obligately_acidophilic.yaml obligately_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='reversed_membrane_potential' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus +data/traits/environment/obligately_acidophilic.yaml obligately_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='superoxide' label='superoxide' type=CHEMICAL — in an island with no path to obligate_aerobic_trait data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide' label='hydrogen peroxide' type=CHEMICAL — in an island with no path to obligate_aerobic_trait data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='superoxide_dismutase' label='superoxide dismutase activity' type=MOLECULAR_FUNCTION — in an island with no path to obligate_aerobic_trait data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='catalase' label='catalase / catalase-peroxidase activity' type=MOLECULAR_FUNCTION — in an island with no path to obligate_aerobic_trait data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='fe_s_cluster_enzymes' label='Fe-S cluster enzymes' type=GENE_OR_PROTEIN — in an island with no path to obligate_aerobic_trait +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=BIOLOGICAL_PROCESS here — also PATHWAY×4 elsewhere in the corpus +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='superoxide_dismutase' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×2 elsewhere in the corpus +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×4 elsewhere in the corpus data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration FRAGMENTED_GRAPH WARN components=3 of 12 node(s) (sizes: 7, 3, 2) — one record, several unrelated mechanisms data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to obligately_alkaphilic_trait data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='proton' label='proton' type=CHEMICAL — in an island with no path to obligately_alkaphilic_trait data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_proton_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to obligately_alkaphilic_trait data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='secondary_cell_wall_polymers' label='secondary cell wall polymers / S-layer' type=CELLULAR_LOCALIZATION — in an island with no path to obligately_alkaphilic_trait data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='net_negative_surface_charge' label='net negative surface charge' type=QUALITY — in an island with no path to obligately_alkaphilic_trait +data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cation_proton_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 9, 5) — one record, several unrelated mechanisms data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide' label='hydrogen peroxide' type=CHEMICAL — in an island with no path to obligate_anaerobic_trait data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity UNREACHABLE_FROM_TRAIT WARN node_id='ferrous_iron' label='ferrous iron (Fe(II))' type=CHEMICAL — in an island with no path to obligate_anaerobic_trait data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity UNREACHABLE_FROM_TRAIT WARN node_id='hydroxyl_radical' label='hydroxyl radical' type=CHEMICAL — in an island with no path to obligate_anaerobic_trait data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity UNREACHABLE_FROM_TRAIT WARN node_id='dna_damage' label='DNA damage' type=BIOLOGICAL_PROCESS — in an island with no path to obligate_anaerobic_trait +data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity INCONSISTENT_NODE_TYPE WARN node_id='dna_damage' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 10, 4) — one record, several unrelated mechanisms data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporters' label='Na+/H+ antiporters' type=GENE_OR_PROTEIN — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_ph_homeostasis' label='intracellular pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum @@ -324,18 +405,27 @@ data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phe data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible-solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='amino_acid_decarboxylation' label='amino-acid decarboxylation' type=BIOLOGICAL_PROCESS — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum +data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='hyperosmotic_stress' type=ENVIRONMENTAL_FACTOR here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 5, 5, 2, 2) — one record, several unrelated mechanisms data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis UNREACHABLE_FROM_TRAIT WARN node_id='catalase' label='catalase' type=GENE_OR_PROTEIN — in an island with no path to oxygen_preference_trait/aerobic_phenotype/anaerobic_phenotype/microaerophilic_phenotype/facultative_phenotype data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide' label='hydrogen peroxide' type=CHEMICAL — in an island with no path to oxygen_preference_trait/aerobic_phenotype/anaerobic_phenotype/microaerophilic_phenotype/facultative_phenotype +data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis INCONSISTENT_NODE_TYPE WARN node_id='superoxide_dismutase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta.yaml ph_delta_homeostasis_flexibility UNREACHABLE_FROM_TRAIT WARN node_id='membrane_lipid_remodeling' label='saturated membrane fatty acid remodeling' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_trait data/traits/environment/ph_delta.yaml ph_delta_homeostasis_flexibility UNREACHABLE_FROM_TRAIT WARN node_id='proton_permeability' label='membrane proton permeability' type=QUALITY — in an island with no path to ph_delta_trait +data/traits/environment/ph_delta.yaml ph_delta_homeostasis_flexibility INCONSISTENT_NODE_TYPE WARN node_id='oxidative_phosphorylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/ph_delta.yaml ph_delta_homeostasis_flexibility FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ph_homeostasis' label='cytoplasmic pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='respiratory_proton_pumps' label='respiratory proton-pumping enzymes' type=GENE_OR_PROTEIN — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering_capacity' label='cytoplasmic buffering capacity' type=CAPACITY — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='membrane_lipid_porin_changes' label='membrane lipid/porin composition changes' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='inward_proton_leakage' label='inward proton leakage' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 +data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth INCONSISTENT_NODE_TYPE WARN node_id='cytoplasmic_buffering_capacity' type=CAPACITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth INCONSISTENT_NODE_TYPE WARN node_id='near_neutral_cytoplasmic_ph' type=QUALITY here — also STATE×1 elsewhere in the corpus data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 7, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_stress' label='external pH stress' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_delta_low_trait/ph_delta data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ph_homeostasis' label='cytoplasmic pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_low_trait/ph_delta @@ -345,6 +435,7 @@ data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHAB data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='electrogenic_na_h_antiport' label='electrogenic Na+/H+ antiport' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_low_trait/ph_delta data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='alkaline_ph_homeostasis' label='alkaline pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_low_trait/ph_delta data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='f1fo_atpase' label='F1Fo-ATPase' type=GENE_OR_PROTEIN — in an island with no path to ph_delta_low_trait/ph_delta +data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth INCONSISTENT_NODE_TYPE WARN node_id='electrogenic_na_h_antiport' type=BIOLOGICAL_PROCESS here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth FRAGMENTED_GRAPH WARN components=4 of 11 node(s) (sizes: 4, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='gln_glu_decarboxylation_pathway' label='glutamine/glutamate decarboxylation pathway' type=PATHWAY — in an island with no path to ph_delta_mid1_trait/ph_delta data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_proton' label='intracellular proton (H+)' type=CHEMICAL — in an island with no path to ph_delta_mid1_trait/ph_delta @@ -352,6 +443,8 @@ data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREAC data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='ammonia' label='ammonia' type=CHEMICAL — in an island with no path to ph_delta_mid1_trait/ph_delta data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='membrane_saturated_fatty_acids' label='membrane saturated fatty acid content' type=QUALITY — in an island with no path to ph_delta_mid1_trait/ph_delta data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='proton_diffusion_across_membrane' label='proton diffusion across membrane' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid1_trait/ph_delta +data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth INCONSISTENT_NODE_TYPE WARN node_id='oxidative_phosphorylation' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 7, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_stress' label='external pH stress' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_delta_mid2_trait/ph_delta data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='pmf_component_balance' label='PMF component balance' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid2_trait/ph_delta @@ -365,6 +458,7 @@ data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHAB data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_proton' label='intracellular H+' type=CHEMICAL — in an island with no path to ph_delta_mid2_trait/ph_delta data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffers' label='cytoplasmic buffering molecules' type=CHEMICAL — in an island with no path to ph_delta_mid2_trait/ph_delta data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ph_buffering' label='cytoplasmic pH buffering' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid2_trait/ph_delta +data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth INCONSISTENT_NODE_TYPE WARN node_id='glutamate_decarboxylase_system' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth FRAGMENTED_GRAPH WARN components=7 of 15 node(s) (sizes: 3, 2, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='external_alkaline_ph' label='external alkaline pH' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_delta_mid3_trait/ph_delta data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiport' label='electrogenic Na+/H+ antiport' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid3_trait/ph_delta @@ -378,6 +472,9 @@ data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABL data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='aa_decarboxylation' label='amino-acid decarboxylation pathways' type=PATHWAY — in an island with no path to ph_delta_mid3_trait/ph_delta data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='membrane_lipid_remodeling' label='membrane lipid composition shifts' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid3_trait/ph_delta data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='proton_permeability' label='membrane proton permeability' type=QUALITY — in an island with no path to ph_delta_mid3_trait/ph_delta +data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiport' type=BIOLOGICAL_PROCESS here — also MOLECULAR_FUNCTION×2 elsewhere in the corpus +data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth INCONSISTENT_NODE_TYPE WARN node_id='phosphate_buffering' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 3, 3, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_stress' label='external pH stress' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_delta_very_low_trait/ph_delta data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='pmf_partitioning' label='PMF partitioning (delta-pH / delta-psi)' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_very_low_trait/ph_delta @@ -389,9 +486,17 @@ data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNRE data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='acid_stress_survival' label='acid stress survival' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_very_low_trait/ph_delta data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='glutamate_decarboxylase_system' label='glutamate decarboxylase GadB + GABA/glutamate antiporter' type=PATHWAY — in an island with no path to ph_delta_very_low_trait/ph_delta data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_proton_consumption' label='cytoplasmic proton consumption' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_very_low_trait/ph_delta +data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic INCONSISTENT_NODE_TYPE WARN node_id='glutamate_decarboxylase_system' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic FRAGMENTED_GRAPH WARN components=6 of 13 node(s) (sizes: 3, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/ph_growth_preference.yaml ph_growth_preference_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/environment/ph_growth_preference.yaml ph_growth_preference_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering_capacity' label='cytoplasmic buffering capacity' type=CAPACITY — in an island with no path to ph_optimum_trait data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='internal_ph' label='internal pH' type=STATE — in an island with no path to ph_optimum_trait +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cytoplasm_acidification' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cytoplasmic_buffering_capacity' type=CAPACITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='internal_ph' type=STATE here — also QUALITY×1 elsewhere in the corpus data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis FRAGMENTED_GRAPH WARN components=2 of 12 node(s) (sizes: 10, 2) — one record, several unrelated mechanisms data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cpa_nha_antiporters' label='CPA/Nha family Na+/H+ antiporters' type=GENE_OR_PROTEIN — in an island with no path to ph_optimum_high_trait/ph_optimum data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_na' label='intracellular Na+ concentration' type=CHEMICAL — in an island with no path to ph_optimum_high_trait/ph_optimum @@ -402,6 +507,7 @@ data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoin data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='acidic_membrane_polymers' label='acidic plasma membrane polymers' type=CHEMICAL — in an island with no path to ph_optimum_high_trait/ph_optimum data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='organic_acid_secretion' label='organic acid secretion' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_high_trait/ph_optimum data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='ph_balance' label='pH balance' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_high_trait/ph_optimum +data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint FRAGMENTED_GRAPH WARN components=5 of 15 node(s) (sizes: 6, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='low_external_ph' label='low external pH' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_optimum_low_trait/ph_optimum data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='transmembrane_ph_gradient' label='large transmembrane pH gradient' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_low_trait/ph_optimum @@ -411,7 +517,9 @@ data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint U data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_proton_load' label='cytoplasmic proton load' type=STATE — in an island with no path to ph_optimum_low_trait/ph_optimum data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='proton_impermeable_membrane' label='rigid proton-impermeable membrane' type=CELLULAR_LOCALIZATION — in an island with no path to ph_optimum_low_trait/ph_optimum data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='passive_proton_permeability' label='passive proton permeability' type=QUALITY — in an island with no path to ph_optimum_low_trait/ph_optimum +data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='inside_positive_membrane_potential' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint FRAGMENTED_GRAPH WARN components=5 of 12 node(s) (sizes: 4, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/ph_optimum_mid1.yaml ph_optimum_mid1_neutrophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=PATHWAY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering_capacity' label='cytoplasmic buffering capacity' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_mid2_trait/ph_optimum data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_ph_homeostasis' label='intracellular pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_mid2_trait/ph_optimum data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporters' label='Na+/H+ antiporters' type=GENE_OR_PROTEIN — in an island with no path to ph_optimum_mid2_trait/ph_optimum @@ -420,6 +528,9 @@ data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_s data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='metabolite_decarboxylation' label='metabolite decarboxylation pathways' type=PATHWAY — in an island with no path to ph_optimum_mid2_trait/ph_optimum data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_mid2_trait/ph_optimum data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='f0f1_atp_synthase' label='F0F1-ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to ph_optimum_mid2_trait/ph_optimum +data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='cytoplasmic_buffering_capacity' type=BIOLOGICAL_PROCESS here — also CAPACITY×3 elsewhere in the corpus +data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='respiratory_proton_pumping' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus +data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint FRAGMENTED_GRAPH WARN components=3 of 12 node(s) (sizes: 5, 4, 3) — one record, several unrelated mechanisms data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='f0f1_atpase' label='F0F1-ATPase / ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthesis_from_pmf' label='ATP synthesis from proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta @@ -430,9 +541,17 @@ data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_num data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_proton' label='intracellular H+' type=CHEMICAL — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='phosphate_buffering' label='cytoplasmic buffering by phosphate pools' type=BIOLOGICAL_PROCESS — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='internal_ph' label='internal pH' type=STATE — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×6 elsewhere in the corpus +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='aa_decarboxylase_antiporter' type=PATHWAY here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='phosphate_buffering' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='internal_ph' type=STATE here — also QUALITY×1 elsewhere in the corpus data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis FRAGMENTED_GRAPH WARN components=5 of 15 node(s) (sizes: 6, 3, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/ph_range.yaml ph_range_bounded_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='membrane_potential' type=CHEMICAL here — also BIOLOGICAL_PROCESS×1, QUALITY×1, STATE×1 elsewhere in the corpus +data/traits/environment/ph_range.yaml ph_range_bounded_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/ph_range_high.yaml ph_range_high_extreme_alkaliphile UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_high' label='external pH > 10.3' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_range_high_trait/ph_range data/traits/environment/ph_range_high.yaml ph_range_high_extreme_alkaliphile UNREACHABLE_FROM_TRAIT WARN node_id='carbonate_speciation' label='carbonate (CO3 2-) speciation' type=CHEMICAL — in an island with no path to ph_range_high_trait/ph_range +data/traits/environment/ph_range_high.yaml ph_range_high_extreme_alkaliphile INCONSISTENT_NODE_TYPE WARN node_id='membrane_potential' type=QUALITY here — also BIOLOGICAL_PROCESS×1, CHEMICAL×1, STATE×1 elsewhere in the corpus data/traits/environment/ph_range_high.yaml ph_range_high_extreme_alkaliphile FRAGMENTED_GRAPH WARN components=2 of 12 node(s) (sizes: 10, 2) — one record, several unrelated mechanisms data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_low_trait/ph_range data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthase_atp_formation' label='ATP synthase-mediated ATP formation' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_low_trait/ph_range @@ -442,7 +561,12 @@ data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHA data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='weak_acid_influx' label='weak organic acid influx into cell' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_low_trait/ph_range data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='weak_acid_dissociation' label='intracellular dissociation of weak organic acids' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_low_trait/ph_range data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='internal_ph' label='internal (cytoplasmic) pH' type=QUALITY — in an island with no path to ph_range_low_trait/ph_range +data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range INCONSISTENT_NODE_TYPE WARN node_id='membrane_proton_permeability' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range INCONSISTENT_NODE_TYPE WARN node_id='internal_ph' type=QUALITY here — also STATE×2 elsewhere in the corpus data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 5, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/ph_range_mid1.yaml ph_range_mid1_neutrophile_range INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_range_mid1.yaml ph_range_mid1_neutrophile_range INCONSISTENT_NODE_TYPE WARN node_id='respiratory_proton_pumping' type=GENE_OR_PROTEIN here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_7_8' label='external pH 7-8' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_range_mid2_trait/ph_range data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ph_homeostasis' label='cytoplasmic pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid2_trait/ph_range data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering' label='cytoplasmic buffering' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid2_trait/ph_range @@ -455,12 +579,15 @@ data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthesis' label='ATP synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid2_trait/ph_range data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='proton_ion_antiporters' label='proton:ion antiporters' type=GENE_OR_PROTEIN — in an island with no path to ph_range_mid2_trait/ph_range data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='membrane_potential' label='membrane potential (Δψ)' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid2_trait/ph_range +data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance INCONSISTENT_NODE_TYPE WARN node_id='membrane_potential' type=BIOLOGICAL_PROCESS here — also CHEMICAL×1, QUALITY×1, STATE×1 elsewhere in the corpus data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 3, 3, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='mrp_antiporter' label='Mrp Na+/H+ antiporter complex' type=GENE_OR_PROTEIN — in an island with no path to ph_range_mid3_trait/ph_range data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_ph_homeostasis' label='intracellular pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid3_trait/ph_range data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='nahplus_antiport_activity' label='Na+/H+ antiport activity' type=MOLECULAR_FUNCTION — in an island with no path to ph_range_mid3_trait/ph_range data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasm_acidification' label='cytoplasm acidification during alkaline growth' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid3_trait/ph_range data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='cardiolipin_membrane' label='cardiolipin-rich negatively charged membrane' type=CELLULAR_LOCALIZATION — in an island with no path to ph_range_mid3_trait/ph_range +data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range INCONSISTENT_NODE_TYPE WARN node_id='cytoplasm_acidification' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='potassium_influx' label='potassium influx / K+ transport' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_very_low_trait/ph_range data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='reversed_membrane_potential' label='inside-positive (reversed) membrane potential' type=STATE — in an island with no path to ph_range_very_low_trait/ph_range @@ -470,7 +597,10 @@ data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidoph data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='weak_organic_acids' label='protonated weak organic acids' type=CHEMICAL — in an island with no path to ph_range_very_low_trait/ph_range data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasm' label='cytoplasm' type=CELLULAR_LOCALIZATION — in an island with no path to ph_range_very_low_trait/ph_range data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_acidification' label='cytoplasmic acidification' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_very_low_trait/ph_range +data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile INCONSISTENT_NODE_TYPE WARN node_id='reversed_membrane_potential' type=STATE here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile INCONSISTENT_NODE_TYPE WARN node_id='near_neutral_cytoplasmic_ph' type=STATE here — also QUALITY×1 elsewhere in the corpus data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile FRAGMENTED_GRAPH WARN components=4 of 11 node(s) (sizes: 3, 3, 3, 2) — one record, several unrelated mechanisms +data/traits/environment/piezotolerant.yaml piezotolerance_pressure_range INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity_maintenance' label='membrane fluidity maintenance under high pressure' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_delta_trait data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='unsaturated_fatty_acid_production' label='unsaturated fatty acid production' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_delta_trait data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solutes' label='intracellular osmolytes / compatible solutes' type=CHEMICAL — in an island with no path to pressure_delta_trait @@ -478,27 +608,34 @@ data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UN data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='nuo_complex_i' label='nuo NADH dehydrogenase I complex' type=GENE_OR_PROTEIN — in an island with no path to pressure_delta_trait data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='high_pressure_energy_conservation' label='high-pressure respiratory energy conservation' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_delta_trait data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor FRAGMENTED_GRAPH WARN components=4 of 12 node(s) (sizes: 6, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/pressure_optimum.yaml pressure_optimum_balanced_adaptation INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/environment/pressure_optimum.yaml pressure_optimum_balanced_adaptation FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 5, 4) — one record, several unrelated mechanisms data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span UNREACHABLE_FROM_TRAIT WARN node_id='tmao' label='trimethylamine N-oxide (TMAO)' type=CHEMICAL — in an island with no path to pressure_range_trait data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span UNREACHABLE_FROM_TRAIT WARN node_id='protein_stabilization' label='protein stabilization via preferential hydration' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_range_trait data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_range_trait +data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span INCONSISTENT_NODE_TYPE WARN node_id='pufa_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 6, 3) — one record, several unrelated mechanisms data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solutes' label='compatible solutes' type=CHEMICAL — in an island with no path to psychrophilic_trait data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='trehalose' label='trehalose' type=CHEMICAL — in an island with no path to psychrophilic_trait data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='protein_membrane_stability' label='protein and membrane stability' type=QUALITY — in an island with no path to psychrophilic_trait +data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 10, 3) — one record, several unrelated mechanisms data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to psychrotolerant_trait data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='protein_membrane_stability' label='protein and membrane stability under cold stress' type=QUALITY — in an island with no path to psychrotolerant_trait data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='extracellular_polymeric_substances' label='extracellular polymeric substances (EPS)' type=CHEMICAL — in an island with no path to psychrotolerant_trait data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='freeze_thaw_cryoprotection' label='cryoprotection against freeze-thaw cycles' type=BIOLOGICAL_PROCESS — in an island with no path to psychrotolerant_trait +data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=QUALITY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_osmotic_balance' label='intracellular osmotic balance across salinity' type=BIOLOGICAL_PROCESS — in an island with no path to salinity_phenotype_trait/nacl_optimum/nacl_range/nacl_delta data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='salt_out_compatible_solute_strategy' label='compatible-solute (salt-out) strategy' type=PATHWAY — in an island with no path to salinity_phenotype_trait/nacl_optimum/nacl_range/nacl_delta data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='salt_in_strategy' label='salt-in strategy' type=PATHWAY — in an island with no path to salinity_phenotype_trait/nacl_optimum/nacl_range/nacl_delta data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='glycine_betaine' label='glycine betaine' type=CHEMICAL — in an island with no path to salinity_phenotype_trait/nacl_optimum/nacl_range/nacl_delta +data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=PATHWAY here — also BIOLOGICAL_PROCESS×7 elsewhere in the corpus data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 9, 4) — one record, several unrelated mechanisms data/traits/environment/slightly_halophilic.yaml slight_halophile_low_salt_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='ion_homeostasis' label='ion homeostasis during salt stress' type=BIOLOGICAL_PROCESS — in an island with no path to slightly_halophilic_trait data/traits/environment/slightly_halophilic.yaml slight_halophile_low_salt_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='na_k_transcription' label='Na+/K+ transcriptional induction' type=BIOLOGICAL_PROCESS — in an island with no path to slightly_halophilic_trait +data/traits/environment/slightly_halophilic.yaml slight_halophile_low_salt_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/slightly_halophilic.yaml slight_halophile_low_salt_osmoadaptation FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 8, 2) — one record, several unrelated mechanisms data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='c_di_amp' label='cyclic di-AMP' type=CHEMICAL — in an island with no path to stenohaline_trait data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='k_import_systems' label='K+ import systems' type=GENE_OR_PROTEIN — in an island with no path to stenohaline_trait @@ -512,6 +649,8 @@ data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance U data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='aquaporin_water_channel' label='aquaporin water-channel activity' type=MOLECULAR_FUNCTION — in an island with no path to stenohaline_trait data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='facilitated_water_diffusion' label='facilitated water diffusion' type=BIOLOGICAL_PROCESS — in an island with no path to stenohaline_trait data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance FRAGMENTED_GRAPH WARN components=6 of 17 node(s) (sizes: 6, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/strictly_anaerobic.yaml strict_anaerobe_oxygen_sensitivity INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/temperature_delta.yaml temperature_delta_thermal_flexibility INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='decreased_growth_temperature' label='decreased growth temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_delta_high_trait/temperature_delta data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='unsaturated_fatty_acid_biosynthesis' label='unsaturated fatty acid biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_high_trait/temperature_delta data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='homoviscous_adaptation' label='homoviscous adaptation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_high_trait/temperature_delta @@ -524,14 +663,19 @@ data/traits/environment/temperature_delta_high.yaml temperature_delta_high_euryt data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='increased_fatty_acid_diversity' label='increased short-/branched-/unsaturated fatty acids' type=CHEMICAL — in an island with no path to temperature_delta_high_trait/temperature_delta data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='thermostable_enzyme' label='hyperthermophilic enzyme thermostability' type=QUALITY — in an island with no path to temperature_delta_high_trait/temperature_delta data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='irreversible_protein_inactivation' label='irreversible inactivation at high temperatures' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_high_trait/temperature_delta +data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity_homeostasis' type=STATE here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 3, 3, 3, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/temperature_delta_low.yaml temperature_delta_low_limited_breadth INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=BIOLOGICAL_PROCESS here — also QUALITY×3 elsewhere in the corpus data/traits/environment/temperature_delta_mid1.yaml temperature_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='membrane_physical_state_change' label='membrane physical-state change' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_mid1_trait/temperature_delta data/traits/environment/temperature_delta_mid1.yaml temperature_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='two_component_cold_signaling' label='two-component cold signaling' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_mid1_trait/temperature_delta +data/traits/environment/temperature_delta_mid1.yaml temperature_delta_mid1_moderate_breadth INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_delta_mid1.yaml temperature_delta_mid1_moderate_breadth FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='rpos_sigma_factor' label='RpoS sigma factor (sigma-S)' type=GENE_OR_PROTEIN — in an island with no path to temperature_delta_mid2_trait/temperature_delta data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='otsab_operon' label='otsAB trehalose biosynthesis operon' type=PATHWAY — in an island with no path to temperature_delta_mid2_trait/temperature_delta data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='trehalose' label='trehalose' type=CHEMICAL — in an island with no path to temperature_delta_mid2_trait/temperature_delta data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cold_tolerance' label='cold / cold-shock tolerance' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_mid2_trait/temperature_delta +data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=BIOLOGICAL_PROCESS here — also QUALITY×24 elsewhere in the corpus data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 6, 4) — one record, several unrelated mechanisms data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='unsaturated_fatty_acid_content' label='unsaturated fatty acid content' type=CHEMICAL — in an island with no path to temperature_delta_very_low_trait/temperature_delta data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to temperature_delta_very_low_trait/temperature_delta @@ -539,9 +683,12 @@ data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_l data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='cspa_protein' label='CspA cold-shock protein' type=GENE_OR_PROTEIN — in an island with no path to temperature_delta_very_low_trait/temperature_delta data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='csda_helicase' label='CsdA DEAD-box RNA helicase' type=GENE_OR_PROTEIN — in an island with no path to temperature_delta_very_low_trait/temperature_delta data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='translation_under_cold' label='translation under cold shock' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_very_low_trait/temperature_delta +data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal FRAGMENTED_GRAPH WARN components=4 of 9 node(s) (sizes: 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='arrhenius_plot_deviation' label='Arrhenius plot deviation from linearity' type=EXPERIMENTAL_FACTOR — in an island with no path to temperature_optimum_trait data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='stress_growth_regime' label='stress / non-physiological growth regime' type=STATE — in an island with no path to temperature_optimum_trait +data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 7, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='reverse_gyrase' label='reverse gyrase' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_high_trait/temperature_optimum data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='positive_dna_supercoiling' label='positive DNA supercoiling' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_high_trait/temperature_optimum @@ -554,6 +701,8 @@ data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_t data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='denatured_protein_refolding' label='refolding of denatured proteins' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_high_trait/temperature_optimum data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='membrane_lipid_composition' label='altered membrane lipid composition' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_high_trait/temperature_optimum data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='membrane_thermostability' label='cytoplasmic membrane thermostability' type=QUALITY — in an island with no path to temperature_optimum_high_trait/temperature_optimum +data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='positive_dna_supercoiling' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='membrane_lipid_composition' type=BIOLOGICAL_PROCESS here — also CELLULAR_LOCALIZATION×2, QUALITY×1 elsewhere in the corpus data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint FRAGMENTED_GRAPH WARN components=6 of 16 node(s) (sizes: 5, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='low_temperature' label='low temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_optimum_low_trait/temperature_optimum data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to temperature_optimum_low_trait/temperature_optimum @@ -565,9 +714,15 @@ data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psy data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='ice_crystal_growth' label='ice crystal growth' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_low_trait/temperature_optimum data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='oxidative_stress' label='oxidative stress' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_low_trait/temperature_optimum data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='pufa_biosynthesis' label='PUFA biosynthesis' type=PATHWAY — in an island with no path to temperature_optimum_low_trait/temperature_optimum +data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='pufa_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 5, 4, 3, 2) — one record, several unrelated mechanisms +data/traits/environment/temperature_optimum_mid1.yaml temperature_optimum_mid1_lower_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_decrease' label='temperature decrease' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_optimum_mid2_trait/temperature_optimum data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_rigidification' label='membrane rigidification' type=QUALITY — in an island with no path to temperature_optimum_mid2_trait/temperature_optimum +data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=QUALITY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 7, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='decreased_temperature' label='decreased temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_bilayer' label='membrane bilayer' type=CELLULAR_LOCALIZATION — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum @@ -577,6 +732,7 @@ data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_u data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='chaperone_network' label='molecular chaperone network' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='proteostasis' label='proteostasis' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum +data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile FRAGMENTED_GRAPH WARN components=5 of 12 node(s) (sizes: 4, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_downshift' label='temperature downshift' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='unsaturated_fatty_acid_proportion' label='unsaturated fatty acid proportion' type=CHEMICAL — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum @@ -589,6 +745,8 @@ data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_w data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='dnak_chaperone' label='DnaK chaperone' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='rpoh_sigma_factor' label='RpoH (sigma-32) heat-shock sigma factor' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='ftsh_protease' label='FtsH protease' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum +data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='unsaturated_fatty_acid_proportion' type=CHEMICAL here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity_homeostasis' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile FRAGMENTED_GRAPH WARN components=4 of 15 node(s) (sizes: 4, 4, 4, 3) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cold_shock_proteins' label='cold shock proteins / RNA chaperones' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='translation_low_temperature' label='translation at low temperature' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum @@ -600,15 +758,23 @@ data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_ve data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='thermal_hysteresis' label='thermal hysteresis / lowered freezing point' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='enzyme_structural_flexibility' label='increased enzyme structural flexibility' type=QUALITY — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='catalytic_activity_low_temperature' label='catalytic activity at low temperature' type=MOLECULAR_FUNCTION — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum +data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='fatty_acid_desaturase' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×2 elsewhere in the corpus data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint FRAGMENTED_GRAPH WARN components=6 of 17 node(s) (sizes: 7, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='membrane_cooling_rigidification' label='membrane rigidification during cooling' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_phenotype_trait/temperature_optimum/temperature_range/temperature_delta/growth_at_low_temperature data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='desk_desr_signaling' label='DesK/DesR two-component signaling' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_phenotype_trait/temperature_optimum/temperature_range/temperature_delta/growth_at_low_temperature data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='cold_adapted_enzymes' label='cold-adapted enzymes' type=GENE_OR_PROTEIN — in an island with no path to temperature_phenotype_trait/temperature_optimum/temperature_range/temperature_delta/growth_at_low_temperature data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='high_catalytic_efficiency_low_temp' label='high catalytic efficiency at low temperature' type=MOLECULAR_FUNCTION — in an island with no path to temperature_phenotype_trait/temperature_optimum/temperature_range/temperature_delta/growth_at_low_temperature +data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 5, 4, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology UNREACHABLE_FROM_TRAIT WARN node_id='environmental_temperature' label='environmental temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_preference_trait data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology UNREACHABLE_FROM_TRAIT WARN node_id='growth_rate' label='microbial growth rate' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_preference_trait +data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology INCONSISTENT_NODE_TYPE WARN node_id='fatty_acid_desaturase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms +data/traits/environment/temperature_range.yaml temperature_range_bounded_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_range.yaml temperature_range_bounded_adaptation INCONSISTENT_NODE_TYPE WARN node_id='chaperone_systems' type=BIOLOGICAL_PROCESS here — also GENE_OR_PROTEIN×1 elsewhere in the corpus +data/traits/environment/temperature_range_high.yaml temperature_range_high_thermophile INCONSISTENT_NODE_TYPE WARN node_id='positive_dna_supercoiling' type=QUALITY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='low_temperature' label='low temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_low_trait/temperature_range data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to temperature_range_low_trait/temperature_range data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='fatty_acid_desaturase_activity' label='fatty acid desaturase activity' type=MOLECULAR_FUNCTION — in an island with no path to temperature_range_low_trait/temperature_range @@ -619,6 +785,8 @@ data/traits/environment/temperature_range_low.yaml temperature_range_low_psychro data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='cryoprotection' label='cryoprotection' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_low_trait/temperature_range data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='molecular_chaperones' label='GroEL/DnaK molecular chaperones' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_low_trait/temperature_range data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='protein_misfolding' label='protein misfolding' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_low_trait/temperature_range +data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant INCONSISTENT_NODE_TYPE WARN node_id='unsaturated_fatty_acid_proportion' type=QUALITY here — also CHEMICAL×1 elsewhere in the corpus data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 4, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_decrease' label='temperature decrease' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid1_trait/temperature_range data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_rigidification' label='membrane rigidification/thickening' type=QUALITY — in an island with no path to temperature_range_mid1_trait/temperature_range @@ -630,12 +798,15 @@ data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='shine_dalgarno_exposure' label='Shine-Dalgarno sequence exposure' type=MOLECULAR_FUNCTION — in an island with no path to temperature_range_mid1_trait/temperature_range data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_shift' label='temperature shift' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid1_trait/temperature_range data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='dna_supercoiling' label='DNA supercoiling' type=QUALITY — in an island with no path to temperature_range_mid1_trait/temperature_range +data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=QUALITY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 4, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='elevated_temperature' label='elevated temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid2_trait/temperature_range data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='rna_thermometer' label='RNA thermometer 5′-UTR structure' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_mid2_trait/temperature_range data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_shift' label='temperature shift / heat shock' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid2_trait/temperature_range data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='heat_shock_proteins' label='heat-shock proteins / chaperones' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_mid2_trait/temperature_range data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='protein_denaturation' label='protein denaturation / aggregation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid2_trait/temperature_range +data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 8, 3, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_order' label='membrane order / fluidity state' type=QUALITY — in an island with no path to temperature_range_mid3_trait/temperature_range data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='desk_kinase_state' label='DesK kinase-dominant state' type=STATE — in an island with no path to temperature_range_mid3_trait/temperature_range @@ -648,6 +819,7 @@ data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_decrease' label='temperature decrease' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid3_trait/temperature_range data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='homeoviscous_adaptation' label='homeoviscous adaptation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid3_trait/temperature_range data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='liquid_crystalline_membrane' label='liquid-crystalline membrane state' type=STATE — in an island with no path to temperature_range_mid3_trait/temperature_range +data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=BIOLOGICAL_PROCESS here — also QUALITY×3 elsewhere in the corpus data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile FRAGMENTED_GRAPH WARN components=6 of 14 node(s) (sizes: 3, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='fab_branchpoint_valve' label='FabI/FabB fatty-acid branchpoint valve' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid4_trait/temperature_range data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='homeoviscous_adaptation' label='homeoviscous adaptation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid4_trait/temperature_range @@ -663,6 +835,9 @@ data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_ data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='rpoh_regulon' label='sigma-32 (RpoH) heat-shock regulon' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid4_trait/temperature_range data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='chaperone_systems' label='DnaK/DnaJ/GrpE and GroES/GroEL chaperone systems' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_mid4_trait/temperature_range data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='heat_stress_protection' label='protection against heat stress' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid4_trait/temperature_range +data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_lipid_composition' type=QUALITY here — also BIOLOGICAL_PROCESS×1, CELLULAR_LOCALIZATION×2 elsewhere in the corpus +data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='chaperone_systems' type=GENE_OR_PROTEIN here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile FRAGMENTED_GRAPH WARN components=6 of 17 node(s) (sizes: 5, 3, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='low_temperature' label='low temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_very_low_trait/temperature_range data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fatty_acid_desaturation' label='membrane fatty-acid desaturation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_very_low_trait/temperature_range @@ -676,6 +851,7 @@ data/traits/environment/temperature_range_very_low.yaml temperature_range_very_l data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='protein_membrane_stabilization' label='protein and membrane stabilization' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_very_low_trait/temperature_range data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='ice_binding_proteins' label='ice-binding/antifreeze proteins' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_very_low_trait/temperature_range data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='ice_crystal_growth' label='ice-crystal growth/recrystallization' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_very_low_trait/temperature_range +data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile FRAGMENTED_GRAPH WARN components=7 of 15 node(s) (sizes: 3, 2, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='reverse_gyrase' label='reverse gyrase' type=GENE_OR_PROTEIN — in an island with no path to thermophilic_trait data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='positive_dna_supercoiling' label='positive DNA supercoiling' type=BIOLOGICAL_PROCESS — in an island with no path to thermophilic_trait @@ -685,6 +861,9 @@ data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHAB data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='denatured_proteins' label='denatured proteins' type=GENE_OR_PROTEIN — in an island with no path to thermophilic_trait data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='cyclopentane_ring_number' label='tetraether lipid cyclopentane ring number' type=QUALITY — in an island with no path to thermophilic_trait data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_rigidity' label='membrane rigidity' type=QUALITY — in an island with no path to thermophilic_trait +data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_lipid_composition' type=CELLULAR_LOCALIZATION here — also BIOLOGICAL_PROCESS×1, QUALITY×1 elsewhere in the corpus +data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_proton_permeability' type=BIOLOGICAL_PROCESS here — also QUALITY×2 elsewhere in the corpus +data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation INCONSISTENT_NODE_TYPE WARN node_id='positive_dna_supercoiling' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 6, 4, 2, 2) — one record, several unrelated mechanisms data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='elevated_temperature' label='elevated temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to thermotolerant_trait data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='heat_shock_response' label='heat-shock response' type=BIOLOGICAL_PROCESS — in an island with no path to thermotolerant_trait @@ -693,6 +872,7 @@ data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adap data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='rpoE_envelope_sigma' label='RpoE envelope-stress sigma factor' type=GENE_OR_PROTEIN — in an island with no path to thermotolerant_trait data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_protein_folding_lps' label='membrane protein folding and LPS biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to thermotolerant_trait data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms +data/traits/environment/uv_radiation_tolerant.yaml uv_tolerance_excision_repair INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/xerophilic.yaml xerophilic_low_water_activity_growth UNREACHABLE_FROM_TRAIT WARN node_id='low_mw_polyols' label='low-molecular-weight polyols (glycerol, erythritol, arabitol)' type=CHEMICAL — in an island with no path to xerophilic_trait data/traits/environment/xerophilic.yaml xerophilic_low_water_activity_growth UNREACHABLE_FROM_TRAIT WARN node_id='osmotic_adjustment' label='osmotic adjustment' type=BIOLOGICAL_PROCESS — in an island with no path to xerophilic_trait data/traits/environment/xerophilic.yaml xerophilic_low_water_activity_growth FRAGMENTED_GRAPH WARN components=2 of 8 node(s) (sizes: 6, 2) — one record, several unrelated mechanisms @@ -730,6 +910,7 @@ data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt UNREACHABLE_F data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt UNREACHABLE_FROM_TRAIT WARN node_id='plasmid_methylase' label='plasmid-encoded methylase' type=MOLECULAR_FUNCTION — in an island with no path to plasmid_carriage_trait data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt UNREACHABLE_FROM_TRAIT WARN node_id='restriction_of_plasmid_dna' label='restriction of incoming plasmid DNA' type=BIOLOGICAL_PROCESS — in an island with no path to plasmid_carriage_trait data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt UNREACHABLE_FROM_TRAIT WARN node_id='anti_restriction_genes' label='plasmid-encoded anti-restriction genes' type=GENE_OR_PROTEIN — in an island with no path to plasmid_carriage_trait +data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt INCONSISTENT_NODE_TYPE WARN node_id='plasmid_methylase' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 6, 3, 2) — one record, several unrelated mechanisms data/traits/genomics/ploidy.yaml ploidy_repair_survival FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 5, 4) — one record, several unrelated mechanisms data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN node_id='ci_repressor' label='CI master repressor' type=GENE_OR_PROTEIN — in an island with no path to prophage_trait @@ -741,10 +922,13 @@ data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN node_id='prophage_induction' label='prophage induction' type=BIOLOGICAL_PROCESS — in an island with no path to prophage_trait data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN node_id='phage_plasmid' label='phage-plasmid' type=GENE_OR_PROTEIN — in an island with no path to prophage_trait data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN node_id='extrachromosomal_maintenance' label='extrachromosomal prophage maintenance' type=BIOLOGICAL_PROCESS — in an island with no path to prophage_trait +data/traits/genomics/prophage.yaml prophage_lysogeny INCONSISTENT_NODE_TYPE WARN node_id='dna_damage' type=ENVIRONMENTAL_FACTOR here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/genomics/prophage.yaml prophage_lysogeny FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 5, 4, 2, 2) — one record, several unrelated mechanisms data/traits/genomics/restriction_modification_system.yaml rm_self_nonself_defense UNREACHABLE_FROM_TRAIT WARN node_id='type_iv_restriction_enzyme' label='type IV restriction enzyme' type=GENE_OR_PROTEIN — in an island with no path to rm_trait data/traits/genomics/restriction_modification_system.yaml rm_self_nonself_defense UNREACHABLE_FROM_TRAIT WARN node_id='methylated_dna_motif' label='methylated DNA motif' type=CHEMICAL — in an island with no path to rm_trait +data/traits/genomics/restriction_modification_system.yaml rm_self_nonself_defense INCONSISTENT_NODE_TYPE WARN node_id='plasmid_methylase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/genomics/restriction_modification_system.yaml rm_self_nonself_defense FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms +data/traits/genomics/rrna_operon_copy_number.yaml rrn_copy_growth_rate INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=QUALITY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/genomics/transposable_element.yaml te_transposition_rearrangement UNREACHABLE_FROM_TRAIT WARN node_id='te_insertion' label='transposable element insertion' type=BIOLOGICAL_PROCESS — in an island with no path to te_trait data/traits/genomics/transposable_element.yaml te_transposition_rearrangement UNREACHABLE_FROM_TRAIT WARN node_id='target_site_duplication' label='target site duplication' type=QUALITY — in an island with no path to te_trait data/traits/genomics/transposable_element.yaml te_transposition_rearrangement UNREACHABLE_FROM_TRAIT WARN node_id='gene_disruption' label='gene disruption' type=BIOLOGICAL_PROCESS — in an island with no path to te_trait @@ -752,6 +936,9 @@ data/traits/genomics/transposable_element.yaml te_transposition_rearrangement FR data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='cytochrome_c_oxidase' label='cytochrome c oxidase' type=GENE_OR_PROTEIN — in an island with no path to aerobic_respiration_trait data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='molecular_oxygen' label='molecular oxygen' type=CHEMICAL — in an island with no path to aerobic_respiration_trait data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='water' label='water' type=CHEMICAL — in an island with no path to aerobic_respiration_trait +data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase FRAGMENTED_GRAPH WARN components=2 of 8 node(s) (sizes: 5, 3) — one record, several unrelated mechanisms data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='oxygen_limitation' label='oxygen limitation / anoxic transition' type=ENVIRONMENTAL_FACTOR — in an island with no path to anaerobic_respiration_trait data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='denitrification_reductases' label='denitrification reductases' type=GENE_OR_PROTEIN — in an island with no path to anaerobic_respiration_trait @@ -761,6 +948,7 @@ data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrif data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='nitrous_oxide_reductase' label='nitrous oxide reductase (NosZ)' type=GENE_OR_PROTEIN — in an island with no path to anaerobic_respiration_trait data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='nitrous_oxide' label='nitrous oxide' type=CHEMICAL — in an island with no path to anaerobic_respiration_trait data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='dinitrogen' label='dinitrogen' type=CHEMICAL — in an island with no path to anaerobic_respiration_trait +data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=MOLECULAR_FUNCTION here — also CHEMICAL×3 elsewhere in the corpus data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 6, 3, 3, 2) — one record, several unrelated mechanisms data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis UNREACHABLE_FROM_TRAIT WARN node_id='endoglucanase' label='endoglucanase' type=GENE_OR_PROTEIN — in an island with no path to biopolymer_degradation_trait data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis UNREACHABLE_FROM_TRAIT WARN node_id='cello_oligosaccharides' label='cello-oligosaccharides' type=CHEMICAL — in an island with no path to biopolymer_degradation_trait @@ -774,6 +962,7 @@ data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extrac data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis UNREACHABLE_FROM_TRAIT WARN node_id='lignin_oxidative_enzymes' label='lignin-oxidizing redox enzymes (LiP/MnP/VP/laccase/DyP)' type=GENE_OR_PROTEIN — in an island with no path to biopolymer_degradation_trait data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis UNREACHABLE_FROM_TRAIT WARN node_id='lignin' label='lignin' type=CHEMICAL — in an island with no path to biopolymer_degradation_trait data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis FRAGMENTED_GRAPH WARN components=6 of 14 node(s) (sizes: 3, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/metabolism/cable_bacteria_metabolism.yaml cable_bacteria_long_distance_electron_transport INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/metabolism/calvin_benson_bassham_cycle.yaml cbb_rubisco_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='cbbr' label='CbbR transcriptional regulator' type=GENE_OR_PROTEIN — in an island with no path to cbb_trait data/traits/metabolism/calvin_benson_bassham_cycle.yaml cbb_rubisco_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='cbb_operon' label='cbb operon' type=GENE_OR_PROTEIN — in an island with no path to cbb_trait data/traits/metabolism/calvin_benson_bassham_cycle.yaml cbb_rubisco_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ca' label='cytoplasmic carbonic anhydrase' type=GENE_OR_PROTEIN — in an island with no path to cbb_trait @@ -804,11 +993,13 @@ data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_ data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 UNREACHABLE_FROM_TRAIT WARN node_id='no_reduction_to_n2o' label='nitric oxide reduction to nitrous oxide' type=BIOLOGICAL_PROCESS — in an island with no path to denitrification_trait data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 UNREACHABLE_FROM_TRAIT WARN node_id='denitrification_modularity' label='denitrification pathway modularity' type=QUALITY — in an island with no path to denitrification_trait data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 UNREACHABLE_FROM_TRAIT WARN node_id='transient_intermediate_accumulation' label='transient accumulation of intermediates' type=STATE — in an island with no path to denitrification_trait +data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 5, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='bicarbonate' label='bicarbonate' type=CHEMICAL — in an island with no path to dc_four_hb_trait data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='pep_carboxylase' label='phosphoenolpyruvate carboxylase' type=GENE_OR_PROTEIN — in an island with no path to dc_four_hb_trait data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='phosphoenolpyruvate' label='phosphoenolpyruvate' type=CHEMICAL — in an island with no path to dc_four_hb_trait data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='oxaloacetate' label='oxaloacetate' type=CHEMICAL — in an island with no path to dc_four_hb_trait +data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 10, 4) — one record, several unrelated mechanisms data/traits/metabolism/dissimilatory_metal_reduction.yaml metal_reduction_anaerobic_respiration UNREACHABLE_FROM_TRAIT WARN node_id='organic_matter_oxidation' label='organic compound oxidation' type=BIOLOGICAL_PROCESS — in an island with no path to metal_reduction_trait data/traits/metabolism/dissimilatory_metal_reduction.yaml metal_reduction_anaerobic_respiration UNREACHABLE_FROM_TRAIT WARN node_id='fe3_reduction' label='Fe(III) reduction' type=BIOLOGICAL_PROCESS — in an island with no path to metal_reduction_trait @@ -847,6 +1038,8 @@ data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers U data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers UNREACHABLE_FROM_TRAIT WARN node_id='terminal_oxidase' label='terminal oxidase' type=GENE_OR_PROTEIN — in an island with no path to electron_transfer_trait data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='oxygen' type=CHEMICAL — in an island with no path to electron_transfer_trait data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to electron_transfer_trait +data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus +data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers FRAGMENTED_GRAPH WARN components=4 of 17 node(s) (sizes: 7, 5, 3, 2) — one record, several unrelated mechanisms data/traits/metabolism/fermentation.yaml fermentation_redox_energy UNREACHABLE_FROM_TRAIT WARN node_id='glycolysis_emp' label='glycolysis (Embden-Meyerhof-Parnas pathway)' type=PATHWAY — in an island with no path to fermentation_trait data/traits/metabolism/fermentation.yaml fermentation_redox_energy UNREACHABLE_FROM_TRAIT WARN node_id='pyruvate' label='pyruvate' type=CHEMICAL — in an island with no path to fermentation_trait @@ -879,6 +1072,7 @@ data/traits/metabolism/lignin_degradation.yaml lignin_degradation_peroxidase_lac data/traits/metabolism/lignin_degradation.yaml lignin_degradation_peroxidase_laccase UNREACHABLE_FROM_TRAIT WARN node_id='beta_o4_bond' label='beta-O-4 aryl ether bond' type=CHEMICAL — in an island with no path to lignin_degradation_trait data/traits/metabolism/lignin_degradation.yaml lignin_degradation_peroxidase_laccase UNREACHABLE_FROM_TRAIT WARN node_id='ca_cb_bond' label='Calpha-Cbeta bond' type=CHEMICAL — in an island with no path to lignin_degradation_trait data/traits/metabolism/lignin_degradation.yaml lignin_degradation_peroxidase_laccase FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 5, 3, 3, 2) — one record, several unrelated mechanisms +data/traits/metabolism/manganese_oxidation.yaml manganese_oxidation_multicopper_oxidase INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='respiratory_electron_transport' label='respiratory electron transport chain' type=BIOLOGICAL_PROCESS — in an island with no path to metabolism_trait data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=CHEMICAL — in an island with no path to metabolism_trait data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthase' label='ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to metabolism_trait @@ -887,6 +1081,7 @@ data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABL data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='carbon_use_efficiency' label='carbon use efficiency' type=QUALITY — in an island with no path to metabolism_trait data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='substrate_complexity' label='substrate complexity' type=QUALITY — in an island with no path to metabolism_trait data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='metabolic_energy_cost' label='energetic cost of metabolism' type=QUALITY — in an island with no path to metabolism_trait +data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=CHEMICAL here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, STATE×18 elsewhere in the corpus data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 6, 4, 2, 2) — one record, several unrelated mechanisms data/traits/metabolism/methanogenesis.yaml methanogenesis_c1_reduction UNREACHABLE_FROM_TRAIT WARN node_id='carbon_dioxide' label='carbon dioxide' type=CHEMICAL — in an island with no path to methanogenesis_trait data/traits/metabolism/methanogenesis.yaml methanogenesis_c1_reduction UNREACHABLE_FROM_TRAIT WARN node_id='molecular_hydrogen' label='molecular hydrogen' type=CHEMICAL — in an island with no path to methanogenesis_trait @@ -898,7 +1093,9 @@ data/traits/metabolism/methanogenesis.yaml methanogenesis_c1_reduction UNREACHAB data/traits/metabolism/methanogenesis.yaml methanogenesis_c1_reduction FRAGMENTED_GRAPH WARN components=4 of 15 node(s) (sizes: 8, 3, 2, 2) — one record, several unrelated mechanisms data/traits/metabolism/mixed_acid_fermentation.yaml mixed_acid_fermentation_enterobacterial UNREACHABLE_FROM_TRAIT WARN node_id='pta_acka' label='phosphotransacetylase / acetate kinase (Pta/AckA)' type=GENE_OR_PROTEIN — in an island with no path to mixed_acid_fermentation_trait data/traits/metabolism/mixed_acid_fermentation.yaml mixed_acid_fermentation_enterobacterial UNREACHABLE_FROM_TRAIT WARN node_id='acetate' label='acetate' type=CHEMICAL — in an island with no path to mixed_acid_fermentation_trait +data/traits/metabolism/mixed_acid_fermentation.yaml mixed_acid_fermentation_enterobacterial INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=ENVIRONMENTAL_FACTOR here — also CHEMICAL×20 elsewhere in the corpus data/traits/metabolism/mixed_acid_fermentation.yaml mixed_acid_fermentation_enterobacterial FRAGMENTED_GRAPH WARN components=2 of 15 node(s) (sizes: 13, 2) — one record, several unrelated mechanisms +data/traits/metabolism/nitrogen_fixation.yaml nitrogen_fixation_nitrogenase INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='nadh' label='NADH' type=CHEMICAL — in an island with no path to oxidative_phosphorylation_trait data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='complex_i' label='Complex I / NADH:quinone oxidoreductase (NDH-1)' type=GENE_OR_PROTEIN — in an island with no path to oxidative_phosphorylation_trait data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='succinate' label='succinate' type=CHEMICAL — in an island with no path to oxidative_phosphorylation_trait @@ -908,6 +1105,9 @@ data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_ data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='terminal_oxidase' label='terminal oxidase' type=GENE_OR_PROTEIN — in an island with no path to oxidative_phosphorylation_trait data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='oxygen' type=CHEMICAL — in an island with no path to oxidative_phosphorylation_trait data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='heme_copper_oxidase' label='heme-copper oxidase' type=GENE_OR_PROTEIN — in an island with no path to oxidative_phosphorylation_trait +data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling FRAGMENTED_GRAPH WARN components=4 of 16 node(s) (sizes: 7, 5, 2, 2) — one record, several unrelated mechanisms data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='water' label='water' type=CHEMICAL — in an island with no path to oxygenic_photosynthesis_trait data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='molecular_oxygen' label='molecular oxygen' type=CHEMICAL — in an island with no path to oxygenic_photosynthesis_trait @@ -918,6 +1118,8 @@ data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_wate data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='ferredoxin' label='ferredoxin' type=GENE_OR_PROTEIN — in an island with no path to oxygenic_photosynthesis_trait data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='fnr' label='ferredoxin-NADP+ reductase' type=GENE_OR_PROTEIN — in an island with no path to oxygenic_photosynthesis_trait data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='nadph' label='NADPH' type=CHEMICAL — in an island with no path to oxygenic_photosynthesis_trait +data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=CHEMICAL here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, STATE×18 elsewhere in the corpus data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 7, 4, 2) — one record, several unrelated mechanisms data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='light_energy' label='light energy' type=ENVIRONMENTAL_FACTOR — in an island with no path to photosynthesis_trait data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='light_harvesting' label='light harvesting / excitation transfer' type=BIOLOGICAL_PROCESS — in an island with no path to photosynthesis_trait @@ -925,12 +1127,15 @@ data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_c data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='electron_transport' label='photosynthetic electron transport' type=BIOLOGICAL_PROCESS — in an island with no path to photosynthesis_trait data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='proton_gradient' label='transmembrane electrochemical proton gradient' type=STATE — in an island with no path to photosynthesis_trait data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthesis' label='ATP synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to photosynthesis_trait +data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CHEMICAL here — also CAPACITY×4 elsewhere in the corpus data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 6, 4) — one record, several unrelated mechanisms data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='photosystem_ii' label='photosystem II' type=GENE_OR_PROTEIN — in an island with no path to phototrophy_trait data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='photosynthetic_electron_transport' label='photosynthetic electron transport chain' type=BIOLOGICAL_PROCESS — in an island with no path to phototrophy_trait data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='nadph' label='NADPH' type=CHEMICAL — in an island with no path to phototrophy_trait data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='atp' label='ATP' type=CHEMICAL — in an island with no path to phototrophy_trait data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='high_light' label='high light intensity' type=ENVIRONMENTAL_FACTOR — in an island with no path to phototrophy_trait +data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=BIOLOGICAL_PROCESS here — also PATHWAY×5 elsewhere in the corpus data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate UNREACHABLE_FROM_TRAIT WARN node_id='pyruvate' label='pyruvate' type=CHEMICAL — in an island with no path to propionic_acid_fermentation_trait data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate UNREACHABLE_FROM_TRAIT WARN node_id='oxaloacetate' label='oxaloacetate' type=CHEMICAL — in an island with no path to propionic_acid_fermentation_trait @@ -942,11 +1147,15 @@ data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentat data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate UNREACHABLE_FROM_TRAIT WARN node_id='mmc_carboxytransferase' label='methylmalonyl-CoA carboxytransferase' type=GENE_OR_PROTEIN — in an island with no path to propionic_acid_fermentation_trait data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate UNREACHABLE_FROM_TRAIT WARN node_id='biotin' label='biotin' type=CHEMICAL — in an island with no path to propionic_acid_fermentation_trait data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate FRAGMENTED_GRAPH WARN components=4 of 15 node(s) (sizes: 6, 5, 2, 2) — one record, several unrelated mechanisms +data/traits/metabolism/proteorhodopsin_phototrophy.yaml proteorhodopsin_light_driven_proton_pump INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_electron_transport_chain' label='membrane electron transport chain' type=PATHWAY — in an island with no path to respiration_trait data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=STATE — in an island with no path to respiration_trait data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthase' label='ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to respiration_trait data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='atp' label='ATP' type=CHEMICAL — in an island with no path to respiration_trait data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='complex_i' label='respiratory Complex I (NADH:quinone oxidoreductase)' type=GENE_OR_PROTEIN — in an island with no path to respiration_trait +data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=CHEMICAL here — also MOLECULAR_FUNCTION×2 elsewhere in the corpus +data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus +data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 8, 5) — one record, several unrelated mechanisms data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='high_energy_phosphorylated_intermediate' label='high-energy phosphorylated intermediate' type=CHEMICAL — in an island with no path to substrate_level_phosphorylation_trait data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='adp' label='ADP' type=CHEMICAL — in an island with no path to substrate_level_phosphorylation_trait @@ -955,6 +1164,7 @@ data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phos data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='acetyl_phosphate' label='acetyl phosphate' type=CHEMICAL — in an island with no path to substrate_level_phosphorylation_trait data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='acetate_kinase' label='acetate kinase' type=GENE_OR_PROTEIN — in an island with no path to substrate_level_phosphorylation_trait data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='acetate' label='acetate' type=CHEMICAL — in an island with no path to substrate_level_phosphorylation_trait +data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 6, 5, 2) — one record, several unrelated mechanisms data/traits/metabolism/syntrophy.yaml syntrophy_interspecies_electron_transfer UNREACHABLE_FROM_TRAIT WARN node_id='direct_interspecies_electron_transfer' label='direct interspecies electron transfer' type=BIOLOGICAL_PROCESS — in an island with no path to syntrophy_trait data/traits/metabolism/syntrophy.yaml syntrophy_interspecies_electron_transfer UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_pressure_inhibition' label='hydrogen pressure inhibition' type=STATE — in an island with no path to syntrophy_trait @@ -992,10 +1202,12 @@ data/traits/morphology/amphitrichous.yaml amphitrichous_bipolar_flagella UNREACH data/traits/morphology/amphitrichous.yaml amphitrichous_bipolar_flagella UNREACHABLE_FROM_TRAIT WARN node_id='flhf_polar_localization' label='FlhF polar localization' type=BIOLOGICAL_PROCESS — in an island with no path to amphitrichous_trait data/traits/morphology/amphitrichous.yaml amphitrichous_bipolar_flagella UNREACHABLE_FROM_TRAIT WARN node_id='polar_flagellar_number' label='polar flagellar number' type=QUALITY — in an island with no path to amphitrichous_trait data/traits/morphology/amphitrichous.yaml amphitrichous_bipolar_flagella FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 8, 3) — one record, several unrelated mechanisms +data/traits/morphology/axially_filamented.yaml axially_filamented_periplasmic_flagella INCONSISTENT_NODE_TYPE WARN node_id='periplasmic_flagella' type=CELLULAR_LOCALIZATION here — also ORGANELLE×2 elsewhere in the corpus data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation UNREACHABLE_FROM_TRAIT WARN node_id='rodA_pbp2_synthase' label='RodA-PBP2 synthase (Rod complex)' type=GENE_OR_PROTEIN — in an island with no path to bacillus_shaped_trait/spherical_morphology data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation UNREACHABLE_FROM_TRAIT WARN node_id='bacterial_elongation' label='bacterial cell elongation' type=BIOLOGICAL_PROCESS — in an island with no path to bacillus_shaped_trait/spherical_morphology data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation UNREACHABLE_FROM_TRAIT WARN node_id='moenomycin' label='moenomycin' type=CHEMICAL — in an island with no path to bacillus_shaped_trait/spherical_morphology data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation UNREACHABLE_FROM_TRAIT WARN node_id='class_a_pbps' label='class A penicillin-binding proteins' type=GENE_OR_PROTEIN — in an island with no path to bacillus_shaped_trait/spherical_morphology +data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=GENE_OR_PROTEIN here — also PATHWAY×2 elsewhere in the corpus data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 8, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/black_pigmented.yaml black_pigmented_melanin_polymer UNREACHABLE_FROM_TRAIT WARN node_id='dopaquinone' label='dopaquinone/dihydroxyindole intermediates' type=CHEMICAL — in an island with no path to black_pigmented_trait data/traits/morphology/black_pigmented.yaml black_pigmented_melanin_polymer UNREACHABLE_FROM_TRAIT WARN node_id='dhn_precursor' label='DHN (1,8-dihydroxynaphthalene)' type=CHEMICAL — in an island with no path to black_pigmented_trait @@ -1026,7 +1238,12 @@ data/traits/morphology/capsule.yaml capsule_polysaccharide_protection UNREACHABL data/traits/morphology/capsule.yaml capsule_polysaccharide_protection UNREACHABLE_FROM_TRAIT WARN node_id='lipid_linked_repeat_unit' label='lipid-linked capsule repeat unit' type=CHEMICAL — in an island with no path to capsule_trait data/traits/morphology/capsule.yaml capsule_polysaccharide_protection UNREACHABLE_FROM_TRAIT WARN node_id='wzb_phosphatase_cycle' label='Wzb phosphatase cycle' type=BIOLOGICAL_PROCESS — in an island with no path to capsule_trait data/traits/morphology/capsule.yaml capsule_polysaccharide_protection UNREACHABLE_FROM_TRAIT WARN node_id='wzc_capsule_assembly' label='Wzc-regulated capsule assembly' type=BIOLOGICAL_PROCESS — in an island with no path to capsule_trait +data/traits/morphology/capsule.yaml capsule_polysaccharide_protection INCONSISTENT_NODE_TYPE WARN node_id='immune_evasion' type=QUALITY here — also BIOLOGICAL_PROCESS×3 elsewhere in the corpus data/traits/morphology/capsule.yaml capsule_polysaccharide_protection FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms +data/traits/morphology/carboxysome.yaml carboxysome_co2_concentrating INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus +data/traits/morphology/carotenoid_pigmentation.yaml carotenoid_pigmentation_crt_pathway INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/morphology/cell_length.yaml cell_length_division_growth_control INCONSISTENT_NODE_TYPE WARN node_id='ftsz_ring' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×2 elsewhere in the corpus +data/traits/morphology/cell_length.yaml cell_length_division_growth_control INCONSISTENT_NODE_TYPE WARN node_id='elongasome' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus data/traits/morphology/cell_length_large.yaml cell_length_large_division_delay UNREACHABLE_FROM_TRAIT WARN node_id='sos_response' label='SOS response' type=BIOLOGICAL_PROCESS — in an island with no path to cell_length_large_trait/cell_length_trait data/traits/morphology/cell_length_large.yaml cell_length_large_division_delay UNREACHABLE_FROM_TRAIT WARN node_id='sula_division_inhibition' label='SulA-mediated division inhibition' type=BIOLOGICAL_PROCESS — in an island with no path to cell_length_large_trait/cell_length_trait data/traits/morphology/cell_length_large.yaml cell_length_large_division_delay UNREACHABLE_FROM_TRAIT WARN node_id='sula_protein' label='SulA' type=GENE_OR_PROTEIN — in an island with no path to cell_length_large_trait/cell_length_trait @@ -1040,6 +1257,8 @@ data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate UN data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate UNREACHABLE_FROM_TRAIT WARN node_id='pbp2_activity' label='PBP2 transpeptidase activity' type=MOLECULAR_FUNCTION — in an island with no path to cell_length_medium_trait/cell_length_trait/rod_shape data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate UNREACHABLE_FROM_TRAIT WARN node_id='membrane_synthesis' label='membrane synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to cell_length_medium_trait/cell_length_trait/rod_shape data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate UNREACHABLE_FROM_TRAIT WARN node_id='envelope_balance_state' label='PG-membrane envelope balance' type=STATE — in an island with no path to cell_length_medium_trait/cell_length_trait/rod_shape +data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=PATHWAY here — also GENE_OR_PROTEIN×3 elsewhere in the corpus +data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate INCONSISTENT_NODE_TYPE WARN node_id='rod_shape' type=TRAIT here — also QUALITY×1 elsewhere in the corpus data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 4, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/cell_length_small.yaml cell_length_small_size_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='ftsz_abundance' label='FtsZ abundance' type=GENE_OR_PROTEIN — in an island with no path to cell_length_small_trait/cell_length_trait data/traits/morphology/cell_length_small.yaml cell_length_small_size_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='division_timing' label='cell division timing' type=BIOLOGICAL_PROCESS — in an island with no path to cell_length_small_trait/cell_length_trait @@ -1057,6 +1276,8 @@ data/traits/morphology/cell_length_very_small.yaml cell_length_very_small_stream data/traits/morphology/cell_length_very_small.yaml cell_length_very_small_streamlining FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 7, 2) — one record, several unrelated mechanisms data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton UNREACHABLE_FROM_TRAIT WARN node_id='flotillins' label='flotillins' type=GENE_OR_PROTEIN — in an island with no path to cell_shape_trait data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton UNREACHABLE_FROM_TRAIT WARN node_id='cell_wall_synthesis' label='cell wall synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to cell_shape_trait +data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=PATHWAY here — also GENE_OR_PROTEIN×3 elsewhere in the corpus +data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton INCONSISTENT_NODE_TYPE WARN node_id='rod_shape' type=QUALITY here — also TRAIT×1 elsewhere in the corpus data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 12, 2) — one record, several unrelated mechanisms data/traits/morphology/cell_width_large.yaml cell_width_large_setpoint_increase UNREACHABLE_FROM_TRAIT WARN node_id='roda_pbp2_activation' label='RodA-PBP2 allosteric activation' type=BIOLOGICAL_PROCESS — in an island with no path to cell_width_large_trait/cell_width_trait data/traits/morphology/cell_width_large.yaml cell_width_large_setpoint_increase UNREACHABLE_FROM_TRAIT WARN node_id='pg_polymerization_crosslinking' label='peptidoglycan polymerization and crosslinking' type=BIOLOGICAL_PROCESS — in an island with no path to cell_width_large_trait/cell_width_trait @@ -1075,6 +1296,7 @@ data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamli data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining UNREACHABLE_FROM_TRAIT WARN node_id='nutrient_uptake_efficiency' label='nutrient uptake efficiency' type=CAPACITY — in an island with no path to cell_width_very_small_trait/cell_width_trait data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining UNREACHABLE_FROM_TRAIT WARN node_id='small_cell_bacteria' label='small-cell bacteria' type=STATE — in an island with no path to cell_width_very_small_trait/cell_width_trait data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining UNREACHABLE_FROM_TRAIT WARN node_id='oligotrophic_waters' label='oligotrophic waters' type=ENVIRONMENTAL_FACTOR — in an island with no path to cell_width_very_small_trait/cell_width_trait +data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=GENE_OR_PROTEIN here — also PATHWAY×2 elsewhere in the corpus data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/dumbbell_shaped.yaml dumbbell_shaped_snapping_division UNREACHABLE_FROM_TRAIT WARN node_id='septal_pg_hydrolysis' label='septal peptidoglycan hydrolysis' type=BIOLOGICAL_PROCESS — in an island with no path to dumbbell_shaped_trait data/traits/morphology/dumbbell_shaped.yaml dumbbell_shaped_snapping_division UNREACHABLE_FROM_TRAIT WARN node_id='daughter_cell_separation' label='daughter cell separation' type=BIOLOGICAL_PROCESS — in an island with no path to dumbbell_shaped_trait @@ -1087,6 +1309,7 @@ data/traits/morphology/dumbbell_shaped.yaml dumbbell_shaped_snapping_division FR data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation UNREACHABLE_FROM_TRAIT WARN node_id='divisome' label='divisome (FtsZ/PBP2x/FtsW)' type=GENE_OR_PROTEIN — in an island with no path to ellipsoidal_trait data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation UNREACHABLE_FROM_TRAIT WARN node_id='septal_pg_synthesis' label='septal peptidoglycan synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to ellipsoidal_trait data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation UNREACHABLE_FROM_TRAIT WARN node_id='undecaprenyl_phosphate' label='undecaprenyl phosphate (Und-P)' type=CHEMICAL — in an island with no path to ellipsoidal_trait +data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation INCONSISTENT_NODE_TYPE WARN node_id='elongasome' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 10, 3) — one record, several unrelated mechanisms data/traits/morphology/flagellar_arrangement.yaml flagellar_arrangement_flhf_flhg UNREACHABLE_FROM_TRAIT WARN node_id='flhf' label='FlhF' type=GENE_OR_PROTEIN — in an island with no path to flagellar_arrangement_trait data/traits/morphology/flagellar_arrangement.yaml flagellar_arrangement_flhf_flhg UNREACHABLE_FROM_TRAIT WARN node_id='flhg' label='FlhG' type=GENE_OR_PROTEIN — in an island with no path to flagellar_arrangement_trait @@ -1110,6 +1333,7 @@ data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth UN data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='cell_wall_biosynthesis' label='cell wall biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to flask_shaped_trait data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='bactofilin_cytoskeleton' label='bactofilin cytoskeleton' type=GENE_OR_PROTEIN — in an island with no path to flask_shaped_trait data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='asymmetric_compartment_growth' label='asymmetric compartment growth' type=BIOLOGICAL_PROCESS — in an island with no path to flask_shaped_trait +data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth INCONSISTENT_NODE_TYPE WARN node_id='bactofilin_lmdc_module' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth FRAGMENTED_GRAPH WARN components=5 of 12 node(s) (sizes: 4, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='mreb' label='MreB' type=GENE_OR_PROTEIN — in an island with no path to fusiform_shaped_trait data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='lateral_pg_synthesis' label='lateral peptidoglycan synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to fusiform_shaped_trait @@ -1121,6 +1345,7 @@ data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='roda' label='RodA' type=GENE_OR_PROTEIN — in an island with no path to fusiform_shaped_trait data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='ftsw' label='FtsW' type=GENE_OR_PROTEIN — in an island with no path to fusiform_shaped_trait data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='septal_pg_incorporation' label='septal peptidoglycan incorporation' type=BIOLOGICAL_PROCESS — in an island with no path to fusiform_shaped_trait +data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth INCONSISTENT_NODE_TYPE WARN node_id='elongasome' type=CELLULAR_LOCALIZATION here — also GENE_OR_PROTEIN×2 elsewhere in the corpus data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth FRAGMENTED_GRAPH WARN components=5 of 14 node(s) (sizes: 4, 3, 3, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TRAIT WARN node_id='gvpa_protein' label='GvpA' type=GENE_OR_PROTEIN — in an island with no path to gas_vesicle_trait/buoyancy data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TRAIT WARN node_id='gas_vesicle_shell' label='gas vesicle shell' type=CELLULAR_LOCALIZATION — in an island with no path to gas_vesicle_trait/buoyancy @@ -1133,6 +1358,7 @@ data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TR data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TRAIT WARN node_id='gas_vesicle_formation' label='gas vesicle formation' type=BIOLOGICAL_PROCESS — in an island with no path to gas_vesicle_trait/buoyancy data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TRAIT WARN node_id='ultrasound_scattering' label='ultrasound scattering' type=BIOLOGICAL_PROCESS — in an island with no path to gas_vesicle_trait/buoyancy data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 4, 3, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/morphology/gliding.yaml gliding_surface_motility INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/morphology/gram_negative.yaml gram_negative_outer_membrane_dye_loss UNREACHABLE_FROM_TRAIT WARN node_id='thin_peptidoglycan_layer' label='thin peptidoglycan layer' type=CELLULAR_LOCALIZATION — in an island with no path to gram_negative_trait data/traits/morphology/gram_negative.yaml gram_negative_outer_membrane_dye_loss UNREACHABLE_FROM_TRAIT WARN node_id='periplasmic_space' label='periplasmic space' type=CELLULAR_LOCALIZATION — in an island with no path to gram_negative_trait data/traits/morphology/gram_negative.yaml gram_negative_outer_membrane_dye_loss UNREACHABLE_FROM_TRAIT WARN node_id='crystal_violet_iodine_complex' label='crystal violet-iodine complex' type=CHEMICAL — in an island with no path to gram_negative_trait @@ -1149,6 +1375,7 @@ data/traits/morphology/gram_positive.yaml gram_positive_cell_wall_retention FRAG data/traits/morphology/gram_stain.yaml gram_stain_cell_envelope_retention UNREACHABLE_FROM_TRAIT WARN node_id='crystal_violet' label='crystal violet' type=CHEMICAL — in an island with no path to gram_stain_trait data/traits/morphology/gram_stain.yaml gram_stain_cell_envelope_retention UNREACHABLE_FROM_TRAIT WARN node_id='iodine_mordant' label='iodine mordant' type=CHEMICAL — in an island with no path to gram_stain_trait data/traits/morphology/gram_stain.yaml gram_stain_cell_envelope_retention FRAGMENTED_GRAPH WARN components=2 of 7 node(s) (sizes: 5, 2) — one record, several unrelated mechanisms +data/traits/morphology/green_pigmented.yaml green_pigmented_pyocyanin_phenazine INCONSISTENT_NODE_TYPE WARN node_id='phenazine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='het_diff_process' label='heterocyst differentiation' type=BIOLOGICAL_PROCESS — in an island with no path to heterocyst_trait data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='hetr_regulator' label='HetR transcriptional regulator' type=GENE_OR_PROTEIN — in an island with no path to heterocyst_trait data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='furc_perr' label='FurC / PerR' type=GENE_OR_PROTEIN — in an island with no path to heterocyst_trait @@ -1158,6 +1385,7 @@ data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UN data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='oxygen' type=CHEMICAL — in an island with no path to heterocyst_trait data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='pats_peptide' label='PatS peptide' type=GENE_OR_PROTEIN — in an island with no path to heterocyst_trait data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='hetn_regulator' label='HetN regulator' type=GENE_OR_PROTEIN — in an island with no path to heterocyst_trait +data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 5, 4, 3, 2) — one record, several unrelated mechanisms data/traits/morphology/intracellular_inclusion.yaml inclusion_compartmentalization UNREACHABLE_FROM_TRAIT WARN node_id='pha_synthase_pathway' label='PhaA/PhaB/PhaC pathway' type=PATHWAY — in an island with no path to inclusion_trait/buoyancy data/traits/morphology/intracellular_inclusion.yaml inclusion_compartmentalization UNREACHABLE_FROM_TRAIT WARN node_id='pha_granule' label='PHA granule' type=CELLULAR_LOCALIZATION — in an island with no path to inclusion_trait/buoyancy @@ -1189,6 +1417,10 @@ data/traits/morphology/monotrichous.yaml monotrichous_single_polar_flagellum UNR data/traits/morphology/monotrichous.yaml monotrichous_single_polar_flagellum UNREACHABLE_FROM_TRAIT WARN node_id='flif_msring' label='FliF MS-ring protein' type=GENE_OR_PROTEIN — in an island with no path to monotrichous_trait data/traits/morphology/monotrichous.yaml monotrichous_single_polar_flagellum UNREACHABLE_FROM_TRAIT WARN node_id='flim_flin' label='FliM/FliN C-ring partners' type=GENE_OR_PROTEIN — in an island with no path to monotrichous_trait data/traits/morphology/monotrichous.yaml monotrichous_single_polar_flagellum FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 7, 3) — one record, several unrelated mechanisms +data/traits/morphology/motile.yaml motile_energy_dependent_locomotion INCONSISTENT_NODE_TYPE WARN node_id='type_iv_pilus' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus +data/traits/morphology/motile.yaml motile_energy_dependent_locomotion INCONSISTENT_NODE_TYPE WARN node_id='twitching_motility' type=BIOLOGICAL_PROCESS here — also TRAIT×1 elsewhere in the corpus +data/traits/morphology/motility.yaml motility_locomotion_machinery INCONSISTENT_NODE_TYPE WARN node_id='type_iv_pilus' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus +data/traits/morphology/motility.yaml motility_locomotion_machinery INCONSISTENT_NODE_TYPE WARN node_id='twitching_motility' type=TRAIT here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/morphology/mycelial_growth.yaml mycelial_branching_hyphal_growth UNREACHABLE_FROM_TRAIT WARN node_id='polarisome_splitting' label='polarisome splitting' type=BIOLOGICAL_PROCESS — in an island with no path to mycelial_growth_trait data/traits/morphology/mycelial_growth.yaml mycelial_branching_hyphal_growth UNREACHABLE_FROM_TRAIT WARN node_id='branch_emergence' label='new branch emergence' type=BIOLOGICAL_PROCESS — in an island with no path to mycelial_growth_trait data/traits/morphology/mycelial_growth.yaml mycelial_branching_hyphal_growth UNREACHABLE_FROM_TRAIT WARN node_id='cglA_ligase' label='CglA glycopolymer ligase' type=GENE_OR_PROTEIN — in an island with no path to mycelial_growth_trait @@ -1205,7 +1437,10 @@ data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumul data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation UNREACHABLE_FROM_TRAIT WARN node_id='zeaxanthin' label='zeaxanthin' type=CHEMICAL — in an island with no path to orange_pigmented_trait data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation UNREACHABLE_FROM_TRAIT WARN node_id='crt_w_ketolase' label='carotenoid ketolase (CrtW)' type=GENE_OR_PROTEIN — in an island with no path to orange_pigmented_trait data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation UNREACHABLE_FROM_TRAIT WARN node_id='ketocarotenoid_biosynthesis' label='ketocarotenoid biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to orange_pigmented_trait +data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=ENVIRONMENTAL_FACTOR here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 8, 5, 2) — one record, several unrelated mechanisms +data/traits/morphology/ovoid_shaped.yaml ovoid_shaped_midcell_pg_assembly INCONSISTENT_NODE_TYPE WARN node_id='ftsz_ring' type=CELLULAR_LOCALIZATION here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/morphology/peritrichous.yaml peritrichous_surface_distributed_flagella UNREACHABLE_FROM_TRAIT WARN node_id='flhg_regulator' label='FlhG' type=GENE_OR_PROTEIN — in an island with no path to peritrichous_trait data/traits/morphology/peritrichous.yaml peritrichous_surface_distributed_flagella UNREACHABLE_FROM_TRAIT WARN node_id='flagellar_assembly_progression' label='progression of flagellar assembly' type=BIOLOGICAL_PROCESS — in an island with no path to peritrichous_trait data/traits/morphology/peritrichous.yaml peritrichous_surface_distributed_flagella UNREACHABLE_FROM_TRAIT WARN node_id='flagellar_filament_number' label='flagellar filament number' type=QUALITY — in an island with no path to peritrichous_trait @@ -1224,7 +1459,11 @@ data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants UNR data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants UNREACHABLE_FROM_TRAIT WARN node_id='homogentisate' label='homogentisate' type=CHEMICAL — in an island with no path to pigmentation_trait data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants UNREACHABLE_FROM_TRAIT WARN node_id='pyomelanin' label='pyomelanin' type=CHEMICAL — in an island with no path to pigmentation_trait data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants UNREACHABLE_FROM_TRAIT WARN node_id='hmga_gene' label='hmgA homogentisate 1,2-dioxygenase' type=GENE_OR_PROTEIN — in an island with no path to pigmentation_trait +data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×5 elsewhere in the corpus +data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants INCONSISTENT_NODE_TYPE WARN node_id='phenazine_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants FRAGMENTED_GRAPH WARN components=4 of 16 node(s) (sizes: 5, 5, 4, 2) — one record, several unrelated mechanisms +data/traits/morphology/pink_pigmented.yaml pink_pigmented_carotenoid_color INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/morphology/pink_pigmented.yaml pink_pigmented_carotenoid_color INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=ENVIRONMENTAL_FACTOR here — also CHEMICAL×11 elsewhere in the corpus data/traits/morphology/polyhydroxyalkanoate_granule.yaml pha_granule_carbon_energy_storage UNREACHABLE_FROM_TRAIT WARN node_id='nutrient_limitation_high_cn' label='nutrient limitation / high C:N ratio' type=ENVIRONMENTAL_FACTOR — in an island with no path to pha_granule_trait data/traits/morphology/polyhydroxyalkanoate_granule.yaml pha_granule_carbon_energy_storage UNREACHABLE_FROM_TRAIT WARN node_id='pha_accumulation' label='polyhydroxyalkanoate accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to pha_granule_trait data/traits/morphology/polyhydroxyalkanoate_granule.yaml pha_granule_carbon_energy_storage UNREACHABLE_FROM_TRAIT WARN node_id='phar_regulator' label='PhaR regulator' type=GENE_OR_PROTEIN — in an island with no path to pha_granule_trait @@ -1240,6 +1479,7 @@ data/traits/morphology/prosthecate.yaml prosthecate_stalk_nutrient_uptake UNREAC data/traits/morphology/prosthecate.yaml prosthecate_stalk_nutrient_uptake UNREACHABLE_FROM_TRAIT WARN node_id='stpabcd_complex' label='StpABCD complex' type=GENE_OR_PROTEIN — in an island with no path to prosthecate_trait data/traits/morphology/prosthecate.yaml prosthecate_stalk_nutrient_uptake UNREACHABLE_FROM_TRAIT WARN node_id='stalk_diffusion' label='diffusion along stalk' type=BIOLOGICAL_PROCESS — in an island with no path to prosthecate_trait data/traits/morphology/prosthecate.yaml prosthecate_stalk_nutrient_uptake FRAGMENTED_GRAPH WARN components=3 of 10 node(s) (sizes: 5, 3, 2) — one record, several unrelated mechanisms +data/traits/morphology/red_pigmented.yaml red_pigmented_prodiginine_pathway INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='mreb_filaments' label='MreB filaments' type=GENE_OR_PROTEIN — in an island with no path to ring_shaped_trait data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='cell_wall_growth_rate' label='rate of cell wall growth' type=BIOLOGICAL_PROCESS — in an island with no path to ring_shaped_trait data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='pg_insertion_perpendicular' label='peptidoglycan insertion perpendicular to long axis' type=BIOLOGICAL_PROCESS — in an island with no path to ring_shaped_trait @@ -1251,12 +1491,14 @@ data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREAC data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='pg_synthesis_rate_skew' label='skewed peptidoglycan synthesis rates' type=BIOLOGICAL_PROCESS — in an island with no path to ring_shaped_trait data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='crescentin' label='crescentin' type=GENE_OR_PROTEIN — in an island with no path to ring_shaped_trait data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='cell_curvature' label='cell curvature' type=QUALITY — in an island with no path to ring_shaped_trait +data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure INCONSISTENT_NODE_TYPE WARN node_id='bactofilin_lmdc_module' type=GENE_OR_PROTEIN here — also PATHWAY×1 elsewhere in the corpus data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 4, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='pbp2_structural_opening' label='PBP2 structural opening' type=MOLECULAR_FUNCTION — in an island with no path to rod_shaped_trait data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='rodA_polymerization' label='RodA polymerization activity' type=MOLECULAR_FUNCTION — in an island with no path to rod_shaped_trait data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='pg_crosslinking' label='peptidoglycan crosslinking' type=BIOLOGICAL_PROCESS — in an island with no path to rod_shaped_trait data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='elongasome_processivity' label='elongasome processivity' type=BIOLOGICAL_PROCESS — in an island with no path to rod_shaped_trait data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='sidewall_reinforcement' label='rod-shaped sidewall reinforcement' type=BIOLOGICAL_PROCESS — in an island with no path to rod_shaped_trait +data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=GENE_OR_PROTEIN here — also PATHWAY×2 elsewhere in the corpus data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 8, 5) — one record, several unrelated mechanisms data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet UNREACHABLE_FROM_TRAIT WARN node_id='ftsz_protein' label='FtsZ' type=GENE_OR_PROTEIN — in an island with no path to sarcina_trait data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet UNREACHABLE_FROM_TRAIT WARN node_id='z_ring' label='Z ring' type=CELLULAR_LOCALIZATION — in an island with no path to sarcina_trait @@ -1270,6 +1512,8 @@ data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_pac data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet UNREACHABLE_FROM_TRAIT WARN node_id='peripheral_pg_bridge' label='peripheral peptidoglycan bridge' type=CELLULAR_LOCALIZATION — in an island with no path to sarcina_trait data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet UNREACHABLE_FROM_TRAIT WARN node_id='daughter_cell_separation' label='daughter-cell separation' type=BIOLOGICAL_PROCESS — in an island with no path to sarcina_trait data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet FRAGMENTED_GRAPH WARN components=5 of 14 node(s) (sizes: 4, 3, 3, 2, 2) — one record, several unrelated mechanisms +data/traits/morphology/spiral_shaped.yaml spiral_shaped_curvature_mechanisms INCONSISTENT_NODE_TYPE WARN node_id='periplasmic_flagella' type=ORGANELLE here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus +data/traits/morphology/spirochete_shaped.yaml spirochete_shaped_periplasmic_flagella INCONSISTENT_NODE_TYPE WARN node_id='periplasmic_flagella' type=ORGANELLE here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus data/traits/morphology/spore_forming.yaml spore_forming_endospore_assembly UNREACHABLE_FROM_TRAIT WARN node_id='spoIID' label='SpoIID' type=GENE_OR_PROTEIN — in an island with no path to spore_forming_trait data/traits/morphology/spore_forming.yaml spore_forming_endospore_assembly UNREACHABLE_FROM_TRAIT WARN node_id='spoIIM' label='SpoIIM' type=GENE_OR_PROTEIN — in an island with no path to spore_forming_trait data/traits/morphology/spore_forming.yaml spore_forming_endospore_assembly UNREACHABLE_FROM_TRAIT WARN node_id='spoIIP' label='SpoIIP' type=GENE_OR_PROTEIN — in an island with no path to spore_forming_trait @@ -1300,6 +1544,7 @@ data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis UN data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis UNREACHABLE_FROM_TRAIT WARN node_id='spore_dna_protection' label='spore DNA protection' type=BIOLOGICAL_PROCESS — in an island with no path to sporulation_trait data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis UNREACHABLE_FROM_TRAIT WARN node_id='spore_coat_cortex' label='spore coat and cortex' type=CELLULAR_LOCALIZATION — in an island with no path to sporulation_trait data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis UNREACHABLE_FROM_TRAIT WARN node_id='stress_resistance' label='heat and chemical resistance' type=QUALITY — in an island with no path to sporulation_trait +data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis INCONSISTENT_NODE_TYPE WARN node_id='stress_resistance' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis FRAGMENTED_GRAPH WARN components=6 of 19 node(s) (sizes: 8, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/square_shaped.yaml square_shaped_planar_anisotropic_growth UNREACHABLE_FROM_TRAIT WARN node_id='archaeal_slayer' label='archaeal S-layer' type=ORGANELLE — in an island with no path to square_shaped_trait data/traits/morphology/square_shaped.yaml square_shaped_planar_anisotropic_growth UNREACHABLE_FROM_TRAIT WARN node_id='cell_shape' label='cell shape' type=QUALITY — in an island with no path to square_shaped_trait @@ -1312,6 +1557,7 @@ data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_ data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster UNREACHABLE_FROM_TRAIT WARN node_id='ftsz' label='FtsZ' type=GENE_OR_PROTEIN — in an island with no path to staphylococcus_trait data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster UNREACHABLE_FROM_TRAIT WARN node_id='ftsz_ring' label='FtsZ Z-ring' type=CELLULAR_LOCALIZATION — in an island with no path to staphylococcus_trait data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster UNREACHABLE_FROM_TRAIT WARN node_id='divisome_pg_synthesis' label='divisome peptidoglycan synthesis at division site' type=BIOLOGICAL_PROCESS — in an island with no path to staphylococcus_trait +data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster INCONSISTENT_NODE_TYPE WARN node_id='ftsz_ring' type=CELLULAR_LOCALIZATION here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster FRAGMENTED_GRAPH WARN components=2 of 8 node(s) (sizes: 5, 3) — one record, several unrelated mechanisms data/traits/morphology/star_shaped.yaml star_shaped_multiple_prosthecae UNREACHABLE_FROM_TRAIT WARN node_id='baca_lmdc_module' label='BacA-LmdC morphogenesis module' type=GENE_OR_PROTEIN — in an island with no path to star_shaped_trait data/traits/morphology/star_shaped.yaml star_shaped_multiple_prosthecae UNREACHABLE_FROM_TRAIT WARN node_id='local_pg_remodeling' label='local peptidoglycan remodeling' type=BIOLOGICAL_PROCESS — in an island with no path to star_shaped_trait @@ -1325,6 +1571,7 @@ data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retractio data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction UNREACHABLE_FROM_TRAIT WARN node_id='pilus_filament_surface_exposure' label='type IV pilus surface exposure' type=BIOLOGICAL_PROCESS — in an island with no path to twitching_trait data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction UNREACHABLE_FROM_TRAIT WARN node_id='pilmnop_alignment_complex' label='PilM/N/O/P alignment complex' type=CELLULAR_LOCALIZATION — in an island with no path to twitching_trait data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction UNREACHABLE_FROM_TRAIT WARN node_id='t4p_machine' label='type IV pilus machine' type=CELLULAR_LOCALIZATION — in an island with no path to twitching_trait +data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction INCONSISTENT_NODE_TYPE WARN node_id='type_iv_pilus' type=CELLULAR_LOCALIZATION here — also GENE_OR_PROTEIN×2 elsewhere in the corpus data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction FRAGMENTED_GRAPH WARN components=4 of 11 node(s) (sizes: 5, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='ipp_dmapp' label='IPP/DMAPP' type=CHEMICAL — in an island with no path to yellow_pigmented_trait data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='ggpp' label='geranylgeranyl diphosphate (GGPP)' type=CHEMICAL — in an island with no path to yellow_pigmented_trait @@ -1332,6 +1579,7 @@ data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color U data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='lycopene' label='lycopene' type=CHEMICAL — in an island with no path to yellow_pigmented_trait data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='crti' label='CrtI (phytoene desaturase)' type=GENE_OR_PROTEIN — in an island with no path to yellow_pigmented_trait data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='lycopene_biosynthesis' label='lycopene biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to yellow_pigmented_trait +data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color FRAGMENTED_GRAPH WARN components=2 of 15 node(s) (sizes: 9, 6) — one record, several unrelated mechanisms data/traits/physiology/antibiotic_resistance.yaml antibiotic_resistance_mechanisms UNREACHABLE_FROM_TRAIT WARN node_id='outer_membrane_porin' label='outer membrane porin' type=GENE_OR_PROTEIN — in an island with no path to antibiotic_resistance_trait data/traits/physiology/antibiotic_resistance.yaml antibiotic_resistance_mechanisms UNREACHABLE_FROM_TRAIT WARN node_id='antibiotic_influx' label='antibiotic influx' type=BIOLOGICAL_PROCESS — in an island with no path to antibiotic_resistance_trait @@ -1345,19 +1593,28 @@ data/traits/physiology/antibiotic_resistance.yaml antibiotic_resistance_mechanis data/traits/physiology/autotrophic.yaml autotrophic_inorganic_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='environmental_ph' label='environmental pH' type=ENVIRONMENTAL_FACTOR — in an island with no path to autotrophic_trait data/traits/physiology/autotrophic.yaml autotrophic_inorganic_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='dissolved_inorganic_carbon' label='dissolved inorganic carbon' type=CHEMICAL — in an island with no path to autotrophic_trait data/traits/physiology/autotrophic.yaml autotrophic_inorganic_carbon_fixation FRAGMENTED_GRAPH WARN components=2 of 18 node(s) (sizes: 16, 2) — one record, several unrelated mechanisms +data/traits/physiology/bioluminescence.yaml bioluminescence_luciferase INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='nife_codh' label='Ni,Fe-carbon monoxide dehydrogenase' type=GENE_OR_PROTEIN — in an island with no path to carboxydotrophic_trait data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='oxygen_sensitivity' label='oxygen sensitivity' type=QUALITY — in an island with no path to carboxydotrophic_trait data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='coo_operon' label='coo operon' type=GENE_OR_PROTEIN — in an island with no path to carboxydotrophic_trait data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='cooa_regulator' label='CooA' type=GENE_OR_PROTEIN — in an island with no path to carboxydotrophic_trait +data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation FRAGMENTED_GRAPH WARN components=2 of 18 node(s) (sizes: 14, 4) — one record, several unrelated mechanisms +data/traits/physiology/catalase_activity.yaml catalase_activity_h2o2_detoxification INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/physiology/catalase_activity.yaml catalase_activity_h2o2_detoxification INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/physiology/chemoheterotrophic.yaml chemoheterotrophic_organic_energy_carbon UNREACHABLE_FROM_TRAIT WARN node_id='mannitol_pts' label='PEP-dependent phosphotransferase system (mannitol PTS)' type=GENE_OR_PROTEIN — in an island with no path to chemoheterotrophic_trait data/traits/physiology/chemoheterotrophic.yaml chemoheterotrophic_organic_energy_carbon UNREACHABLE_FROM_TRAIT WARN node_id='mannitol' label='mannitol' type=CHEMICAL — in an island with no path to chemoheterotrophic_trait +data/traits/physiology/chemoheterotrophic.yaml chemoheterotrophic_organic_energy_carbon INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=PATHWAY here — also BIOLOGICAL_PROCESS×3 elsewhere in the corpus data/traits/physiology/chemoheterotrophic.yaml chemoheterotrophic_organic_energy_carbon FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 12, 2) — one record, several unrelated mechanisms +data/traits/physiology/chemolithoautotrophic.yaml chemolithoautotrophic_energy_and_fixation INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/physiology/chemolithoautotrophic.yaml chemolithoautotrophic_energy_and_fixation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/physiology/chemolithoautotrophic.yaml chemolithoautotrophic_energy_and_fixation INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CAPACITY here — also CHEMICAL×1 elsewhere in the corpus data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='sox_pathway' label='Sox sulfur-oxidation pathway' type=PATHWAY — in an island with no path to chemolithoheterotrophic_trait data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='thiosulfate' label='thiosulfate' type=CHEMICAL — in an island with no path to chemolithoheterotrophic_trait data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='sulfate' label='sulfate' type=CHEMICAL — in an island with no path to chemolithoheterotrophic_trait data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='branched_thiosulfate_oxidation' label='branched thiosulfate oxidation pathway' type=PATHWAY — in an island with no path to chemolithoheterotrophic_trait data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='elemental_sulfur' label='elemental sulfur' type=CHEMICAL — in an island with no path to chemolithoheterotrophic_trait +data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon FRAGMENTED_GRAPH WARN components=3 of 16 node(s) (sizes: 11, 3, 2) — one record, several unrelated mechanisms data/traits/physiology/chemolithotrophic.yaml chemolithotrophic_inorganic_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='ammonia' label='ammonia' type=CHEMICAL — in an island with no path to chemolithotrophic_trait data/traits/physiology/chemolithotrophic.yaml chemolithotrophic_inorganic_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='ammonia_monooxygenase' label='ammonia monooxygenase' type=GENE_OR_PROTEIN — in an island with no path to chemolithotrophic_trait @@ -1373,11 +1630,16 @@ data/traits/physiology/chemolithotrophic.yaml chemolithotrophic_inorganic_oxidat data/traits/physiology/chemolithotrophic.yaml chemolithotrophic_inorganic_oxidation FRAGMENTED_GRAPH WARN components=5 of 15 node(s) (sizes: 4, 4, 3, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/chemoorganoheterotrophic.yaml chemoorganoheterotrophic_organic_energy_carbon UNREACHABLE_FROM_TRAIT WARN node_id='extracellular_cazymes' label='extracellular carbohydrate-active enzymes' type=MOLECULAR_FUNCTION — in an island with no path to chemoorganoheterotrophic_trait data/traits/physiology/chemoorganoheterotrophic.yaml chemoorganoheterotrophic_organic_energy_carbon UNREACHABLE_FROM_TRAIT WARN node_id='complex_polysaccharides' label='complex polysaccharides' type=CHEMICAL — in an island with no path to chemoorganoheterotrophic_trait +data/traits/physiology/chemoorganoheterotrophic.yaml chemoorganoheterotrophic_organic_energy_carbon INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=PATHWAY here — also BIOLOGICAL_PROCESS×3 elsewhere in the corpus data/traits/physiology/chemoorganoheterotrophic.yaml chemoorganoheterotrophic_organic_energy_carbon FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy UNREACHABLE_FROM_TRAIT WARN node_id='aerobic_respiration' label='aerobic respiration' type=BIOLOGICAL_PROCESS — in an island with no path to chemoorganotrophic_trait data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy UNREACHABLE_FROM_TRAIT WARN node_id='anaerobic_respiration' label='anaerobic respiration' type=BIOLOGICAL_PROCESS — in an island with no path to chemoorganotrophic_trait data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='oxygen' type=ENVIRONMENTAL_FACTOR — in an island with no path to chemoorganotrophic_trait data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy UNREACHABLE_FROM_TRAIT WARN node_id='nitrate_nitrite' label='nitrate/nitrite' type=ENVIRONMENTAL_FACTOR — in an island with no path to chemoorganotrophic_trait +data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=CHEMICAL here — also MOLECULAR_FUNCTION×2 elsewhere in the corpus +data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=ENVIRONMENTAL_FACTOR here — also CHEMICAL×11 elsewhere in the corpus +data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy FRAGMENTED_GRAPH WARN components=3 of 17 node(s) (sizes: 13, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_FROM_TRAIT WARN node_id='chemoreceptor_mcp' label='chemoreceptor (MCP)' type=GENE_OR_PROTEIN — in an island with no path to chemotaxis_trait data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_FROM_TRAIT WARN node_id='chea_kinase' label='CheA histidine kinase' type=GENE_OR_PROTEIN — in an island with no path to chemotaxis_trait @@ -1389,6 +1651,8 @@ data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_ data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_FROM_TRAIT WARN node_id='chew' label='CheW coupling protein' type=GENE_OR_PROTEIN — in an island with no path to chemotaxis_trait data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_FROM_TRAIT WARN node_id='cw_flagellar_rotation' label='clockwise flagellar rotation' type=BIOLOGICAL_PROCESS — in an island with no path to chemotaxis_trait data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response FRAGMENTED_GRAPH WARN components=2 of 12 node(s) (sizes: 9, 3) — one record, several unrelated mechanisms +data/traits/physiology/chemotrophic.yaml chemotrophic_chemical_redox_energy INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=CHEMICAL here — also MOLECULAR_FUNCTION×2 elsewhere in the corpus +data/traits/physiology/chemotrophic.yaml chemotrophic_chemical_redox_energy INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/copiotrophic.yaml copiotrophic_high_nutrient_fast_growth UNREACHABLE_FROM_TRAIT WARN node_id='catabolite_repression' label='catabolite repression / dynamic transcriptional regulation' type=BIOLOGICAL_PROCESS — in an island with no path to copiotrophic_trait data/traits/physiology/copiotrophic.yaml copiotrophic_high_nutrient_fast_growth UNREACHABLE_FROM_TRAIT WARN node_id='proteome_reallocation' label='proteome reallocation' type=BIOLOGICAL_PROCESS — in an island with no path to copiotrophic_trait data/traits/physiology/copiotrophic.yaml copiotrophic_high_nutrient_fast_growth FRAGMENTED_GRAPH WARN components=2 of 15 node(s) (sizes: 13, 2) — one record, several unrelated mechanisms @@ -1396,6 +1660,9 @@ data/traits/physiology/dormancy.yaml dormancy_seed_bank UNREACHABLE_FROM_TRAIT W data/traits/physiology/dormancy.yaml dormancy_seed_bank UNREACHABLE_FROM_TRAIT WARN node_id='protein_synthesis' label='protein synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to dormancy_trait data/traits/physiology/dormancy.yaml dormancy_seed_bank UNREACHABLE_FROM_TRAIT WARN node_id='ribosome' label='ribosome' type=ORGANELLE — in an island with no path to dormancy_trait data/traits/physiology/dormancy.yaml dormancy_seed_bank FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 7, 3) — one record, several unrelated mechanisms +data/traits/physiology/heterotrophic.yaml heterotrophic_organic_carbon_assimilation INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/physiology/hydrogenotrophic.yaml hydrogenotrophic_hydrogen_oxidation_fixation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/physiology/hydrogenotrophic.yaml hydrogenotrophic_hydrogen_oxidation_fixation INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_dehydrogenase' label='membrane-bound (de)hydrogenase' type=GENE_OR_PROTEIN — in an island with no path to lithoautotrophic_trait data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='electron_transport_chain' label='electron transport chain' type=BIOLOGICAL_PROCESS — in an island with no path to lithoautotrophic_trait data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=CAPACITY — in an island with no path to lithoautotrophic_trait @@ -1403,9 +1670,13 @@ data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='reverse_electron_flow' label='reverse electron flow' type=BIOLOGICAL_PROCESS — in an island with no path to lithoautotrophic_trait data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='nadh_reducing_equivalents' label='NAD(H) reducing equivalents' type=CHEMICAL — in an island with no path to lithoautotrophic_trait data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='cytbc1_nadh_dehydrogenase' label='cytochrome bc1 and NADH dehydrogenase' type=GENE_OR_PROTEIN — in an island with no path to lithoautotrophic_trait +data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CAPACITY here — also CHEMICAL×1 elsewhere in the corpus +data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=BIOLOGICAL_PROCESS here — also PATHWAY×4 elsewhere in the corpus +data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=CAPACITY here — also BIOLOGICAL_PROCESS×13, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 8, 4, 3) — one record, several unrelated mechanisms data/traits/physiology/lithoheterotrophic.yaml lithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='conductive_pili_cytochromes' label='conductive pili and c-type cytochromes' type=GENE_OR_PROTEIN — in an island with no path to lithoheterotrophic_trait data/traits/physiology/lithoheterotrophic.yaml lithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='diet' label='direct interspecies electron transfer' type=BIOLOGICAL_PROCESS — in an island with no path to lithoheterotrophic_trait +data/traits/physiology/lithoheterotrophic.yaml lithoheterotrophic_inorganic_energy_organic_carbon INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/physiology/lithoheterotrophic.yaml lithoheterotrophic_inorganic_energy_organic_carbon FRAGMENTED_GRAPH WARN components=2 of 18 node(s) (sizes: 16, 2) — one record, several unrelated mechanisms data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='thiosulfate' label='thiosulfate' type=CHEMICAL — in an island with no path to lithotrophic_trait data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='sox_multienzyme_system' label='Sox multienzyme system' type=GENE_OR_PROTEIN — in an island with no path to lithotrophic_trait @@ -1419,6 +1690,8 @@ data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNR data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='nitrite_oxidoreductase' label='nitrite oxidoreductase (NXR)' type=GENE_OR_PROTEIN — in an island with no path to lithotrophic_trait data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='molecular oxygen' type=CHEMICAL — in an island with no path to lithotrophic_trait data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='sulfur_oxidation_process' label='sulfur oxidation' type=BIOLOGICAL_PROCESS — in an island with no path to lithotrophic_trait +data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy FRAGMENTED_GRAPH WARN components=7 of 19 node(s) (sizes: 7, 2, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='formaldehyde' label='formaldehyde' type=CHEMICAL — in an island with no path to methanotrophic_trait data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='formaldehyde_assimilation' label='formaldehyde assimilation' type=PATHWAY — in an island with no path to methanotrophic_trait @@ -1432,6 +1705,7 @@ data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNRE data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='methanobactin' label='methanobactin' type=CHEMICAL — in an island with no path to methanotrophic_trait data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='cuprous_ion' label='Cu(I)' type=CHEMICAL — in an island with no path to methanotrophic_trait data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='copper_acquisition' label='copper acquisition' type=BIOLOGICAL_PROCESS — in an island with no path to methanotrophic_trait +data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation FRAGMENTED_GRAPH WARN components=5 of 20 node(s) (sizes: 8, 6, 2, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation UNREACHABLE_FROM_TRAIT WARN node_id='formaldehyde_dehydrogenase' label='formaldehyde dehydrogenase (Fld/FDH)' type=GENE_OR_PROTEIN — in an island with no path to methylotrophic_trait data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation UNREACHABLE_FROM_TRAIT WARN node_id='formate' label='formate' type=CHEMICAL — in an island with no path to methylotrophic_trait @@ -1441,6 +1715,8 @@ data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation UNREACHABLE_FROM_TRAIT WARN node_id='pqq' label='pyrroloquinoline quinone (PQQ)' type=CHEMICAL — in an island with no path to methylotrophic_trait data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation UNREACHABLE_FROM_TRAIT WARN node_id='calcium_ion' label='calcium ion (Ca2+)' type=CHEMICAL — in an island with no path to methylotrophic_trait data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation FRAGMENTED_GRAPH WARN components=4 of 19 node(s) (sizes: 12, 3, 2, 2) — one record, several unrelated mechanisms +data/traits/physiology/mixotrophic.yaml mixotrophic_dual_carbon_energy_use INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/physiology/mixotrophic.yaml mixotrophic_dual_carbon_energy_use INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/physiology/natural_competence.yaml natural_competence_dna_uptake UNREACHABLE_FROM_TRAIT WARN node_id='pilus_retraction' label='competence pilus retraction' type=BIOLOGICAL_PROCESS — in an island with no path to natural_competence_trait data/traits/physiology/natural_competence.yaml natural_competence_dna_uptake UNREACHABLE_FROM_TRAIT WARN node_id='dna_uptake' label='extracellular DNA uptake' type=BIOLOGICAL_PROCESS — in an island with no path to natural_competence_trait data/traits/physiology/natural_competence.yaml natural_competence_dna_uptake UNREACHABLE_FROM_TRAIT WARN node_id='comec' label='ComEC' type=GENE_OR_PROTEIN — in an island with no path to natural_competence_trait @@ -1456,14 +1732,19 @@ data/traits/physiology/nutrient_adaptation.yaml nutrient_adaptation_life_history data/traits/physiology/nutrient_adaptation.yaml nutrient_adaptation_life_history_axis UNREACHABLE_FROM_TRAIT WARN node_id='maximum_growth_potential' label='maximum growth potential' type=CAPACITY — in an island with no path to nutrient_adaptation_trait/copiotrophic_phenotype/oligotrophic_phenotype data/traits/physiology/nutrient_adaptation.yaml nutrient_adaptation_life_history_axis UNREACHABLE_FROM_TRAIT WARN node_id='carbohydrate_acquisition_genes' label='carbohydrate acquisition gene abundance' type=GENE_OR_PROTEIN — in an island with no path to nutrient_adaptation_trait/copiotrophic_phenotype/oligotrophic_phenotype data/traits/physiology/nutrient_adaptation.yaml nutrient_adaptation_life_history_axis FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 8, 3, 2) — one record, several unrelated mechanisms +data/traits/physiology/organoheterotrophic.yaml organoheterotrophic_organic_donor_carbon INCONSISTENT_NODE_TYPE WARN node_id='oxidative_phosphorylation' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/physiology/organotrophic.yaml organotrophic_organic_compound_oxidation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='family_a_cytochrome_c_oxidase' label='family A cytochrome c oxidase' type=GENE_OR_PROTEIN — in an island with no path to oxidase_activity_trait data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='reduced_cytochrome_c' label='reduced cytochrome c' type=CHEMICAL — in an island with no path to oxidase_activity_trait data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='cua_center' label='CuA center' type=CHEMICAL — in an island with no path to oxidase_activity_trait data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='heme_a' label='heme a' type=CHEMICAL — in an island with no path to oxidase_activity_trait data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='cua_cub_copper_centers' label='CuA/CuB copper centers' type=CHEMICAL — in an island with no path to oxidase_activity_trait +data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='antibiotic_resistance' label='antibiotic resistance' type=BIOLOGICAL_PROCESS — in an island with no path to persister_trait data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='elevated_mic' label='elevated minimum inhibitory concentration' type=QUALITY — in an island with no path to persister_trait +data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance INCONSISTENT_NODE_TYPE WARN node_id='oxidative_phosphorylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 8, 2) — one record, several unrelated mechanisms data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='photosystem_ii' label='photosystem II' type=GENE_OR_PROTEIN — in an island with no path to photoautotrophic_trait data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='water' label='water' type=CHEMICAL — in an island with no path to photoautotrophic_trait @@ -1479,15 +1760,21 @@ data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_car data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='carboxysome' label='carboxysome' type=ORGANELLE — in an island with no path to photoautotrophic_trait data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='carboxysomal_carbonic_anhydrase' label='carboxysomal carbonic anhydrase' type=GENE_OR_PROTEIN — in an island with no path to photoautotrophic_trait data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='bicarbonate' label='bicarbonate' type=CHEMICAL — in an island with no path to photoautotrophic_trait +data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation FRAGMENTED_GRAPH WARN components=4 of 16 node(s) (sizes: 9, 3, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='proteorhodopsin' label='proteorhodopsin' type=GENE_OR_PROTEIN — in an island with no path to photoheterotrophic_trait/aerobic_anoxygenic_phototrophs data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='nadph_anabolic' label='NAD(P)H for anabolic metabolism' type=CHEMICAL — in an island with no path to photoheterotrophic_trait/aerobic_anoxygenic_phototrophs +data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon INCONSISTENT_NODE_TYPE WARN node_id='membrane_potential' type=STATE here — also BIOLOGICAL_PROCESS×1, CHEMICAL×1, QUALITY×1 elsewhere in the corpus data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon FRAGMENTED_GRAPH WARN components=2 of 16 node(s) (sizes: 14, 2) — one record, several unrelated mechanisms data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='sulfide' label='sulfide' type=CHEMICAL — in an island with no path to photolithoautotrophic_trait data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='sulfur_oxidation' label='sulfur oxidation' type=BIOLOGICAL_PROCESS — in an island with no path to photolithoautotrophic_trait data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='carbonic_anhydrase' label='carbonic anhydrase' type=GENE_OR_PROTEIN — in an island with no path to photolithoautotrophic_trait data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='bicarbonate' label='bicarbonate' type=CHEMICAL — in an island with no path to photolithoautotrophic_trait data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='dic_transporter' label='inorganic carbon transporter' type=GENE_OR_PROTEIN — in an island with no path to photolithoautotrophic_trait +data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CAPACITY here — also CHEMICAL×1 elsewhere in the corpus data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 10, 3, 2) — one record, several unrelated mechanisms data/traits/physiology/photolithotrophic.yaml photolithotrophic_inorganic_electron_donors UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_sulfide_oxidation' label='hydrogen sulfide oxidation' type=BIOLOGICAL_PROCESS — in an island with no path to photolithotrophic_trait/photoferrotrophy data/traits/physiology/photolithotrophic.yaml photolithotrophic_inorganic_electron_donors UNREACHABLE_FROM_TRAIT WARN node_id='elemental_sulfur' label='elemental sulfur' type=CHEMICAL — in an island with no path to photolithotrophic_trait/photoferrotrophy @@ -1498,15 +1785,22 @@ data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_li data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons UNREACHABLE_FROM_TRAIT WARN node_id='bchl_photoheterotrophy' label='bacteriochlorophyll-based anoxygenic photoheterotrophy' type=PATHWAY — in an island with no path to photoorganoheterotrophic_trait data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons UNREACHABLE_FROM_TRAIT WARN node_id='diurnal_cycle' label='diurnal dark-light cycle' type=ENVIRONMENTAL_FACTOR — in an island with no path to photoorganoheterotrophic_trait data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons UNREACHABLE_FROM_TRAIT WARN node_id='rhythmic_transcription' label='rhythmic transcription' type=BIOLOGICAL_PROCESS — in an island with no path to photoorganoheterotrophic_trait +data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons FRAGMENTED_GRAPH WARN components=4 of 16 node(s) (sizes: 10, 2, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='rhodopsin' label='rhodopsin' type=GENE_OR_PROTEIN — in an island with no path to phototrophic_trait data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='ion_transport' label='ion transport across membrane' type=BIOLOGICAL_PROCESS — in an island with no path to phototrophic_trait +data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CAPACITY here — also CHEMICAL×1 elsewhere in the corpus +data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=CAPACITY here — also BIOLOGICAL_PROCESS×13, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='rpos' label='RpoS sigma factor' type=GENE_OR_PROTEIN — in an island with no path to vbnc_trait data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='resuscitation' label='resuscitation from VBNC' type=BIOLOGICAL_PROCESS — in an island with no path to vbnc_trait data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='atp' label='ATP' type=CHEMICAL — in an island with no path to vbnc_trait data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='nad_synthesis' label='NAD+ biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to vbnc_trait data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='tca_oxphos' label='TCA cycle flux and oxidative phosphorylation' type=BIOLOGICAL_PROCESS — in an island with no path to vbnc_trait +data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy INCONSISTENT_NODE_TYPE WARN node_id='stress_resistance' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms data/traits/upper/observation.yaml observation_measurement_upper_context UNREACHABLE_FROM_TRAIT WARN node_id='metadata' label='metadata' type=EXPERIMENTAL_FACTOR — in an island with no path to measured_quality/material_entity/material_entity_evaluant/sample data/traits/upper/observation.yaml observation_measurement_upper_context UNREACHABLE_FROM_TRAIT WARN node_id='mixs_standard' label='MIxS reporting standard' type=EXPERIMENTAL_FACTOR — in an island with no path to measured_quality/material_entity/material_entity_evaluant/sample diff --git a/docs/CURATION_PLAYBOOK.md b/docs/CURATION_PLAYBOOK.md index 84b9cf80..21ddc41c 100644 --- a/docs/CURATION_PLAYBOOK.md +++ b/docs/CURATION_PLAYBOOK.md @@ -203,6 +203,50 @@ Those numbers came from measuring the graphs by hand. #359 makes it routine — `reports/causal_graph_connectivity.tsv`, one row per graph, arriving with **#363**. Once it lands, quote that table rather than the finding counts. +### One `node_id` means one thing — across the whole corpus + +`audit-graphs` flags `INCONSISTENT_NODE_TYPE` when one `node_id` carries +different `node_type`s in different records (#356). It is the only +**cross-record** check here, and that is exactly why the defect survived: read +alone, neither record is wrong. + +Baselined at **294 occurrences across 63 `node_id`s**. The worst is +`proton_motive_force` — `STATE`×18, `BIOLOGICAL_PROCESS`×13, `CHEMICAL`×2, +`CAPACITY`×2, for one concept. + +**Why it stopped being cosmetic.** #355 minted `powers` (`METPO:2007900`) gated +to `subject_types = BIOLOGICAL_PROCESS|STATE`. Two byte-identical assertions now +behave differently purely by subject typing: + +``` +physiology/carboxydotrophic.yaml proton_motive_force (STATE) -> atp_synthase grounds +physiology/phototrophic.yaml proton_motive_force (CAPACITY) -> atp_synthase blocked_by_node_type +``` + +Typing decides groundings now. A disagreement is no longer just untidy. + +**A hit is not automatically a defect.** `terminal electron acceptor` is +deliberately both `CHEMICAL` and `MOLECULAR_FUNCTION`; `mappings/node_grounding.tsv` +carries a row for each, noting that one METPO class covers both senses and the +`MOLECULAR_FUNCTION` typing "surfaces the role-of interpretation". Same +two-senses shape as `reduces` (#330/#333) and the `CAPACITY` table above. + +So ask **does this id mean one thing?** + +| answer | fix | +|---|---| +| yes, and one type is right | normalise the outliers to it | +| yes, but the right type is arguable (`STATE` vs `BIOLOGICAL_PROCESS`) | decide once, record why, normalise | +| **no — it means two things** | **split into two `node_id`s**, not one type | + +The gradient *is* a state; generating and maintaining it *is* a process. If a +record means the second, it should not be reusing the id for the first. + +**Do not repeat #352's mistake.** The test is not "is this type defensible in +isolation" — it is "is it compatible with what the record and its predicates +already assert". #352 spent three review rounds learning that on the +neighbouring `DISPOSITION_MISTYPED` family, and the grounding is what settles it. + ### `enables` needs a process-or-activity object Separately from the domain rule above, `enables` (`RO:0002327`) has a diff --git a/history/infrastructure/inconsistent-node-type/2026-08-12T000912Z-claude-code-779670.yaml b/history/infrastructure/inconsistent-node-type/2026-08-12T000912Z-claude-code-779670.yaml new file mode 100644 index 00000000..c809fbb2 --- /dev/null +++ b/history/infrastructure/inconsistent-node-type/2026-08-12T000912Z-claude-code-779670.yaml @@ -0,0 +1,43 @@ +history_version: 1 +target: + kind: infrastructure + path: scripts/audit_causal_graphs.py + slug: inconsistent-node-type +session: + id: 2026-08-12T000912Z-claude-code-779670 + timestamp: '2026-08-12T00:09:12Z' + actors: + - type: ai_agent + name: claude-code +links: + issues: + - https://github.com/CultureBotAI/TraitMech/issues/356 +events: +- type: EDIT + outcome: changed + sections: + - causal_graphs + summary: Detect one node_id carrying several node_types across records + details: 'Every other check in audit_causal_graphs.py is scoped to one graph. This defect + is not: two records disagree about what a node IS, and neither is wrong read alone, which + is why nothing caught it. Added node_type_index() plus an INCONSISTENT_NODE_TYPE finding, + baselined at 294 occurrences across 63 node_ids. The issue understated the scale by about + 7x: it reports proton_motive_force typed four ways across 9 records; measured, it is 35 + records (STATE 18, BIOLOGICAL_PROCESS 13, CHEMICAL 2, CAPACITY 2), and 63 node_ids disagree + with themselves corpus-wide including membrane_potential at four types. It stopped being + cosmetic when 355 minted powers (METPO:2007900) gated to subject_types BIOLOGICAL_PROCESS + or STATE: carboxydotrophic.yaml''s proton_motive_force (STATE) grounds while phototrophic.yaml''s + (CAPACITY) is blocked_by_node_type, for byte-identical assertions. Reported per occurrence + rather than on a presumed-wrong minority, because nothing here knows which type is right + - proton_motive_force splits 18 STATE to 13 BIOLOGICAL_PROCESS and the gradient genuinely + is a state while generating it is a process, so the majority is an observation and not + a verdict; per-occurrence rows also mean a family clears together the moment it is normalised. + The detail leads with node_id so _key discriminates by node within a graph, deliberately + NOT with the type set, since a family part-way through a burn-down would otherwise re-key + on every step and un-suppress rows nobody has reached yet. A test pins that. Documented + that not every hit is a defect: terminal electron acceptor is deliberately both CHEMICAL + and MOLECULAR_FUNCTION and node_grounding.tsv carries a row for each saying one METPO + class covers both senses, the same two-senses shape as reduces (330/333). Where a family + really means two things the fix is two node_ids rather than one type, which is written + into the playbook as a decision table. Detection only - no data changed, and the burn-down + is the next step. 534 tests pass (4 new), ruff clean.' diff --git a/reports/causal_graph_audit.tsv b/reports/causal_graph_audit.tsv index 156f7496..cc02fac4 100644 --- a/reports/causal_graph_audit.tsv +++ b/reports/causal_graph_audit.tsv @@ -1,11 +1,13 @@ file graph_id defect severity detail data/traits/ecology/animal_pathogen.yaml animal_pathogen_metazoan_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='low_iron_environment' label='low-iron host environment' type=ENVIRONMENTAL_FACTOR — in an island with no path to animal_pathogen_trait data/traits/ecology/animal_pathogen.yaml animal_pathogen_metazoan_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='siderophore_biosynthesis' label='siderophore biosynthesis gene expression' type=BIOLOGICAL_PROCESS — in an island with no path to animal_pathogen_trait +data/traits/ecology/animal_pathogen.yaml animal_pathogen_metazoan_adaptation INCONSISTENT_NODE_TYPE WARN node_id='immune_evasion' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/ecology/animal_pathogen.yaml animal_pathogen_metazoan_adaptation FRAGMENTED_GRAPH WARN components=2 of 17 node(s) (sizes: 15, 2) — one record, several unrelated mechanisms data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community UNREACHABLE_FROM_TRAIT WARN node_id='planktonic_cell' label='planktonic cell' type=STATE — in an island with no path to biofilm_formation_trait data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community UNREACHABLE_FROM_TRAIT WARN node_id='amenable_surface' label='amenable surface' type=ENVIRONMENTAL_FACTOR — in an island with no path to biofilm_formation_trait data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community UNREACHABLE_FROM_TRAIT WARN node_id='nitric_oxide' label='nitric oxide' type=CHEMICAL — in an island with no path to biofilm_formation_trait data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community UNREACHABLE_FROM_TRAIT WARN node_id='biofilm_dispersal' label='biofilm dispersal' type=BIOLOGICAL_PROCESS — in an island with no path to biofilm_formation_trait +data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community INCONSISTENT_NODE_TYPE WARN node_id='eps_matrix' type=CHEMICAL here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus data/traits/ecology/biofilm_formation.yaml biofilm_eps_matrix_community FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 9, 2, 2) — one record, several unrelated mechanisms data/traits/ecology/biosafety_level.yaml biosafety_level_hazard_classification UNREACHABLE_FROM_TRAIT WARN node_id='lack_of_countermeasures' label='lack of effective treatment or vaccine' type=QUALITY — in an island with no path to biosafety_level_trait/bsl1/bsl2/bsl3/bsl4/bsl5 data/traits/ecology/biosafety_level.yaml biosafety_level_hazard_classification UNREACHABLE_FROM_TRAIT WARN node_id='bsl4_containment' label='BSL-4 containment requirement' type=EXPERIMENTAL_FACTOR — in an island with no path to biosafety_level_trait/bsl1/bsl2/bsl3/bsl4/bsl5 @@ -26,6 +28,7 @@ data/traits/ecology/endosymbiosis.yaml endosymbiosis_intracellular_genome_reduct data/traits/ecology/endosymbiosis.yaml endosymbiosis_intracellular_genome_reduction FRAGMENTED_GRAPH WARN components=3 of 10 node(s) (sizes: 6, 2, 2) — one record, several unrelated mechanisms data/traits/ecology/free_living.yaml free_living_environmental_habitat UNREACHABLE_FROM_TRAIT WARN node_id='trehalose_biosynthesis' label='trehalose biosynthesis/transport' type=PATHWAY — in an island with no path to free_living_trait data/traits/ecology/free_living.yaml free_living_environmental_habitat UNREACHABLE_FROM_TRAIT WARN node_id='environmental_stress_tolerance' label='stress tolerance in fluctuating environments' type=BIOLOGICAL_PROCESS — in an island with no path to free_living_trait +data/traits/ecology/free_living.yaml free_living_environmental_habitat INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/ecology/free_living.yaml free_living_environmental_habitat FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 7, 2) — one record, several unrelated mechanisms data/traits/ecology/gut_associated.yaml gut_associated_microbiota_metabolism UNREACHABLE_FROM_TRAIT WARN node_id='peristalsis' label='intestinal peristalsis' type=ENVIRONMENTAL_FACTOR — in an island with no path to gut_associated_trait data/traits/ecology/gut_associated.yaml gut_associated_microbiota_metabolism UNREACHABLE_FROM_TRAIT WARN node_id='duodenal_retention' label='colonization/retention in duodenum' type=BIOLOGICAL_PROCESS — in an island with no path to gut_associated_trait @@ -37,6 +40,7 @@ data/traits/ecology/habitat_association.yaml habitat_association_biogeographic_s data/traits/ecology/habitat_association.yaml habitat_association_biogeographic_structure UNREACHABLE_FROM_TRAIT WARN node_id='ecological_drift' label='ecological drift in community assembly' type=BIOLOGICAL_PROCESS — in an island with no path to habitat_association_trait data/traits/ecology/habitat_association.yaml habitat_association_biogeographic_structure UNREACHABLE_FROM_TRAIT WARN node_id='dispersal_limitation' label='dispersal limitation in community assembly' type=BIOLOGICAL_PROCESS — in an island with no path to habitat_association_trait data/traits/ecology/habitat_association.yaml habitat_association_biogeographic_structure FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 6, 4) — one record, several unrelated mechanisms +data/traits/ecology/host_associated.yaml host_associated_microbiome INCONSISTENT_NODE_TYPE WARN node_id='root_exudates' type=ENVIRONMENTAL_FACTOR here — also CHEMICAL×1 elsewhere in the corpus data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit UNREACHABLE_FROM_TRAIT WARN node_id='cross_feeding_architecture' label='co-auxotrophy / cross-feeding architecture' type=BIOLOGICAL_PROCESS — in an island with no path to mutualism_trait data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit UNREACHABLE_FROM_TRAIT WARN node_id='obligate_mutualism_syntrophy' label='obligate mutualism (syntrophy)' type=STATE — in an island with no path to mutualism_trait data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit UNREACHABLE_FROM_TRAIT WARN node_id='metabolite_secretion_profile' label='metabolite secretion profile' type=CHEMICAL — in an island with no path to mutualism_trait @@ -44,6 +48,7 @@ data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit UNREACHABLE_FROM data/traits/ecology/mutualism.yaml mutualism_reciprocal_benefit FRAGMENTED_GRAPH WARN components=3 of 10 node(s) (sizes: 6, 2, 2) — one record, several unrelated mechanisms data/traits/ecology/pathogenic_to_host.yaml pathogenic_to_host_virulence_factor_program UNREACHABLE_FROM_TRAIT WARN node_id='biofilm_matrix' label='biofilm extracellular matrix' type=CELLULAR_LOCALIZATION — in an island with no path to pathogenic_to_host_trait data/traits/ecology/pathogenic_to_host.yaml pathogenic_to_host_virulence_factor_program UNREACHABLE_FROM_TRAIT WARN node_id='antibiotic_tolerance' label='antibiotic tolerance' type=BIOLOGICAL_PROCESS — in an island with no path to pathogenic_to_host_trait +data/traits/ecology/pathogenic_to_host.yaml pathogenic_to_host_virulence_factor_program INCONSISTENT_NODE_TYPE WARN node_id='immune_evasion' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/ecology/pathogenic_to_host.yaml pathogenic_to_host_virulence_factor_program FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 12, 2) — one record, several unrelated mechanisms data/traits/ecology/plant_pathogen.yaml plant_pathogen_t3ss_effector_program UNREACHABLE_FROM_TRAIT WARN node_id='quorum_sensing' label='quorum sensing' type=BIOLOGICAL_PROCESS — in an island with no path to plant_pathogen_trait data/traits/ecology/plant_pathogen.yaml plant_pathogen_t3ss_effector_program UNREACHABLE_FROM_TRAIT WARN node_id='biofilm_formation' label='biofilm formation' type=BIOLOGICAL_PROCESS — in an island with no path to plant_pathogen_trait @@ -60,6 +65,7 @@ data/traits/ecology/predatory_bacterium.yaml predatory_bacterium_prey_killing FR data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate UNREACHABLE_FROM_TRAIT WARN node_id='bacterial_chemotaxis' label='bacterial chemotaxis' type=BIOLOGICAL_PROCESS — in an island with no path to rhizosphere_trait data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate UNREACHABLE_FROM_TRAIT WARN node_id='mcp_chemoreceptor' label='methyl-accepting chemotaxis protein (MCP)' type=GENE_OR_PROTEIN — in an island with no path to rhizosphere_trait data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate UNREACHABLE_FROM_TRAIT WARN node_id='root_colonization' label='root colonization' type=BIOLOGICAL_PROCESS — in an island with no path to rhizosphere_trait +data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate INCONSISTENT_NODE_TYPE WARN node_id='root_exudates' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/ecology/rhizosphere_association.yaml rhizosphere_root_exudate FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 6, 3) — one record, several unrelated mechanisms data/traits/ecology/saprotrophy.yaml saprotrophy_decomposition_cycling UNREACHABLE_FROM_TRAIT WARN node_id='extracellular_exoenzymes' label='extracellular exoenzymes' type=GENE_OR_PROTEIN — in an island with no path to saprotrophy_trait data/traits/ecology/saprotrophy.yaml saprotrophy_decomposition_cycling UNREACHABLE_FROM_TRAIT WARN node_id='soluble_organic_compounds' label='soluble organic compounds' type=CHEMICAL — in an island with no path to saprotrophy_trait @@ -91,37 +97,54 @@ data/traits/ecology/symbiosis.yaml symbiosis_host_interaction UNREACHABLE_FROM_T data/traits/ecology/symbiosis.yaml symbiosis_host_interaction UNREACHABLE_FROM_TRAIT WARN node_id='o_antigen' label='O-antigen' type=CHEMICAL — in an island with no path to symbiosis_trait data/traits/ecology/symbiosis.yaml symbiosis_host_interaction UNREACHABLE_FROM_TRAIT WARN node_id='immune_evasion' label='immune evasion' type=BIOLOGICAL_PROCESS — in an island with no path to symbiosis_trait data/traits/ecology/symbiosis.yaml symbiosis_host_interaction UNREACHABLE_FROM_TRAIT WARN node_id='adhesins' label='adhesins' type=GENE_OR_PROTEIN — in an island with no path to symbiosis_trait +data/traits/ecology/symbiosis.yaml symbiosis_host_interaction INCONSISTENT_NODE_TYPE WARN node_id='immune_evasion' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/ecology/symbiosis.yaml symbiosis_host_interaction FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 7, 6) — one record, several unrelated mechanisms data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='hopanoid_and_membrane_proteins' label='hopanoid lipids and membrane proteins (Omp40, PspA)' type=CELLULAR_LOCALIZATION — in an island with no path to acidophilic_trait data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='proton_exclusion' label='proton exclusion' type=BIOLOGICAL_PROCESS — in an island with no path to acidophilic_trait data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='bipolar_tetraether_lipids' label='bipolar tetraether lipids (GDNT/GDGT)' type=CHEMICAL — in an island with no path to acidophilic_trait data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='low_passive_proton_permeability' label='low passive proton permeability' type=QUALITY — in an island with no path to acidophilic_trait +data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='reversed_membrane_potential' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus data/traits/environment/acidophilic.yaml acidophilic_ph_homeostasis FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 9, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/acidotolerant.yaml acidotolerant_acid_stress_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=PATHWAY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus +data/traits/environment/aerobic.yaml aerobic_trait_mechanism INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/aerobic.yaml aerobic_trait_mechanism INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=MOLECULAR_FUNCTION here — also CHEMICAL×3 elsewhere in the corpus +data/traits/environment/aerobic.yaml aerobic_trait_mechanism INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide' label='hydrogen peroxide' type=CHEMICAL — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide_detoxification' label='hydrogen peroxide detoxification' type=BIOLOGICAL_PROCESS — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='catalase' label='catalase' type=GENE_OR_PROTEIN — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='rubrerythrin' label='rubrerythrin' type=GENE_OR_PROTEIN — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='nadh_peroxidase' label='NADH peroxidase' type=GENE_OR_PROTEIN — in an island with no path to aerotolerant_trait data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense UNREACHABLE_FROM_TRAIT WARN node_id='nadph_peroxidase' label='NADPH peroxidase' type=GENE_OR_PROTEIN — in an island with no path to aerotolerant_trait +data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense INCONSISTENT_NODE_TYPE WARN node_id='superoxide_dismutase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/aerotolerant.yaml aerotolerant_anaerobe_ros_defense FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 5, 4, 2) — one record, several unrelated mechanisms data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='alkaline_external_ph' label='alkaline external pH' type=ENVIRONMENTAL_FACTOR — in an island with no path to alkalotolerant_trait data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='electrogenic_na_h_antiport' label='electrogenic Na+/H+ antiport' type=MOLECULAR_FUNCTION — in an island with no path to alkalotolerant_trait +data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cation_proton_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='electrogenic_na_h_antiport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/alkalotolerant.yaml alkalotolerant_alkaline_stress_homeostasis FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms data/traits/environment/alkaphilic.yaml alkaliphilic_na_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to alkaphilic_trait data/traits/environment/alkaphilic.yaml alkaliphilic_na_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='proton' label='proton' type=CHEMICAL — in an island with no path to alkaphilic_trait data/traits/environment/alkaphilic.yaml alkaliphilic_na_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_proton_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to alkaphilic_trait data/traits/environment/alkaphilic.yaml alkaliphilic_na_cycle_homeostasis FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 8, 3) — one record, several unrelated mechanisms +data/traits/environment/anaerobic.yaml anaerobic_trait_oxygen_exclusion INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/delta_phenotype_with_numerical_limits.yaml delta_phenotype_breadth_descriptor INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='trehalose' label='trehalose' type=CHEMICAL — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='plasma_membrane' label='plasma membrane' type=CELLULAR_LOCALIZATION — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='vitrification' label='vitrification / glass formation' type=BIOLOGICAL_PROCESS — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='chaperone_activity' label='heat shock protein / chaperone activity' type=MOLECULAR_FUNCTION — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='protein_aggregation' label='protein aggregation' type=BIOLOGICAL_PROCESS — in an island with no path to desiccation_tolerant_trait data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair UNREACHABLE_FROM_TRAIT WARN node_id='desiccation_idps' label='desiccation-related intrinsically disordered proteins' type=GENE_OR_PROTEIN — in an island with no path to desiccation_tolerant_trait +data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/desiccation_tolerant.yaml desiccation_anhydrobiosis_repair FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 7, 4, 2) — one record, several unrelated mechanisms data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='mechanosensitive_channels' label='mechanosensitive channels (Msc)' type=GENE_OR_PROTEIN — in an island with no path to euryhaline_trait data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='osmotic_downshock' label='osmotic downshock' type=BIOLOGICAL_PROCESS — in an island with no path to euryhaline_trait data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to euryhaline_trait data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_sodium' label='cytoplasmic sodium ions' type=CHEMICAL — in an island with no path to euryhaline_trait +data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_transport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/euryhaline.yaml euryhaline_wide_salinity_tolerance FRAGMENTED_GRAPH WARN components=3 of 17 node(s) (sizes: 13, 2, 2) — one record, several unrelated mechanisms data/traits/environment/extreme_hyperthermophilic.yaml extreme_hyperthermophilic_archaeal_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='reverse_gyrase' label='reverse gyrase' type=GENE_OR_PROTEIN — in an island with no path to extreme_hyperthermophilic_trait data/traits/environment/extreme_hyperthermophilic.yaml extreme_hyperthermophilic_archaeal_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='dna_positive_supercoiling' label='DNA positive supercoiling' type=BIOLOGICAL_PROCESS — in an island with no path to extreme_hyperthermophilic_trait @@ -130,12 +153,22 @@ data/traits/environment/extreme_hyperthermophilic.yaml extreme_hyperthermophilic data/traits/environment/extreme_hyperthermophilic.yaml extreme_hyperthermophilic_archaeal_adaptation FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 7, 4) — one record, several unrelated mechanisms data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to extremely_halophilic_trait data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome UNREACHABLE_FROM_TRAIT WARN node_id='sodium_efflux' label='sodium efflux' type=BIOLOGICAL_PROCESS — in an island with no path to extremely_halophilic_trait +data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/extremely_halophilic.yaml extreme_halophile_salt_in_acidic_proteome FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms +data/traits/environment/facultative_oxygen_preference.yaml facultative_oxygen_preference_switching INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/facultative_oxygen_preference.yaml facultative_oxygen_preference_switching INCONSISTENT_NODE_TYPE WARN node_id='anaerobic_metabolism_genes' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='exopolysaccharides' label='extracellular polymeric substances (EPS)' type=CHEMICAL — in an island with no path to facultative_psychrophilic_trait data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='freeze_thaw_cycles' label='freeze-thaw cycles' type=ENVIRONMENTAL_FACTOR — in an island with no path to facultative_psychrophilic_trait +data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance INCONSISTENT_NODE_TYPE WARN node_id='fatty_acid_desaturase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/facultative_psychrophilic.yaml facultative_psychrophilic_cold_tolerance FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='hopanoid_biosynthesis' label='hopanoid biosynthetic process' type=BIOLOGICAL_PROCESS — in an island with no path to facultatively_acidophilic_trait data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='membrane_proton_permeability' label='membrane proton permeability' type=QUALITY — in an island with no path to facultatively_acidophilic_trait +data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='inside_positive_membrane_potential' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='membrane_proton_permeability' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='glutamate_decarboxylase_system' type=GENE_OR_PROTEIN here — also PATHWAY×2 elsewhere in the corpus +data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='intracellular_ph' type=QUALITY here — also STATE×1 elsewhere in the corpus data/traits/environment/facultatively_acidophilic.yaml facultatively_acidophilic_ph_homeostasis FRAGMENTED_GRAPH WARN components=2 of 15 node(s) (sizes: 13, 2) — one record, several unrelated mechanisms data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='molecular_oxygen' label='molecular oxygen' type=CHEMICAL — in an island with no path to facultative_aerobic_trait data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='aerobic_respiration' label='aerobic respiration' type=BIOLOGICAL_PROCESS — in an island with no path to facultative_aerobic_trait @@ -146,6 +179,8 @@ data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_fle data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='anaerobic_metabolism_genes' label='anaerobic metabolism genes' type=GENE_OR_PROTEIN — in an island with no path to facultative_aerobic_trait data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='aerobic_metabolism_genes' label='aerobic metabolism genes' type=GENE_OR_PROTEIN — in an island with no path to facultative_aerobic_trait data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth UNREACHABLE_FROM_TRAIT WARN node_id='cytochrome_bd_oxidase' label='cytochrome bd oxidase' type=GENE_OR_PROTEIN — in an island with no path to facultative_aerobic_trait +data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth INCONSISTENT_NODE_TYPE WARN node_id='anaerobic_metabolism_genes' type=GENE_OR_PROTEIN here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/facultatively_aerobic.yaml facultative_aerobe_oxygen_flexible_growth FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to facultatively_alkaphilic_trait data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='proton' label='proton' type=CHEMICAL — in an island with no path to facultatively_alkaphilic_trait @@ -154,22 +189,38 @@ data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_s data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='f1fo_atp_synthase' label='F1Fo-ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to facultatively_alkaphilic_trait data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='atp_production_alkaline' label='ATP production at alkaline pH' type=BIOLOGICAL_PROCESS — in an island with no path to facultatively_alkaphilic_trait data/traits/environment/facultatively_alkaphilic.yaml facultatively_alkaphilic_sodium_cycle_homeostasis FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 5, 4, 2) — one record, several unrelated mechanisms +data/traits/environment/facultatively_anaerobic.yaml facultative_anaerobe_oxygen_switch INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='proton_pumping_atpase_respiration' label='F0F1-ATPase / proton-pumping respiratory chain activity' type=MOLECULAR_FUNCTION — in an island with no path to growth_range_phenotype_trait/nacl_range/ph_range/temperature_range data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='prevent_cytoplasm_acidification' label='prevention of cytoplasmic acidification' type=BIOLOGICAL_PROCESS — in an island with no path to growth_range_phenotype_trait/nacl_range/ph_range/temperature_range data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='hypertonic_salinity_increase' label='hypertonic salinity increase' type=ENVIRONMENTAL_FACTOR — in an island with no path to growth_range_phenotype_trait/nacl_range/ph_range/temperature_range data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='cell_shrinkage_low_turgor' label='cell shrinkage and lowered turgor' type=STATE — in an island with no path to growth_range_phenotype_trait/nacl_range/ph_range/temperature_range +data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='cation_proton_antiporter' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×3 elsewhere in the corpus +data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='cytoplasm_acidification' type=STATE here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='aa_decarboxylase_antiporter' type=MOLECULAR_FUNCTION here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/growth_range_phenotype_with_numerical_limits.yaml growth_range_phenotype_descriptor FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 11, 2, 2) — one record, several unrelated mechanisms data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='choline_oxidation_pathway' label='choline oxidation pathway' type=PATHWAY — in an island with no path to haloalkaliphilic_trait data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='glycine_betaine' label='glycine betaine' type=CHEMICAL — in an island with no path to haloalkaliphilic_trait +data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/haloalkaliphilic.yaml haloalkaliphilic_salt_alkaline_adaptation FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/environment/halophilic.yaml halophilic_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to halophilic_trait data/traits/environment/halophilic.yaml halophilic_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to halophilic_trait data/traits/environment/halophilic.yaml halophilic_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='k_uniport' label='K+ uniport system' type=GENE_OR_PROTEIN — in an island with no path to halophilic_trait data/traits/environment/halophilic.yaml halophilic_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='potassium_ion' label='potassium ion' type=CHEMICAL — in an island with no path to halophilic_trait +data/traits/environment/halophilic.yaml halophilic_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/halophilic.yaml halophilic_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/halophilic.yaml halophilic_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='acidified_proteome' type=STATE here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/halophilic.yaml halophilic_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/halophilic.yaml halophilic_osmoadaptation FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 11, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/halophily_preference.yaml halophily_preference_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_transport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/halophily_preference.yaml halophily_preference_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/halophily_preference.yaml halophily_preference_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='acidified_proteome' type=QUALITY here — also STATE×1 elsewhere in the corpus +data/traits/environment/halotolerant.yaml halotolerant_salt_stress_response INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_transport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/halotolerant.yaml halotolerant_salt_stress_response INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability UNREACHABLE_FROM_TRAIT WARN node_id='cdpg' label='cyclic 2,3-diphosphoglycerate (cDPG)' type=CHEMICAL — in an island with no path to hyperthermophilic_trait data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability UNREACHABLE_FROM_TRAIT WARN node_id='archaeal_proteins' label='archaeal proteins' type=GENE_OR_PROTEIN — in an island with no path to hyperthermophilic_trait data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability UNREACHABLE_FROM_TRAIT WARN node_id='dna_oxidative_damage' label='DNA oxidative damage by hydroxyl radicals' type=BIOLOGICAL_PROCESS — in an island with no path to hyperthermophilic_trait +data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability INCONSISTENT_NODE_TYPE WARN node_id='membrane_lipid_composition' type=CELLULAR_LOCALIZATION here — also BIOLOGICAL_PROCESS×1, QUALITY×1 elsewhere in the corpus data/traits/environment/hyperthermophilic.yaml hyperthermophilic_thermostability FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 10, 3) — one record, several unrelated mechanisms data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to mesophilic_trait data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='homoviscous_lipid_composition' label='homoviscous lipid composition' type=CELLULAR_LOCALIZATION — in an island with no path to mesophilic_trait @@ -182,6 +233,7 @@ data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREAC data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='rpoh_sigma32' label='sigma-32 (RpoH)' type=GENE_OR_PROTEIN — in an island with no path to mesophilic_trait data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='heat_shock_genes' label='heat shock genes' type=GENE_OR_PROTEIN — in an island with no path to mesophilic_trait data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='dnak' label='DnaK chaperone' type=GENE_OR_PROTEIN — in an island with no path to mesophilic_trait +data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/mesophilic.yaml mesophilic_homoviscous_adaptation FRAGMENTED_GRAPH WARN components=5 of 15 node(s) (sizes: 4, 4, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/metal_tolerant.yaml metal_tolerance_efflux_detoxification UNREACHABLE_FROM_TRAIT WARN node_id='arsenate' label='arsenate As(V)' type=CHEMICAL — in an island with no path to metal_tolerant_trait/arsenic_tolerance data/traits/environment/metal_tolerant.yaml metal_tolerance_efflux_detoxification UNREACHABLE_FROM_TRAIT WARN node_id='arsenite' label='arsenite As(III)' type=CHEMICAL — in an island with no path to metal_tolerant_trait/arsenic_tolerance @@ -194,6 +246,7 @@ data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respirati data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='superoxide_dismutase_sodb' label='superoxide dismutase (SodB)' type=GENE_OR_PROTEIN — in an island with no path to microaerophilic_trait data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='reactive_oxygen_species' label='reactive oxygen species' type=CHEMICAL — in an island with no path to microaerophilic_trait data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='ahpc' label='alkyl hydroperoxide reductase (AhpC)' type=GENE_OR_PROTEIN — in an island with no path to microaerophilic_trait +data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/microaerophilic.yaml microaerophile_low_oxygen_respiration FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 7, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/microaerotolerant.yaml microaerotolerant_low_oxygen_defense UNREACHABLE_FROM_TRAIT WARN node_id='superoxide' label='superoxide' type=CHEMICAL — in an island with no path to microaerotolerant_trait data/traits/environment/microaerotolerant.yaml microaerotolerant_low_oxygen_defense UNREACHABLE_FROM_TRAIT WARN node_id='superoxide_reductase' label='superoxide reductase' type=GENE_OR_PROTEIN — in an island with no path to microaerotolerant_trait @@ -211,6 +264,7 @@ data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth UNREACHABL data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth UNREACHABLE_FROM_TRAIT WARN node_id='high_maximal_nacl_tolerance' label='high maximal NaCl tolerance' type=QUALITY — in an island with no path to nacl_delta_trait data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth UNREACHABLE_FROM_TRAIT WARN node_id='mechanosensitive_channels' label='mechanosensitive channels (MscL/MscS)' type=GENE_OR_PROTEIN — in an island with no path to nacl_delta_trait data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth UNREACHABLE_FROM_TRAIT WARN node_id='hypoosmotic_shock' label='hypoosmotic shock' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_delta_trait +data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/nacl_delta.yaml nacl_delta_euryhaline_breadth FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 5, 4, 2, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline UNREACHABLE_FROM_TRAIT WARN node_id='high_external_salinity' label='high external salinity' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_delta_high_trait/nacl_delta data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible-solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_high_trait/nacl_delta @@ -224,6 +278,7 @@ data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline UNREACHABLE_FROM_TRAIT WARN node_id='hypersaline_environment' label='hypersaline environment' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_delta_high_trait/nacl_delta data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline UNREACHABLE_FROM_TRAIT WARN node_id='halophilic_osmoadaptation' label='halophilic osmoadaptation strategies' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_high_trait/nacl_delta data/traits/environment/nacl_delta_high.yaml nacl_delta_high_extreme_euryhaline FRAGMENTED_GRAPH WARN components=6 of 14 node(s) (sizes: 3, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/nacl_delta_low.yaml nacl_delta_low_stenohaline INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='osmotic_upshift' label='osmotic upshift' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_delta_mid1_trait/nacl_delta data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='k_import' label='potassium import' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_mid1_trait/nacl_delta data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_mid1_trait/nacl_delta @@ -232,6 +287,7 @@ data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNRE data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='ectoine' label='ectoine' type=CHEMICAL — in an island with no path to nacl_delta_mid1_trait/nacl_delta data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='c_di_amp' label='cyclic di-AMP' type=CHEMICAL — in an island with no path to nacl_delta_mid1_trait/nacl_delta data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth UNREACHABLE_FROM_TRAIT WARN node_id='organic_osmolyte_influx_biosynthesis' label='compatible organic osmolyte influx and biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_mid1_trait/nacl_delta +data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/environment/nacl_delta_mid1.yaml nacl_delta_mid1_modest_breadth FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 8, 3) — one record, several unrelated mechanisms data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cyclic_di_amp' label='cyclic di-AMP' type=CHEMICAL — in an island with no path to nacl_delta_mid2_trait/nacl_delta data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='potassium_uptake_systems' label='potassium uptake systems' type=GENE_OR_PROTEIN — in an island with no path to nacl_delta_mid2_trait/nacl_delta @@ -243,6 +299,8 @@ data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREA data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='eps_matrix' label='exopolysaccharide matrix' type=CELLULAR_LOCALIZATION — in an island with no path to nacl_delta_mid2_trait/nacl_delta data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to nacl_delta_mid2_trait/nacl_delta data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='water_retention' label='water retention / reduced pericellular Na+ toxicity' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_delta_mid2_trait/nacl_delta +data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_transport' type=BIOLOGICAL_PROCESS here — also MOLECULAR_FUNCTION×3 elsewhere in the corpus +data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth INCONSISTENT_NODE_TYPE WARN node_id='eps_matrix' type=CELLULAR_LOCALIZATION here — also CHEMICAL×1 elsewhere in the corpus data/traits/environment/nacl_delta_mid2.yaml nacl_delta_mid2_broad_breadth FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 3, 3, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='salt_in_strategy' label='salt-in strategy' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_optimum_trait data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_k_accumulation' label='intracellular K+ accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_optimum_trait @@ -252,9 +310,14 @@ data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation U data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='lower_energetic_cost' label='lower energetic cost than de novo synthesis' type=QUALITY — in an island with no path to nacl_optimum_trait data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='na_antiport_activity' label='Na+/H+ antiport activity' type=MOLECULAR_FUNCTION — in an island with no path to nacl_optimum_trait data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_na_homeostasis' label='cytoplasmic Na+ homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_optimum_trait +data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_uptake' type=BIOLOGICAL_PROCESS here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/environment/nacl_optimum.yaml nacl_optimum_balanced_osmoadaptation FRAGMENTED_GRAPH WARN components=5 of 16 node(s) (sizes: 8, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile UNREACHABLE_FROM_TRAIT WARN node_id='acidic_aa_content' label='increased acidic amino-acid content' type=QUALITY — in an island with no path to nacl_optimum_high_trait/nacl_optimum data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile UNREACHABLE_FROM_TRAIT WARN node_id='protein_solubility_high_salt' label='protein solubility in high salt' type=QUALITY — in an island with no path to nacl_optimum_high_trait/nacl_optimum +data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/nacl_optimum_high.yaml nacl_optimum_high_extreme_halophile FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_optimum_low.yaml nacl_optimum_low_non_halophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cyclic_di_amp' label='cyclic di-AMP' type=CHEMICAL — in an island with no path to nacl_optimum_low_trait/nacl_optimum/non_halophile_optimum_definition/halotolerant_organism data/traits/environment/nacl_optimum_low.yaml nacl_optimum_low_non_halophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='k_uptake_systems' label='K+ uptake systems (Trk/Ktr/Kup/KimA)' type=GENE_OR_PROTEIN — in an island with no path to nacl_optimum_low_trait/nacl_optimum/non_halophile_optimum_definition/halotolerant_organism @@ -263,6 +326,7 @@ data/traits/environment/nacl_optimum_low.yaml nacl_optimum_low_non_halophile_set data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='elevated_nacl' label='elevated external NaCl' type=ENVIRONMENTAL_FACTOR — in an island with no path to nacl_optimum_mid1_trait/nacl_optimum data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='glycine_betaine' label='glycine betaine' type=CHEMICAL — in an island with no path to nacl_optimum_mid1_trait/nacl_optimum data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='l_proline' label='L-proline' type=CHEMICAL — in an island with no path to nacl_optimum_mid1_trait/nacl_optimum +data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/nacl_optimum_mid1.yaml nacl_optimum_mid1_slight_halophile FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 7, 3) — one record, several unrelated mechanisms data/traits/environment/nacl_range_high.yaml nacl_range_high_extreme_halophile UNREACHABLE_FROM_TRAIT WARN node_id='acidic_amino_acid_enrichment' label='acidic amino acid enrichment (Asp/Glu)' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_high_trait/nacl_range data/traits/environment/nacl_range_high.yaml nacl_range_high_extreme_halophile UNREACHABLE_FROM_TRAIT WARN node_id='protein_function_high_ionic' label='protein function at very high ionic strength' type=MOLECULAR_FUNCTION — in an island with no path to nacl_range_high_trait/nacl_range @@ -278,6 +342,7 @@ data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile UNREACH data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile UNREACHABLE_FROM_TRAIT WARN node_id='opu_solute_importers' label='OpuA/OpuC compatible-solute importers' type=GENE_OR_PROTEIN — in an island with no path to nacl_range_low_trait/nacl_range data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile UNREACHABLE_FROM_TRAIT WARN node_id='choline_uptake' label='choline uptake' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_low_trait/nacl_range data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile UNREACHABLE_FROM_TRAIT WARN node_id='glycine_betaine_synthesis' label='glycine betaine biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_low_trait/nacl_range +data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile INCONSISTENT_NODE_TYPE WARN node_id='hyperosmotic_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/nacl_range_low.yaml nacl_range_low_non_halophile FRAGMENTED_GRAPH WARN components=5 of 12 node(s) (sizes: 3, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/nacl_range_mid1.yaml nacl_range_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='potassium_accumulation' label='K+ accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_mid1_trait/nacl_range/slight_halophile/moderate_halophile/halotolerant_and_moderate_halophiles data/traits/environment/nacl_range_mid1.yaml nacl_range_mid1_slight_halophile UNREACHABLE_FROM_TRAIT WARN node_id='osmotic_balance' label='osmotic balance / salt adaptation' type=BIOLOGICAL_PROCESS — in an island with no path to nacl_range_mid1_trait/nacl_range/slight_halophile/moderate_halophile/halotolerant_and_moderate_halophiles @@ -286,6 +351,11 @@ data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis UN data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_proton_influx' label='cytoplasmic proton influx' type=BIOLOGICAL_PROCESS — in an island with no path to neutrophilic_trait data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering_capacity' label='cytoplasmic buffering capacity' type=CAPACITY — in an island with no path to neutrophilic_trait data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_ph' label='intracellular pH' type=STATE — in an island with no path to neutrophilic_trait +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cation_proton_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cytoplasmic_buffering_capacity' type=CAPACITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='intracellular_ph' type=STATE here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/neutrophilic.yaml neutrophilic_neutral_ph_homeostasis FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='high_osmolarity' label='high osmolarity' type=ENVIRONMENTAL_FACTOR — in an island with no path to non_halophilic_trait data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='water_flux' label='water flux across cytoplasmic membrane' type=BIOLOGICAL_PROCESS — in an island with no path to non_halophilic_trait @@ -297,23 +367,34 @@ data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='rapid_k_uptake' label='rapid potassium uptake' type=BIOLOGICAL_PROCESS — in an island with no path to non_halophilic_trait data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='glutamate' label='L-glutamate' type=CHEMICAL — in an island with no path to non_halophilic_trait data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to non_halophilic_trait +data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response INCONSISTENT_NODE_TYPE WARN node_id='compatible_solute_uptake' type=GENE_OR_PROTEIN here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/non_halophilic.yaml non_halophilic_salt_stress_response FRAGMENTED_GRAPH WARN components=3 of 12 node(s) (sizes: 5, 5, 2) — one record, several unrelated mechanisms +data/traits/environment/obligately_acidophilic.yaml obligately_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='reversed_membrane_potential' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus +data/traits/environment/obligately_acidophilic.yaml obligately_acidophilic_ph_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='superoxide' label='superoxide' type=CHEMICAL — in an island with no path to obligate_aerobic_trait data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide' label='hydrogen peroxide' type=CHEMICAL — in an island with no path to obligate_aerobic_trait data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='superoxide_dismutase' label='superoxide dismutase activity' type=MOLECULAR_FUNCTION — in an island with no path to obligate_aerobic_trait data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='catalase' label='catalase / catalase-peroxidase activity' type=MOLECULAR_FUNCTION — in an island with no path to obligate_aerobic_trait data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration UNREACHABLE_FROM_TRAIT WARN node_id='fe_s_cluster_enzymes' label='Fe-S cluster enzymes' type=GENE_OR_PROTEIN — in an island with no path to obligate_aerobic_trait +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=BIOLOGICAL_PROCESS here — also PATHWAY×4 elsewhere in the corpus +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='superoxide_dismutase' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×2 elsewhere in the corpus +data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×4 elsewhere in the corpus data/traits/environment/obligately_aerobic.yaml obligate_aerobe_oxygen_respiration FRAGMENTED_GRAPH WARN components=3 of 12 node(s) (sizes: 7, 3, 2) — one record, several unrelated mechanisms data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_ion' label='sodium ion' type=CHEMICAL — in an island with no path to obligately_alkaphilic_trait data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='proton' label='proton' type=CHEMICAL — in an island with no path to obligately_alkaphilic_trait data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='sodium_proton_antiporter' label='Na+/H+ antiporter' type=GENE_OR_PROTEIN — in an island with no path to obligately_alkaphilic_trait data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='secondary_cell_wall_polymers' label='secondary cell wall polymers / S-layer' type=CELLULAR_LOCALIZATION — in an island with no path to obligately_alkaphilic_trait data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='net_negative_surface_charge' label='net negative surface charge' type=QUALITY — in an island with no path to obligately_alkaphilic_trait +data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cation_proton_antiporter' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/obligately_alkaphilic.yaml obligately_alkaphilic_sodium_cycle_homeostasis FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 9, 5) — one record, several unrelated mechanisms data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide' label='hydrogen peroxide' type=CHEMICAL — in an island with no path to obligate_anaerobic_trait data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity UNREACHABLE_FROM_TRAIT WARN node_id='ferrous_iron' label='ferrous iron (Fe(II))' type=CHEMICAL — in an island with no path to obligate_anaerobic_trait data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity UNREACHABLE_FROM_TRAIT WARN node_id='hydroxyl_radical' label='hydroxyl radical' type=CHEMICAL — in an island with no path to obligate_anaerobic_trait data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity UNREACHABLE_FROM_TRAIT WARN node_id='dna_damage' label='DNA damage' type=BIOLOGICAL_PROCESS — in an island with no path to obligate_anaerobic_trait +data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity INCONSISTENT_NODE_TYPE WARN node_id='dna_damage' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/environment/obligately_anaerobic.yaml obligate_anaerobe_oxygen_toxicity FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 10, 4) — one record, several unrelated mechanisms data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporters' label='Na+/H+ antiporters' type=GENE_OR_PROTEIN — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_ph_homeostasis' label='intracellular pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum @@ -324,18 +405,27 @@ data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phe data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible-solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='amino_acid_decarboxylation' label='amino-acid decarboxylation' type=BIOLOGICAL_PROCESS — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to optimum_phenotype_trait/nacl_optimum/ph_optimum/temperature_optimum +data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='hyperosmotic_stress' type=ENVIRONMENTAL_FACTOR here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/optimum_phenotype_with_numerical_limits.yaml optimum_phenotype_descriptor FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 5, 5, 2, 2) — one record, several unrelated mechanisms data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis UNREACHABLE_FROM_TRAIT WARN node_id='catalase' label='catalase' type=GENE_OR_PROTEIN — in an island with no path to oxygen_preference_trait/aerobic_phenotype/anaerobic_phenotype/microaerophilic_phenotype/facultative_phenotype data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_peroxide' label='hydrogen peroxide' type=CHEMICAL — in an island with no path to oxygen_preference_trait/aerobic_phenotype/anaerobic_phenotype/microaerophilic_phenotype/facultative_phenotype +data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis INCONSISTENT_NODE_TYPE WARN node_id='superoxide_dismutase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/oxygen_preference.yaml oxygen_preference_o2_availability_axis FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta.yaml ph_delta_homeostasis_flexibility UNREACHABLE_FROM_TRAIT WARN node_id='membrane_lipid_remodeling' label='saturated membrane fatty acid remodeling' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_trait data/traits/environment/ph_delta.yaml ph_delta_homeostasis_flexibility UNREACHABLE_FROM_TRAIT WARN node_id='proton_permeability' label='membrane proton permeability' type=QUALITY — in an island with no path to ph_delta_trait +data/traits/environment/ph_delta.yaml ph_delta_homeostasis_flexibility INCONSISTENT_NODE_TYPE WARN node_id='oxidative_phosphorylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/ph_delta.yaml ph_delta_homeostasis_flexibility FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ph_homeostasis' label='cytoplasmic pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='respiratory_proton_pumps' label='respiratory proton-pumping enzymes' type=GENE_OR_PROTEIN — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering_capacity' label='cytoplasmic buffering capacity' type=CAPACITY — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='membrane_lipid_porin_changes' label='membrane lipid/porin composition changes' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth UNREACHABLE_FROM_TRAIT WARN node_id='inward_proton_leakage' label='inward proton leakage' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_high_trait/ph_delta/growth_external_ph_5_5_9 +data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth INCONSISTENT_NODE_TYPE WARN node_id='cytoplasmic_buffering_capacity' type=CAPACITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth INCONSISTENT_NODE_TYPE WARN node_id='near_neutral_cytoplasmic_ph' type=QUALITY here — also STATE×1 elsewhere in the corpus data/traits/environment/ph_delta_high.yaml ph_delta_high_euryphilic_breadth FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 7, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_stress' label='external pH stress' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_delta_low_trait/ph_delta data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ph_homeostasis' label='cytoplasmic pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_low_trait/ph_delta @@ -345,6 +435,7 @@ data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHAB data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='electrogenic_na_h_antiport' label='electrogenic Na+/H+ antiport' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_low_trait/ph_delta data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='alkaline_ph_homeostasis' label='alkaline pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_low_trait/ph_delta data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth UNREACHABLE_FROM_TRAIT WARN node_id='f1fo_atpase' label='F1Fo-ATPase' type=GENE_OR_PROTEIN — in an island with no path to ph_delta_low_trait/ph_delta +data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth INCONSISTENT_NODE_TYPE WARN node_id='electrogenic_na_h_antiport' type=BIOLOGICAL_PROCESS here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/ph_delta_low.yaml ph_delta_low_limited_breadth FRAGMENTED_GRAPH WARN components=4 of 11 node(s) (sizes: 4, 3, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='gln_glu_decarboxylation_pathway' label='glutamine/glutamate decarboxylation pathway' type=PATHWAY — in an island with no path to ph_delta_mid1_trait/ph_delta data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_proton' label='intracellular proton (H+)' type=CHEMICAL — in an island with no path to ph_delta_mid1_trait/ph_delta @@ -352,6 +443,8 @@ data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREAC data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='ammonia' label='ammonia' type=CHEMICAL — in an island with no path to ph_delta_mid1_trait/ph_delta data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='membrane_saturated_fatty_acids' label='membrane saturated fatty acid content' type=QUALITY — in an island with no path to ph_delta_mid1_trait/ph_delta data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='proton_diffusion_across_membrane' label='proton diffusion across membrane' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid1_trait/ph_delta +data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth INCONSISTENT_NODE_TYPE WARN node_id='oxidative_phosphorylation' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/ph_delta_mid1.yaml ph_delta_mid1_moderate_breadth FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 7, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_stress' label='external pH stress' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_delta_mid2_trait/ph_delta data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='pmf_component_balance' label='PMF component balance' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid2_trait/ph_delta @@ -365,6 +458,7 @@ data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHAB data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_proton' label='intracellular H+' type=CHEMICAL — in an island with no path to ph_delta_mid2_trait/ph_delta data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffers' label='cytoplasmic buffering molecules' type=CHEMICAL — in an island with no path to ph_delta_mid2_trait/ph_delta data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ph_buffering' label='cytoplasmic pH buffering' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid2_trait/ph_delta +data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth INCONSISTENT_NODE_TYPE WARN node_id='glutamate_decarboxylase_system' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/environment/ph_delta_mid2.yaml ph_delta_mid2_broad_breadth FRAGMENTED_GRAPH WARN components=7 of 15 node(s) (sizes: 3, 2, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='external_alkaline_ph' label='external alkaline pH' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_delta_mid3_trait/ph_delta data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiport' label='electrogenic Na+/H+ antiport' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid3_trait/ph_delta @@ -378,6 +472,9 @@ data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABL data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='aa_decarboxylation' label='amino-acid decarboxylation pathways' type=PATHWAY — in an island with no path to ph_delta_mid3_trait/ph_delta data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='membrane_lipid_remodeling' label='membrane lipid composition shifts' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_mid3_trait/ph_delta data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth UNREACHABLE_FROM_TRAIT WARN node_id='proton_permeability' label='membrane proton permeability' type=QUALITY — in an island with no path to ph_delta_mid3_trait/ph_delta +data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiport' type=BIOLOGICAL_PROCESS here — also MOLECULAR_FUNCTION×2 elsewhere in the corpus +data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth INCONSISTENT_NODE_TYPE WARN node_id='phosphate_buffering' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/ph_delta_mid3.yaml ph_delta_mid3_wide_breadth FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 3, 3, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_stress' label='external pH stress' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_delta_very_low_trait/ph_delta data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='pmf_partitioning' label='PMF partitioning (delta-pH / delta-psi)' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_very_low_trait/ph_delta @@ -389,9 +486,17 @@ data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNRE data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='acid_stress_survival' label='acid stress survival' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_very_low_trait/ph_delta data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='glutamate_decarboxylase_system' label='glutamate decarboxylase GadB + GABA/glutamate antiporter' type=PATHWAY — in an island with no path to ph_delta_very_low_trait/ph_delta data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_proton_consumption' label='cytoplasmic proton consumption' type=BIOLOGICAL_PROCESS — in an island with no path to ph_delta_very_low_trait/ph_delta +data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic INCONSISTENT_NODE_TYPE WARN node_id='glutamate_decarboxylase_system' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/environment/ph_delta_very_low.yaml ph_delta_very_low_stenotopic FRAGMENTED_GRAPH WARN components=6 of 13 node(s) (sizes: 3, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/ph_growth_preference.yaml ph_growth_preference_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/environment/ph_growth_preference.yaml ph_growth_preference_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiport' type=MOLECULAR_FUNCTION here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering_capacity' label='cytoplasmic buffering capacity' type=CAPACITY — in an island with no path to ph_optimum_trait data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis UNREACHABLE_FROM_TRAIT WARN node_id='internal_ph' label='internal pH' type=STATE — in an island with no path to ph_optimum_trait +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cytoplasm_acidification' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='cytoplasmic_buffering_capacity' type=CAPACITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='internal_ph' type=STATE here — also QUALITY×1 elsewhere in the corpus data/traits/environment/ph_optimum.yaml ph_optimum_balanced_homeostasis FRAGMENTED_GRAPH WARN components=2 of 12 node(s) (sizes: 10, 2) — one record, several unrelated mechanisms data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cpa_nha_antiporters' label='CPA/Nha family Na+/H+ antiporters' type=GENE_OR_PROTEIN — in an island with no path to ph_optimum_high_trait/ph_optimum data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_na' label='intracellular Na+ concentration' type=CHEMICAL — in an island with no path to ph_optimum_high_trait/ph_optimum @@ -402,6 +507,7 @@ data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoin data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='acidic_membrane_polymers' label='acidic plasma membrane polymers' type=CHEMICAL — in an island with no path to ph_optimum_high_trait/ph_optimum data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='organic_acid_secretion' label='organic acid secretion' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_high_trait/ph_optimum data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='ph_balance' label='pH balance' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_high_trait/ph_optimum +data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/ph_optimum_high.yaml ph_optimum_high_alkaliphile_setpoint FRAGMENTED_GRAPH WARN components=5 of 15 node(s) (sizes: 6, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='low_external_ph' label='low external pH' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_optimum_low_trait/ph_optimum data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='transmembrane_ph_gradient' label='large transmembrane pH gradient' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_low_trait/ph_optimum @@ -411,7 +517,9 @@ data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint U data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_proton_load' label='cytoplasmic proton load' type=STATE — in an island with no path to ph_optimum_low_trait/ph_optimum data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='proton_impermeable_membrane' label='rigid proton-impermeable membrane' type=CELLULAR_LOCALIZATION — in an island with no path to ph_optimum_low_trait/ph_optimum data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='passive_proton_permeability' label='passive proton permeability' type=QUALITY — in an island with no path to ph_optimum_low_trait/ph_optimum +data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='inside_positive_membrane_potential' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/environment/ph_optimum_low.yaml ph_optimum_low_acidophile_setpoint FRAGMENTED_GRAPH WARN components=5 of 12 node(s) (sizes: 4, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/ph_optimum_mid1.yaml ph_optimum_mid1_neutrophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=PATHWAY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering_capacity' label='cytoplasmic buffering capacity' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_mid2_trait/ph_optimum data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_ph_homeostasis' label='intracellular pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_mid2_trait/ph_optimum data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='na_h_antiporters' label='Na+/H+ antiporters' type=GENE_OR_PROTEIN — in an island with no path to ph_optimum_mid2_trait/ph_optimum @@ -420,6 +528,9 @@ data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_s data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='metabolite_decarboxylation' label='metabolite decarboxylation pathways' type=PATHWAY — in an island with no path to ph_optimum_mid2_trait/ph_optimum data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to ph_optimum_mid2_trait/ph_optimum data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='f0f1_atp_synthase' label='F0F1-ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to ph_optimum_mid2_trait/ph_optimum +data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='cytoplasmic_buffering_capacity' type=BIOLOGICAL_PROCESS here — also CAPACITY×3 elsewhere in the corpus +data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='respiratory_proton_pumping' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus +data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/environment/ph_optimum_mid2.yaml ph_optimum_mid2_alkaline_tolerant_setpoint FRAGMENTED_GRAPH WARN components=3 of 12 node(s) (sizes: 5, 4, 3) — one record, several unrelated mechanisms data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='f0f1_atpase' label='F0F1-ATPase / ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthesis_from_pmf' label='ATP synthesis from proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta @@ -430,9 +541,17 @@ data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_num data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_proton' label='intracellular H+' type=CHEMICAL — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='phosphate_buffering' label='cytoplasmic buffering by phosphate pools' type=BIOLOGICAL_PROCESS — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='internal_ph' label='internal pH' type=STATE — in an island with no path to ph_phenotype_trait/ph_optimum/ph_range/ph_delta +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='na_h_antiporter' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×6 elsewhere in the corpus +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='aa_decarboxylase_antiporter' type=PATHWAY here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='phosphate_buffering' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='internal_ph' type=STATE here — also QUALITY×1 elsewhere in the corpus data/traits/environment/ph_phenotype_with_numerical_limits.yaml ph_phenotype_numerical_axis FRAGMENTED_GRAPH WARN components=5 of 15 node(s) (sizes: 6, 3, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/ph_range.yaml ph_range_bounded_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='membrane_potential' type=CHEMICAL here — also BIOLOGICAL_PROCESS×1, QUALITY×1, STATE×1 elsewhere in the corpus +data/traits/environment/ph_range.yaml ph_range_bounded_homeostasis INCONSISTENT_NODE_TYPE WARN node_id='amino_acid_decarboxylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/ph_range_high.yaml ph_range_high_extreme_alkaliphile UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_high' label='external pH > 10.3' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_range_high_trait/ph_range data/traits/environment/ph_range_high.yaml ph_range_high_extreme_alkaliphile UNREACHABLE_FROM_TRAIT WARN node_id='carbonate_speciation' label='carbonate (CO3 2-) speciation' type=CHEMICAL — in an island with no path to ph_range_high_trait/ph_range +data/traits/environment/ph_range_high.yaml ph_range_high_extreme_alkaliphile INCONSISTENT_NODE_TYPE WARN node_id='membrane_potential' type=QUALITY here — also BIOLOGICAL_PROCESS×1, CHEMICAL×1, STATE×1 elsewhere in the corpus data/traits/environment/ph_range_high.yaml ph_range_high_extreme_alkaliphile FRAGMENTED_GRAPH WARN components=2 of 12 node(s) (sizes: 10, 2) — one record, several unrelated mechanisms data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_low_trait/ph_range data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthase_atp_formation' label='ATP synthase-mediated ATP formation' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_low_trait/ph_range @@ -442,7 +561,12 @@ data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHA data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='weak_acid_influx' label='weak organic acid influx into cell' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_low_trait/ph_range data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='weak_acid_dissociation' label='intracellular dissociation of weak organic acids' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_low_trait/ph_range data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range UNREACHABLE_FROM_TRAIT WARN node_id='internal_ph' label='internal (cytoplasmic) pH' type=QUALITY — in an island with no path to ph_range_low_trait/ph_range +data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range INCONSISTENT_NODE_TYPE WARN node_id='membrane_proton_permeability' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range INCONSISTENT_NODE_TYPE WARN node_id='internal_ph' type=QUALITY here — also STATE×2 elsewhere in the corpus data/traits/environment/ph_range_low.yaml ph_range_low_acidophile_range FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 5, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/ph_range_mid1.yaml ph_range_mid1_neutrophile_range INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_range_mid1.yaml ph_range_mid1_neutrophile_range INCONSISTENT_NODE_TYPE WARN node_id='respiratory_proton_pumping' type=GENE_OR_PROTEIN here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='external_ph_7_8' label='external pH 7-8' type=ENVIRONMENTAL_FACTOR — in an island with no path to ph_range_mid2_trait/ph_range data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ph_homeostasis' label='cytoplasmic pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid2_trait/ph_range data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_buffering' label='cytoplasmic buffering' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid2_trait/ph_range @@ -455,12 +579,15 @@ data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthesis' label='ATP synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid2_trait/ph_range data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='proton_ion_antiporters' label='proton:ion antiporters' type=GENE_OR_PROTEIN — in an island with no path to ph_range_mid2_trait/ph_range data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='membrane_potential' label='membrane potential (Δψ)' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid2_trait/ph_range +data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus +data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance INCONSISTENT_NODE_TYPE WARN node_id='membrane_potential' type=BIOLOGICAL_PROCESS here — also CHEMICAL×1, QUALITY×1, STATE×1 elsewhere in the corpus data/traits/environment/ph_range_mid2.yaml ph_range_mid2_mild_alkaline_tolerance FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 3, 3, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='mrp_antiporter' label='Mrp Na+/H+ antiporter complex' type=GENE_OR_PROTEIN — in an island with no path to ph_range_mid3_trait/ph_range data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_ph_homeostasis' label='intracellular pH homeostasis' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid3_trait/ph_range data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='nahplus_antiport_activity' label='Na+/H+ antiport activity' type=MOLECULAR_FUNCTION — in an island with no path to ph_range_mid3_trait/ph_range data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasm_acidification' label='cytoplasm acidification during alkaline growth' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_mid3_trait/ph_range data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range UNREACHABLE_FROM_TRAIT WARN node_id='cardiolipin_membrane' label='cardiolipin-rich negatively charged membrane' type=CELLULAR_LOCALIZATION — in an island with no path to ph_range_mid3_trait/ph_range +data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range INCONSISTENT_NODE_TYPE WARN node_id='cytoplasm_acidification' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus data/traits/environment/ph_range_mid3.yaml ph_range_mid3_alkaliphile_range FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='potassium_influx' label='potassium influx / K+ transport' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_very_low_trait/ph_range data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='reversed_membrane_potential' label='inside-positive (reversed) membrane potential' type=STATE — in an island with no path to ph_range_very_low_trait/ph_range @@ -470,7 +597,10 @@ data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidoph data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='weak_organic_acids' label='protonated weak organic acids' type=CHEMICAL — in an island with no path to ph_range_very_low_trait/ph_range data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasm' label='cytoplasm' type=CELLULAR_LOCALIZATION — in an island with no path to ph_range_very_low_trait/ph_range data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_acidification' label='cytoplasmic acidification' type=BIOLOGICAL_PROCESS — in an island with no path to ph_range_very_low_trait/ph_range +data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile INCONSISTENT_NODE_TYPE WARN node_id='reversed_membrane_potential' type=STATE here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile INCONSISTENT_NODE_TYPE WARN node_id='near_neutral_cytoplasmic_ph' type=STATE here — also QUALITY×1 elsewhere in the corpus data/traits/environment/ph_range_very_low.yaml ph_range_very_low_extreme_acidophile FRAGMENTED_GRAPH WARN components=4 of 11 node(s) (sizes: 3, 3, 3, 2) — one record, several unrelated mechanisms +data/traits/environment/piezotolerant.yaml piezotolerance_pressure_range INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity_maintenance' label='membrane fluidity maintenance under high pressure' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_delta_trait data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='unsaturated_fatty_acid_production' label='unsaturated fatty acid production' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_delta_trait data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solutes' label='intracellular osmolytes / compatible solutes' type=CHEMICAL — in an island with no path to pressure_delta_trait @@ -478,27 +608,34 @@ data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UN data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='nuo_complex_i' label='nuo NADH dehydrogenase I complex' type=GENE_OR_PROTEIN — in an island with no path to pressure_delta_trait data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor UNREACHABLE_FROM_TRAIT WARN node_id='high_pressure_energy_conservation' label='high-pressure respiratory energy conservation' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_delta_trait data/traits/environment/pressure_delta.yaml pressure_delta_breadth_descriptor FRAGMENTED_GRAPH WARN components=4 of 12 node(s) (sizes: 6, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/pressure_optimum.yaml pressure_optimum_balanced_adaptation INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/environment/pressure_optimum.yaml pressure_optimum_balanced_adaptation FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 5, 4) — one record, several unrelated mechanisms data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span UNREACHABLE_FROM_TRAIT WARN node_id='tmao' label='trimethylamine N-oxide (TMAO)' type=CHEMICAL — in an island with no path to pressure_range_trait data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span UNREACHABLE_FROM_TRAIT WARN node_id='protein_stabilization' label='protein stabilization via preferential hydration' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_range_trait data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to pressure_range_trait +data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span INCONSISTENT_NODE_TYPE WARN node_id='pufa_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/environment/pressure_range.yaml pressure_range_growth_bounded_span FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 6, 3) — one record, several unrelated mechanisms data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solutes' label='compatible solutes' type=CHEMICAL — in an island with no path to psychrophilic_trait data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='trehalose' label='trehalose' type=CHEMICAL — in an island with no path to psychrophilic_trait data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='protein_membrane_stability' label='protein and membrane stability' type=QUALITY — in an island with no path to psychrophilic_trait +data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/psychrophilic.yaml psychrophilic_cold_adaptation FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 10, 3) — one record, several unrelated mechanisms data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='compatible_solute_accumulation' label='compatible solute accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to psychrotolerant_trait data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='protein_membrane_stability' label='protein and membrane stability under cold stress' type=QUALITY — in an island with no path to psychrotolerant_trait data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='extracellular_polymeric_substances' label='extracellular polymeric substances (EPS)' type=CHEMICAL — in an island with no path to psychrotolerant_trait data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='freeze_thaw_cryoprotection' label='cryoprotection against freeze-thaw cycles' type=BIOLOGICAL_PROCESS — in an island with no path to psychrotolerant_trait +data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=QUALITY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus data/traits/environment/psychrotolerant.yaml psychrotolerant_facultative_cold_adaptation FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='intracellular_osmotic_balance' label='intracellular osmotic balance across salinity' type=BIOLOGICAL_PROCESS — in an island with no path to salinity_phenotype_trait/nacl_optimum/nacl_range/nacl_delta data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='salt_out_compatible_solute_strategy' label='compatible-solute (salt-out) strategy' type=PATHWAY — in an island with no path to salinity_phenotype_trait/nacl_optimum/nacl_range/nacl_delta data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='salt_in_strategy' label='salt-in strategy' type=PATHWAY — in an island with no path to salinity_phenotype_trait/nacl_optimum/nacl_range/nacl_delta data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='glycine_betaine' label='glycine betaine' type=CHEMICAL — in an island with no path to salinity_phenotype_trait/nacl_optimum/nacl_range/nacl_delta +data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='salt_in_strategy' type=PATHWAY here — also BIOLOGICAL_PROCESS×7 elsewhere in the corpus data/traits/environment/salinity_phenotype_with_numerical_limits.yaml salinity_phenotype_numerical_axis FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 9, 4) — one record, several unrelated mechanisms data/traits/environment/slightly_halophilic.yaml slight_halophile_low_salt_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='ion_homeostasis' label='ion homeostasis during salt stress' type=BIOLOGICAL_PROCESS — in an island with no path to slightly_halophilic_trait data/traits/environment/slightly_halophilic.yaml slight_halophile_low_salt_osmoadaptation UNREACHABLE_FROM_TRAIT WARN node_id='na_k_transcription' label='Na+/K+ transcriptional induction' type=BIOLOGICAL_PROCESS — in an island with no path to slightly_halophilic_trait +data/traits/environment/slightly_halophilic.yaml slight_halophile_low_salt_osmoadaptation INCONSISTENT_NODE_TYPE WARN node_id='ectoine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/environment/slightly_halophilic.yaml slight_halophile_low_salt_osmoadaptation FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 8, 2) — one record, several unrelated mechanisms data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='c_di_amp' label='cyclic di-AMP' type=CHEMICAL — in an island with no path to stenohaline_trait data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='k_import_systems' label='K+ import systems' type=GENE_OR_PROTEIN — in an island with no path to stenohaline_trait @@ -512,6 +649,8 @@ data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance U data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='aquaporin_water_channel' label='aquaporin water-channel activity' type=MOLECULAR_FUNCTION — in an island with no path to stenohaline_trait data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='facilitated_water_diffusion' label='facilitated water diffusion' type=BIOLOGICAL_PROCESS — in an island with no path to stenohaline_trait data/traits/environment/stenohaline.yaml stenohaline_narrow_salinity_tolerance FRAGMENTED_GRAPH WARN components=6 of 17 node(s) (sizes: 6, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/strictly_anaerobic.yaml strict_anaerobe_oxygen_sensitivity INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/temperature_delta.yaml temperature_delta_thermal_flexibility INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='decreased_growth_temperature' label='decreased growth temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_delta_high_trait/temperature_delta data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='unsaturated_fatty_acid_biosynthesis' label='unsaturated fatty acid biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_high_trait/temperature_delta data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='homoviscous_adaptation' label='homoviscous adaptation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_high_trait/temperature_delta @@ -524,14 +663,19 @@ data/traits/environment/temperature_delta_high.yaml temperature_delta_high_euryt data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='increased_fatty_acid_diversity' label='increased short-/branched-/unsaturated fatty acids' type=CHEMICAL — in an island with no path to temperature_delta_high_trait/temperature_delta data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='thermostable_enzyme' label='hyperthermophilic enzyme thermostability' type=QUALITY — in an island with no path to temperature_delta_high_trait/temperature_delta data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal UNREACHABLE_FROM_TRAIT WARN node_id='irreversible_protein_inactivation' label='irreversible inactivation at high temperatures' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_high_trait/temperature_delta +data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity_homeostasis' type=STATE here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_delta_high.yaml temperature_delta_high_eurythermal FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 3, 3, 3, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/environment/temperature_delta_low.yaml temperature_delta_low_limited_breadth INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=BIOLOGICAL_PROCESS here — also QUALITY×3 elsewhere in the corpus data/traits/environment/temperature_delta_mid1.yaml temperature_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='membrane_physical_state_change' label='membrane physical-state change' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_mid1_trait/temperature_delta data/traits/environment/temperature_delta_mid1.yaml temperature_delta_mid1_moderate_breadth UNREACHABLE_FROM_TRAIT WARN node_id='two_component_cold_signaling' label='two-component cold signaling' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_mid1_trait/temperature_delta +data/traits/environment/temperature_delta_mid1.yaml temperature_delta_mid1_moderate_breadth INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_delta_mid1.yaml temperature_delta_mid1_moderate_breadth FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='rpos_sigma_factor' label='RpoS sigma factor (sigma-S)' type=GENE_OR_PROTEIN — in an island with no path to temperature_delta_mid2_trait/temperature_delta data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='otsab_operon' label='otsAB trehalose biosynthesis operon' type=PATHWAY — in an island with no path to temperature_delta_mid2_trait/temperature_delta data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='trehalose' label='trehalose' type=CHEMICAL — in an island with no path to temperature_delta_mid2_trait/temperature_delta data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth UNREACHABLE_FROM_TRAIT WARN node_id='cold_tolerance' label='cold / cold-shock tolerance' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_mid2_trait/temperature_delta +data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=BIOLOGICAL_PROCESS here — also QUALITY×24 elsewhere in the corpus data/traits/environment/temperature_delta_mid2.yaml temperature_delta_mid2_broad_breadth FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 6, 4) — one record, several unrelated mechanisms data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='unsaturated_fatty_acid_content' label='unsaturated fatty acid content' type=CHEMICAL — in an island with no path to temperature_delta_very_low_trait/temperature_delta data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to temperature_delta_very_low_trait/temperature_delta @@ -539,9 +683,12 @@ data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_l data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='cspa_protein' label='CspA cold-shock protein' type=GENE_OR_PROTEIN — in an island with no path to temperature_delta_very_low_trait/temperature_delta data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='csda_helicase' label='CsdA DEAD-box RNA helicase' type=GENE_OR_PROTEIN — in an island with no path to temperature_delta_very_low_trait/temperature_delta data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal UNREACHABLE_FROM_TRAIT WARN node_id='translation_under_cold' label='translation under cold shock' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_delta_very_low_trait/temperature_delta +data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_delta_very_low.yaml temperature_delta_very_low_stenothermal FRAGMENTED_GRAPH WARN components=4 of 9 node(s) (sizes: 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='arrhenius_plot_deviation' label='Arrhenius plot deviation from linearity' type=EXPERIMENTAL_FACTOR — in an island with no path to temperature_optimum_trait data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='stress_growth_regime' label='stress / non-physiological growth regime' type=STATE — in an island with no path to temperature_optimum_trait +data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/environment/temperature_optimum.yaml temperature_optimum_balanced_adaptation FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 7, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='reverse_gyrase' label='reverse gyrase' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_high_trait/temperature_optimum data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='positive_dna_supercoiling' label='positive DNA supercoiling' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_high_trait/temperature_optimum @@ -554,6 +701,8 @@ data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_t data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='denatured_protein_refolding' label='refolding of denatured proteins' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_high_trait/temperature_optimum data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='membrane_lipid_composition' label='altered membrane lipid composition' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_high_trait/temperature_optimum data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='membrane_thermostability' label='cytoplasmic membrane thermostability' type=QUALITY — in an island with no path to temperature_optimum_high_trait/temperature_optimum +data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='positive_dna_supercoiling' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='membrane_lipid_composition' type=BIOLOGICAL_PROCESS here — also CELLULAR_LOCALIZATION×2, QUALITY×1 elsewhere in the corpus data/traits/environment/temperature_optimum_high.yaml temperature_optimum_high_thermophile_setpoint FRAGMENTED_GRAPH WARN components=6 of 16 node(s) (sizes: 5, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='low_temperature' label='low temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_optimum_low_trait/temperature_optimum data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to temperature_optimum_low_trait/temperature_optimum @@ -565,9 +714,15 @@ data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psy data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='ice_crystal_growth' label='ice crystal growth' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_low_trait/temperature_optimum data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='oxidative_stress' label='oxidative stress' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_low_trait/temperature_optimum data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='pufa_biosynthesis' label='PUFA biosynthesis' type=PATHWAY — in an island with no path to temperature_optimum_low_trait/temperature_optimum +data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint INCONSISTENT_NODE_TYPE WARN node_id='pufa_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_optimum_low.yaml temperature_optimum_low_psychrotolerant_setpoint FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 5, 4, 3, 2) — one record, several unrelated mechanisms +data/traits/environment/temperature_optimum_mid1.yaml temperature_optimum_mid1_lower_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_decrease' label='temperature decrease' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_optimum_mid2_trait/temperature_optimum data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_rigidification' label='membrane rigidification' type=QUALITY — in an island with no path to temperature_optimum_mid2_trait/temperature_optimum +data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=QUALITY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_optimum_mid2.yaml temperature_optimum_mid2_mesophile FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 7, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='decreased_temperature' label='decreased temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_bilayer' label='membrane bilayer' type=CELLULAR_LOCALIZATION — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum @@ -577,6 +732,7 @@ data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_u data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='chaperone_network' label='molecular chaperone network' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='proteostasis' label='proteostasis' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_mid3_trait/temperature_optimum +data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_optimum_mid3.yaml temperature_optimum_mid3_upper_mesophile FRAGMENTED_GRAPH WARN components=5 of 12 node(s) (sizes: 4, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_downshift' label='temperature downshift' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='unsaturated_fatty_acid_proportion' label='unsaturated fatty acid proportion' type=CHEMICAL — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum @@ -589,6 +745,8 @@ data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_w data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='dnak_chaperone' label='DnaK chaperone' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='rpoh_sigma_factor' label='RpoH (sigma-32) heat-shock sigma factor' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='ftsh_protease' label='FtsH protease' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_mid4_trait/temperature_optimum +data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='unsaturated_fatty_acid_proportion' type=CHEMICAL here — also QUALITY×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity_homeostasis' type=BIOLOGICAL_PROCESS here — also STATE×1 elsewhere in the corpus data/traits/environment/temperature_optimum_mid4.yaml temperature_optimum_mid4_warm_mesophile FRAGMENTED_GRAPH WARN components=4 of 15 node(s) (sizes: 4, 4, 4, 3) — one record, several unrelated mechanisms data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='cold_shock_proteins' label='cold shock proteins / RNA chaperones' type=GENE_OR_PROTEIN — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='translation_low_temperature' label='translation at low temperature' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum @@ -600,15 +758,23 @@ data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_ve data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='thermal_hysteresis' label='thermal hysteresis / lowered freezing point' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='enzyme_structural_flexibility' label='increased enzyme structural flexibility' type=QUALITY — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='catalytic_activity_low_temperature' label='catalytic activity at low temperature' type=MOLECULAR_FUNCTION — in an island with no path to temperature_optimum_very_low_trait/temperature_optimum +data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint INCONSISTENT_NODE_TYPE WARN node_id='fatty_acid_desaturase' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×2 elsewhere in the corpus data/traits/environment/temperature_optimum_very_low.yaml temperature_optimum_very_low_psychrophile_setpoint FRAGMENTED_GRAPH WARN components=6 of 17 node(s) (sizes: 7, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='membrane_cooling_rigidification' label='membrane rigidification during cooling' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_phenotype_trait/temperature_optimum/temperature_range/temperature_delta/growth_at_low_temperature data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='desk_desr_signaling' label='DesK/DesR two-component signaling' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_phenotype_trait/temperature_optimum/temperature_range/temperature_delta/growth_at_low_temperature data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='cold_adapted_enzymes' label='cold-adapted enzymes' type=GENE_OR_PROTEIN — in an island with no path to temperature_phenotype_trait/temperature_optimum/temperature_range/temperature_delta/growth_at_low_temperature data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis UNREACHABLE_FROM_TRAIT WARN node_id='high_catalytic_efficiency_low_temp' label='high catalytic efficiency at low temperature' type=MOLECULAR_FUNCTION — in an island with no path to temperature_phenotype_trait/temperature_optimum/temperature_range/temperature_delta/growth_at_low_temperature +data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_phenotype_with_numerical_limits.yaml temperature_phenotype_numerical_axis FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 5, 4, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology UNREACHABLE_FROM_TRAIT WARN node_id='environmental_temperature' label='environmental temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_preference_trait data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology UNREACHABLE_FROM_TRAIT WARN node_id='growth_rate' label='microbial growth rate' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_preference_trait +data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology INCONSISTENT_NODE_TYPE WARN node_id='fatty_acid_desaturase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/temperature_preference.yaml temperature_preference_growth_physiology FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms +data/traits/environment/temperature_range.yaml temperature_range_bounded_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_range.yaml temperature_range_bounded_adaptation INCONSISTENT_NODE_TYPE WARN node_id='chaperone_systems' type=BIOLOGICAL_PROCESS here — also GENE_OR_PROTEIN×1 elsewhere in the corpus +data/traits/environment/temperature_range_high.yaml temperature_range_high_thermophile INCONSISTENT_NODE_TYPE WARN node_id='positive_dna_supercoiling' type=QUALITY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='low_temperature' label='low temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_low_trait/temperature_range data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fluidity' label='membrane fluidity' type=QUALITY — in an island with no path to temperature_range_low_trait/temperature_range data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='fatty_acid_desaturase_activity' label='fatty acid desaturase activity' type=MOLECULAR_FUNCTION — in an island with no path to temperature_range_low_trait/temperature_range @@ -619,6 +785,8 @@ data/traits/environment/temperature_range_low.yaml temperature_range_low_psychro data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='cryoprotection' label='cryoprotection' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_low_trait/temperature_range data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='molecular_chaperones' label='GroEL/DnaK molecular chaperones' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_low_trait/temperature_range data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant UNREACHABLE_FROM_TRAIT WARN node_id='protein_misfolding' label='protein misfolding' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_low_trait/temperature_range +data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant INCONSISTENT_NODE_TYPE WARN node_id='unsaturated_fatty_acid_proportion' type=QUALITY here — also CHEMICAL×1 elsewhere in the corpus data/traits/environment/temperature_range_low.yaml temperature_range_low_psychrotolerant FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 4, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_decrease' label='temperature decrease' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid1_trait/temperature_range data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_rigidification' label='membrane rigidification/thickening' type=QUALITY — in an island with no path to temperature_range_mid1_trait/temperature_range @@ -630,12 +798,15 @@ data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='shine_dalgarno_exposure' label='Shine-Dalgarno sequence exposure' type=MOLECULAR_FUNCTION — in an island with no path to temperature_range_mid1_trait/temperature_range data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_shift' label='temperature shift' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid1_trait/temperature_range data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='dna_supercoiling' label='DNA supercoiling' type=QUALITY — in an island with no path to temperature_range_mid1_trait/temperature_range +data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=QUALITY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_range_mid1.yaml temperature_range_mid1_lower_mesophile FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 4, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='elevated_temperature' label='elevated temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid2_trait/temperature_range data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='rna_thermometer' label='RNA thermometer 5′-UTR structure' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_mid2_trait/temperature_range data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_shift' label='temperature shift / heat shock' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid2_trait/temperature_range data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='heat_shock_proteins' label='heat-shock proteins / chaperones' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_mid2_trait/temperature_range data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='protein_denaturation' label='protein denaturation / aggregation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid2_trait/temperature_range +data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_range_mid2.yaml temperature_range_mid2_baseline_mesophile FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 8, 3, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_order' label='membrane order / fluidity state' type=QUALITY — in an island with no path to temperature_range_mid3_trait/temperature_range data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='desk_kinase_state' label='DesK kinase-dominant state' type=STATE — in an island with no path to temperature_range_mid3_trait/temperature_range @@ -648,6 +819,7 @@ data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='temperature_decrease' label='temperature decrease' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_mid3_trait/temperature_range data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='homeoviscous_adaptation' label='homeoviscous adaptation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid3_trait/temperature_range data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='liquid_crystalline_membrane' label='liquid-crystalline membrane state' type=STATE — in an island with no path to temperature_range_mid3_trait/temperature_range +data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_rigidification' type=BIOLOGICAL_PROCESS here — also QUALITY×3 elsewhere in the corpus data/traits/environment/temperature_range_mid3.yaml temperature_range_mid3_upper_mesophile FRAGMENTED_GRAPH WARN components=6 of 14 node(s) (sizes: 3, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='fab_branchpoint_valve' label='FabI/FabB fatty-acid branchpoint valve' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid4_trait/temperature_range data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='homeoviscous_adaptation' label='homeoviscous adaptation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid4_trait/temperature_range @@ -663,6 +835,9 @@ data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_ data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='rpoh_regulon' label='sigma-32 (RpoH) heat-shock regulon' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid4_trait/temperature_range data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='chaperone_systems' label='DnaK/DnaJ/GrpE and GroES/GroEL chaperone systems' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_mid4_trait/temperature_range data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile UNREACHABLE_FROM_TRAIT WARN node_id='heat_stress_protection' label='protection against heat stress' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_mid4_trait/temperature_range +data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_lipid_composition' type=QUALITY here — also BIOLOGICAL_PROCESS×1, CELLULAR_LOCALIZATION×2 elsewhere in the corpus +data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile INCONSISTENT_NODE_TYPE WARN node_id='chaperone_systems' type=GENE_OR_PROTEIN here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_range_mid4.yaml temperature_range_mid4_warm_mesophile FRAGMENTED_GRAPH WARN components=6 of 17 node(s) (sizes: 5, 3, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='low_temperature' label='low temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to temperature_range_very_low_trait/temperature_range data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='membrane_fatty_acid_desaturation' label='membrane fatty-acid desaturation' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_very_low_trait/temperature_range @@ -676,6 +851,7 @@ data/traits/environment/temperature_range_very_low.yaml temperature_range_very_l data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='protein_membrane_stabilization' label='protein and membrane stabilization' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_very_low_trait/temperature_range data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='ice_binding_proteins' label='ice-binding/antifreeze proteins' type=GENE_OR_PROTEIN — in an island with no path to temperature_range_very_low_trait/temperature_range data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile UNREACHABLE_FROM_TRAIT WARN node_id='ice_crystal_growth' label='ice-crystal growth/recrystallization' type=BIOLOGICAL_PROCESS — in an island with no path to temperature_range_very_low_trait/temperature_range +data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile INCONSISTENT_NODE_TYPE WARN node_id='membrane_fluidity' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/environment/temperature_range_very_low.yaml temperature_range_very_low_psychrophile FRAGMENTED_GRAPH WARN components=7 of 15 node(s) (sizes: 3, 2, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='reverse_gyrase' label='reverse gyrase' type=GENE_OR_PROTEIN — in an island with no path to thermophilic_trait data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='positive_dna_supercoiling' label='positive DNA supercoiling' type=BIOLOGICAL_PROCESS — in an island with no path to thermophilic_trait @@ -685,6 +861,9 @@ data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHAB data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='denatured_proteins' label='denatured proteins' type=GENE_OR_PROTEIN — in an island with no path to thermophilic_trait data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='cyclopentane_ring_number' label='tetraether lipid cyclopentane ring number' type=QUALITY — in an island with no path to thermophilic_trait data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_rigidity' label='membrane rigidity' type=QUALITY — in an island with no path to thermophilic_trait +data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_lipid_composition' type=CELLULAR_LOCALIZATION here — also BIOLOGICAL_PROCESS×1, QUALITY×1 elsewhere in the corpus +data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation INCONSISTENT_NODE_TYPE WARN node_id='membrane_proton_permeability' type=BIOLOGICAL_PROCESS here — also QUALITY×2 elsewhere in the corpus +data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation INCONSISTENT_NODE_TYPE WARN node_id='positive_dna_supercoiling' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/environment/thermophilic.yaml thermophilic_heat_adaptation FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 6, 4, 2, 2) — one record, several unrelated mechanisms data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='elevated_temperature' label='elevated temperature' type=ENVIRONMENTAL_FACTOR — in an island with no path to thermotolerant_trait data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='heat_shock_response' label='heat-shock response' type=BIOLOGICAL_PROCESS — in an island with no path to thermotolerant_trait @@ -693,6 +872,7 @@ data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adap data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='rpoE_envelope_sigma' label='RpoE envelope-stress sigma factor' type=GENE_OR_PROTEIN — in an island with no path to thermotolerant_trait data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_protein_folding_lps' label='membrane protein folding and LPS biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to thermotolerant_trait data/traits/environment/thermotolerant.yaml thermotolerant_facultative_heat_adaptation FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms +data/traits/environment/uv_radiation_tolerant.yaml uv_tolerance_excision_repair INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/environment/xerophilic.yaml xerophilic_low_water_activity_growth UNREACHABLE_FROM_TRAIT WARN node_id='low_mw_polyols' label='low-molecular-weight polyols (glycerol, erythritol, arabitol)' type=CHEMICAL — in an island with no path to xerophilic_trait data/traits/environment/xerophilic.yaml xerophilic_low_water_activity_growth UNREACHABLE_FROM_TRAIT WARN node_id='osmotic_adjustment' label='osmotic adjustment' type=BIOLOGICAL_PROCESS — in an island with no path to xerophilic_trait data/traits/environment/xerophilic.yaml xerophilic_low_water_activity_growth FRAGMENTED_GRAPH WARN components=2 of 8 node(s) (sizes: 6, 2) — one record, several unrelated mechanisms @@ -730,6 +910,7 @@ data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt UNREACHABLE_F data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt UNREACHABLE_FROM_TRAIT WARN node_id='plasmid_methylase' label='plasmid-encoded methylase' type=MOLECULAR_FUNCTION — in an island with no path to plasmid_carriage_trait data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt UNREACHABLE_FROM_TRAIT WARN node_id='restriction_of_plasmid_dna' label='restriction of incoming plasmid DNA' type=BIOLOGICAL_PROCESS — in an island with no path to plasmid_carriage_trait data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt UNREACHABLE_FROM_TRAIT WARN node_id='anti_restriction_genes' label='plasmid-encoded anti-restriction genes' type=GENE_OR_PROTEIN — in an island with no path to plasmid_carriage_trait +data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt INCONSISTENT_NODE_TYPE WARN node_id='plasmid_methylase' type=MOLECULAR_FUNCTION here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/genomics/plasmid_carriage.yaml plasmid_conjugation_hgt FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 6, 3, 2) — one record, several unrelated mechanisms data/traits/genomics/ploidy.yaml ploidy_repair_survival FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 5, 4) — one record, several unrelated mechanisms data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN node_id='ci_repressor' label='CI master repressor' type=GENE_OR_PROTEIN — in an island with no path to prophage_trait @@ -741,10 +922,13 @@ data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN node_id='prophage_induction' label='prophage induction' type=BIOLOGICAL_PROCESS — in an island with no path to prophage_trait data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN node_id='phage_plasmid' label='phage-plasmid' type=GENE_OR_PROTEIN — in an island with no path to prophage_trait data/traits/genomics/prophage.yaml prophage_lysogeny UNREACHABLE_FROM_TRAIT WARN node_id='extrachromosomal_maintenance' label='extrachromosomal prophage maintenance' type=BIOLOGICAL_PROCESS — in an island with no path to prophage_trait +data/traits/genomics/prophage.yaml prophage_lysogeny INCONSISTENT_NODE_TYPE WARN node_id='dna_damage' type=ENVIRONMENTAL_FACTOR here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/genomics/prophage.yaml prophage_lysogeny FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 5, 4, 2, 2) — one record, several unrelated mechanisms data/traits/genomics/restriction_modification_system.yaml rm_self_nonself_defense UNREACHABLE_FROM_TRAIT WARN node_id='type_iv_restriction_enzyme' label='type IV restriction enzyme' type=GENE_OR_PROTEIN — in an island with no path to rm_trait data/traits/genomics/restriction_modification_system.yaml rm_self_nonself_defense UNREACHABLE_FROM_TRAIT WARN node_id='methylated_dna_motif' label='methylated DNA motif' type=CHEMICAL — in an island with no path to rm_trait +data/traits/genomics/restriction_modification_system.yaml rm_self_nonself_defense INCONSISTENT_NODE_TYPE WARN node_id='plasmid_methylase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus data/traits/genomics/restriction_modification_system.yaml rm_self_nonself_defense FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 9, 2) — one record, several unrelated mechanisms +data/traits/genomics/rrna_operon_copy_number.yaml rrn_copy_growth_rate INCONSISTENT_NODE_TYPE WARN node_id='maximal_growth_rate' type=QUALITY here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/genomics/transposable_element.yaml te_transposition_rearrangement UNREACHABLE_FROM_TRAIT WARN node_id='te_insertion' label='transposable element insertion' type=BIOLOGICAL_PROCESS — in an island with no path to te_trait data/traits/genomics/transposable_element.yaml te_transposition_rearrangement UNREACHABLE_FROM_TRAIT WARN node_id='target_site_duplication' label='target site duplication' type=QUALITY — in an island with no path to te_trait data/traits/genomics/transposable_element.yaml te_transposition_rearrangement UNREACHABLE_FROM_TRAIT WARN node_id='gene_disruption' label='gene disruption' type=BIOLOGICAL_PROCESS — in an island with no path to te_trait @@ -752,6 +936,9 @@ data/traits/genomics/transposable_element.yaml te_transposition_rearrangement FR data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='cytochrome_c_oxidase' label='cytochrome c oxidase' type=GENE_OR_PROTEIN — in an island with no path to aerobic_respiration_trait data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='molecular_oxygen' label='molecular oxygen' type=CHEMICAL — in an island with no path to aerobic_respiration_trait data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='water' label='water' type=CHEMICAL — in an island with no path to aerobic_respiration_trait +data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/metabolism/aerobic_respiration.yaml aerobic_respiration_terminal_oxidase FRAGMENTED_GRAPH WARN components=2 of 8 node(s) (sizes: 5, 3) — one record, several unrelated mechanisms data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='oxygen_limitation' label='oxygen limitation / anoxic transition' type=ENVIRONMENTAL_FACTOR — in an island with no path to anaerobic_respiration_trait data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='denitrification_reductases' label='denitrification reductases' type=GENE_OR_PROTEIN — in an island with no path to anaerobic_respiration_trait @@ -761,6 +948,7 @@ data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrif data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='nitrous_oxide_reductase' label='nitrous oxide reductase (NosZ)' type=GENE_OR_PROTEIN — in an island with no path to anaerobic_respiration_trait data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='nitrous_oxide' label='nitrous oxide' type=CHEMICAL — in an island with no path to anaerobic_respiration_trait data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification UNREACHABLE_FROM_TRAIT WARN node_id='dinitrogen' label='dinitrogen' type=CHEMICAL — in an island with no path to anaerobic_respiration_trait +data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=MOLECULAR_FUNCTION here — also CHEMICAL×3 elsewhere in the corpus data/traits/metabolism/anaerobic_respiration.yaml anaerobic_respiration_denitrification FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 6, 3, 3, 2) — one record, several unrelated mechanisms data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis UNREACHABLE_FROM_TRAIT WARN node_id='endoglucanase' label='endoglucanase' type=GENE_OR_PROTEIN — in an island with no path to biopolymer_degradation_trait data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis UNREACHABLE_FROM_TRAIT WARN node_id='cello_oligosaccharides' label='cello-oligosaccharides' type=CHEMICAL — in an island with no path to biopolymer_degradation_trait @@ -774,6 +962,7 @@ data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extrac data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis UNREACHABLE_FROM_TRAIT WARN node_id='lignin_oxidative_enzymes' label='lignin-oxidizing redox enzymes (LiP/MnP/VP/laccase/DyP)' type=GENE_OR_PROTEIN — in an island with no path to biopolymer_degradation_trait data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis UNREACHABLE_FROM_TRAIT WARN node_id='lignin' label='lignin' type=CHEMICAL — in an island with no path to biopolymer_degradation_trait data/traits/metabolism/biopolymer_degradation.yaml biopolymer_degradation_extracellular_hydrolysis FRAGMENTED_GRAPH WARN components=6 of 14 node(s) (sizes: 3, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/metabolism/cable_bacteria_metabolism.yaml cable_bacteria_long_distance_electron_transport INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/metabolism/calvin_benson_bassham_cycle.yaml cbb_rubisco_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='cbbr' label='CbbR transcriptional regulator' type=GENE_OR_PROTEIN — in an island with no path to cbb_trait data/traits/metabolism/calvin_benson_bassham_cycle.yaml cbb_rubisco_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='cbb_operon' label='cbb operon' type=GENE_OR_PROTEIN — in an island with no path to cbb_trait data/traits/metabolism/calvin_benson_bassham_cycle.yaml cbb_rubisco_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='cytoplasmic_ca' label='cytoplasmic carbonic anhydrase' type=GENE_OR_PROTEIN — in an island with no path to cbb_trait @@ -804,11 +993,13 @@ data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_ data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 UNREACHABLE_FROM_TRAIT WARN node_id='no_reduction_to_n2o' label='nitric oxide reduction to nitrous oxide' type=BIOLOGICAL_PROCESS — in an island with no path to denitrification_trait data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 UNREACHABLE_FROM_TRAIT WARN node_id='denitrification_modularity' label='denitrification pathway modularity' type=QUALITY — in an island with no path to denitrification_trait data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 UNREACHABLE_FROM_TRAIT WARN node_id='transient_intermediate_accumulation' label='transient accumulation of intermediates' type=STATE — in an island with no path to denitrification_trait +data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/metabolism/denitrification.yaml denitrification_stepwise_nitrate_to_n2 FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 5, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='bicarbonate' label='bicarbonate' type=CHEMICAL — in an island with no path to dc_four_hb_trait data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='pep_carboxylase' label='phosphoenolpyruvate carboxylase' type=GENE_OR_PROTEIN — in an island with no path to dc_four_hb_trait data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='phosphoenolpyruvate' label='phosphoenolpyruvate' type=CHEMICAL — in an island with no path to dc_four_hb_trait data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='oxaloacetate' label='oxaloacetate' type=CHEMICAL — in an island with no path to dc_four_hb_trait +data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml dc_four_hb_anaerobic_archaeal_co2_fixation FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 10, 4) — one record, several unrelated mechanisms data/traits/metabolism/dissimilatory_metal_reduction.yaml metal_reduction_anaerobic_respiration UNREACHABLE_FROM_TRAIT WARN node_id='organic_matter_oxidation' label='organic compound oxidation' type=BIOLOGICAL_PROCESS — in an island with no path to metal_reduction_trait data/traits/metabolism/dissimilatory_metal_reduction.yaml metal_reduction_anaerobic_respiration UNREACHABLE_FROM_TRAIT WARN node_id='fe3_reduction' label='Fe(III) reduction' type=BIOLOGICAL_PROCESS — in an island with no path to metal_reduction_trait @@ -847,6 +1038,8 @@ data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers U data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers UNREACHABLE_FROM_TRAIT WARN node_id='terminal_oxidase' label='terminal oxidase' type=GENE_OR_PROTEIN — in an island with no path to electron_transfer_trait data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='oxygen' type=CHEMICAL — in an island with no path to electron_transfer_trait data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=BIOLOGICAL_PROCESS — in an island with no path to electron_transfer_trait +data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus +data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/metabolism/electron_transfer.yaml electron_transfer_redox_carriers FRAGMENTED_GRAPH WARN components=4 of 17 node(s) (sizes: 7, 5, 3, 2) — one record, several unrelated mechanisms data/traits/metabolism/fermentation.yaml fermentation_redox_energy UNREACHABLE_FROM_TRAIT WARN node_id='glycolysis_emp' label='glycolysis (Embden-Meyerhof-Parnas pathway)' type=PATHWAY — in an island with no path to fermentation_trait data/traits/metabolism/fermentation.yaml fermentation_redox_energy UNREACHABLE_FROM_TRAIT WARN node_id='pyruvate' label='pyruvate' type=CHEMICAL — in an island with no path to fermentation_trait @@ -879,6 +1072,7 @@ data/traits/metabolism/lignin_degradation.yaml lignin_degradation_peroxidase_lac data/traits/metabolism/lignin_degradation.yaml lignin_degradation_peroxidase_laccase UNREACHABLE_FROM_TRAIT WARN node_id='beta_o4_bond' label='beta-O-4 aryl ether bond' type=CHEMICAL — in an island with no path to lignin_degradation_trait data/traits/metabolism/lignin_degradation.yaml lignin_degradation_peroxidase_laccase UNREACHABLE_FROM_TRAIT WARN node_id='ca_cb_bond' label='Calpha-Cbeta bond' type=CHEMICAL — in an island with no path to lignin_degradation_trait data/traits/metabolism/lignin_degradation.yaml lignin_degradation_peroxidase_laccase FRAGMENTED_GRAPH WARN components=4 of 13 node(s) (sizes: 5, 3, 3, 2) — one record, several unrelated mechanisms +data/traits/metabolism/manganese_oxidation.yaml manganese_oxidation_multicopper_oxidase INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='respiratory_electron_transport' label='respiratory electron transport chain' type=BIOLOGICAL_PROCESS — in an island with no path to metabolism_trait data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=CHEMICAL — in an island with no path to metabolism_trait data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthase' label='ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to metabolism_trait @@ -887,6 +1081,7 @@ data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABL data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='carbon_use_efficiency' label='carbon use efficiency' type=QUALITY — in an island with no path to metabolism_trait data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='substrate_complexity' label='substrate complexity' type=QUALITY — in an island with no path to metabolism_trait data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth UNREACHABLE_FROM_TRAIT WARN node_id='metabolic_energy_cost' label='energetic cost of metabolism' type=QUALITY — in an island with no path to metabolism_trait +data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=CHEMICAL here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, STATE×18 elsewhere in the corpus data/traits/metabolism/metabolism.yaml metabolism_substrate_to_growth FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 6, 4, 2, 2) — one record, several unrelated mechanisms data/traits/metabolism/methanogenesis.yaml methanogenesis_c1_reduction UNREACHABLE_FROM_TRAIT WARN node_id='carbon_dioxide' label='carbon dioxide' type=CHEMICAL — in an island with no path to methanogenesis_trait data/traits/metabolism/methanogenesis.yaml methanogenesis_c1_reduction UNREACHABLE_FROM_TRAIT WARN node_id='molecular_hydrogen' label='molecular hydrogen' type=CHEMICAL — in an island with no path to methanogenesis_trait @@ -898,7 +1093,9 @@ data/traits/metabolism/methanogenesis.yaml methanogenesis_c1_reduction UNREACHAB data/traits/metabolism/methanogenesis.yaml methanogenesis_c1_reduction FRAGMENTED_GRAPH WARN components=4 of 15 node(s) (sizes: 8, 3, 2, 2) — one record, several unrelated mechanisms data/traits/metabolism/mixed_acid_fermentation.yaml mixed_acid_fermentation_enterobacterial UNREACHABLE_FROM_TRAIT WARN node_id='pta_acka' label='phosphotransacetylase / acetate kinase (Pta/AckA)' type=GENE_OR_PROTEIN — in an island with no path to mixed_acid_fermentation_trait data/traits/metabolism/mixed_acid_fermentation.yaml mixed_acid_fermentation_enterobacterial UNREACHABLE_FROM_TRAIT WARN node_id='acetate' label='acetate' type=CHEMICAL — in an island with no path to mixed_acid_fermentation_trait +data/traits/metabolism/mixed_acid_fermentation.yaml mixed_acid_fermentation_enterobacterial INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=ENVIRONMENTAL_FACTOR here — also CHEMICAL×20 elsewhere in the corpus data/traits/metabolism/mixed_acid_fermentation.yaml mixed_acid_fermentation_enterobacterial FRAGMENTED_GRAPH WARN components=2 of 15 node(s) (sizes: 13, 2) — one record, several unrelated mechanisms +data/traits/metabolism/nitrogen_fixation.yaml nitrogen_fixation_nitrogenase INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='nadh' label='NADH' type=CHEMICAL — in an island with no path to oxidative_phosphorylation_trait data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='complex_i' label='Complex I / NADH:quinone oxidoreductase (NDH-1)' type=GENE_OR_PROTEIN — in an island with no path to oxidative_phosphorylation_trait data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='succinate' label='succinate' type=CHEMICAL — in an island with no path to oxidative_phosphorylation_trait @@ -908,6 +1105,9 @@ data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_ data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='terminal_oxidase' label='terminal oxidase' type=GENE_OR_PROTEIN — in an island with no path to oxidative_phosphorylation_trait data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='oxygen' type=CHEMICAL — in an island with no path to oxidative_phosphorylation_trait data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling UNREACHABLE_FROM_TRAIT WARN node_id='heme_copper_oxidase' label='heme-copper oxidase' type=GENE_OR_PROTEIN — in an island with no path to oxidative_phosphorylation_trait +data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/metabolism/oxidative_phosphorylation.yaml oxidative_phosphorylation_chemiosmotic_coupling FRAGMENTED_GRAPH WARN components=4 of 16 node(s) (sizes: 7, 5, 2, 2) — one record, several unrelated mechanisms data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='water' label='water' type=CHEMICAL — in an island with no path to oxygenic_photosynthesis_trait data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='molecular_oxygen' label='molecular oxygen' type=CHEMICAL — in an island with no path to oxygenic_photosynthesis_trait @@ -918,6 +1118,8 @@ data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_wate data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='ferredoxin' label='ferredoxin' type=GENE_OR_PROTEIN — in an island with no path to oxygenic_photosynthesis_trait data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='fnr' label='ferredoxin-NADP+ reductase' type=GENE_OR_PROTEIN — in an island with no path to oxygenic_photosynthesis_trait data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting UNREACHABLE_FROM_TRAIT WARN node_id='nadph' label='NADPH' type=CHEMICAL — in an island with no path to oxygenic_photosynthesis_trait +data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=CHEMICAL here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, STATE×18 elsewhere in the corpus data/traits/metabolism/oxygenic_photosynthesis.yaml oxygenic_photosynthesis_water_splitting FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 7, 4, 2) — one record, several unrelated mechanisms data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='light_energy' label='light energy' type=ENVIRONMENTAL_FACTOR — in an island with no path to photosynthesis_trait data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='light_harvesting' label='light harvesting / excitation transfer' type=BIOLOGICAL_PROCESS — in an island with no path to photosynthesis_trait @@ -925,12 +1127,15 @@ data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_c data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='electron_transport' label='photosynthetic electron transport' type=BIOLOGICAL_PROCESS — in an island with no path to photosynthesis_trait data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='proton_gradient' label='transmembrane electrochemical proton gradient' type=STATE — in an island with no path to photosynthesis_trait data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthesis' label='ATP synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to photosynthesis_trait +data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CHEMICAL here — also CAPACITY×4 elsewhere in the corpus data/traits/metabolism/photosynthesis.yaml photosynthesis_chlorophyll_reaction_center FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 6, 4) — one record, several unrelated mechanisms data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='photosystem_ii' label='photosystem II' type=GENE_OR_PROTEIN — in an island with no path to phototrophy_trait data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='photosynthetic_electron_transport' label='photosynthetic electron transport chain' type=BIOLOGICAL_PROCESS — in an island with no path to phototrophy_trait data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='nadph' label='NADPH' type=CHEMICAL — in an island with no path to phototrophy_trait data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='atp' label='ATP' type=CHEMICAL — in an island with no path to phototrophy_trait data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='high_light' label='high light intensity' type=ENVIRONMENTAL_FACTOR — in an island with no path to phototrophy_trait +data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=BIOLOGICAL_PROCESS here — also PATHWAY×5 elsewhere in the corpus data/traits/metabolism/phototrophy.yaml phototrophy_light_energy_capture FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate UNREACHABLE_FROM_TRAIT WARN node_id='pyruvate' label='pyruvate' type=CHEMICAL — in an island with no path to propionic_acid_fermentation_trait data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate UNREACHABLE_FROM_TRAIT WARN node_id='oxaloacetate' label='oxaloacetate' type=CHEMICAL — in an island with no path to propionic_acid_fermentation_trait @@ -942,11 +1147,15 @@ data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentat data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate UNREACHABLE_FROM_TRAIT WARN node_id='mmc_carboxytransferase' label='methylmalonyl-CoA carboxytransferase' type=GENE_OR_PROTEIN — in an island with no path to propionic_acid_fermentation_trait data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate UNREACHABLE_FROM_TRAIT WARN node_id='biotin' label='biotin' type=CHEMICAL — in an island with no path to propionic_acid_fermentation_trait data/traits/metabolism/propionic_acid_fermentation.yaml propionic_acid_fermentation_propionate FRAGMENTED_GRAPH WARN components=4 of 15 node(s) (sizes: 6, 5, 2, 2) — one record, several unrelated mechanisms +data/traits/metabolism/proteorhodopsin_phototrophy.yaml proteorhodopsin_light_driven_proton_pump INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_electron_transport_chain' label='membrane electron transport chain' type=PATHWAY — in an island with no path to respiration_trait data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=STATE — in an island with no path to respiration_trait data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='atp_synthase' label='ATP synthase' type=GENE_OR_PROTEIN — in an island with no path to respiration_trait data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='atp' label='ATP' type=CHEMICAL — in an island with no path to respiration_trait data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation UNREACHABLE_FROM_TRAIT WARN node_id='complex_i' label='respiratory Complex I (NADH:quinone oxidoreductase)' type=GENE_OR_PROTEIN — in an island with no path to respiration_trait +data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=CHEMICAL here — also MOLECULAR_FUNCTION×2 elsewhere in the corpus +data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus +data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/metabolism/respiration.yaml respiration_electron_acceptor_energy_conservation FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 8, 5) — one record, several unrelated mechanisms data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='high_energy_phosphorylated_intermediate' label='high-energy phosphorylated intermediate' type=CHEMICAL — in an island with no path to substrate_level_phosphorylation_trait data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='adp' label='ADP' type=CHEMICAL — in an island with no path to substrate_level_phosphorylation_trait @@ -955,6 +1164,7 @@ data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phos data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='acetyl_phosphate' label='acetyl phosphate' type=CHEMICAL — in an island with no path to substrate_level_phosphorylation_trait data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='acetate_kinase' label='acetate kinase' type=GENE_OR_PROTEIN — in an island with no path to substrate_level_phosphorylation_trait data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp UNREACHABLE_FROM_TRAIT WARN node_id='acetate' label='acetate' type=CHEMICAL — in an island with no path to substrate_level_phosphorylation_trait +data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/metabolism/substrate_level_phosphorylation.yaml substrate_level_phosphorylation_direct_atp FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 6, 5, 2) — one record, several unrelated mechanisms data/traits/metabolism/syntrophy.yaml syntrophy_interspecies_electron_transfer UNREACHABLE_FROM_TRAIT WARN node_id='direct_interspecies_electron_transfer' label='direct interspecies electron transfer' type=BIOLOGICAL_PROCESS — in an island with no path to syntrophy_trait data/traits/metabolism/syntrophy.yaml syntrophy_interspecies_electron_transfer UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_pressure_inhibition' label='hydrogen pressure inhibition' type=STATE — in an island with no path to syntrophy_trait @@ -992,10 +1202,12 @@ data/traits/morphology/amphitrichous.yaml amphitrichous_bipolar_flagella UNREACH data/traits/morphology/amphitrichous.yaml amphitrichous_bipolar_flagella UNREACHABLE_FROM_TRAIT WARN node_id='flhf_polar_localization' label='FlhF polar localization' type=BIOLOGICAL_PROCESS — in an island with no path to amphitrichous_trait data/traits/morphology/amphitrichous.yaml amphitrichous_bipolar_flagella UNREACHABLE_FROM_TRAIT WARN node_id='polar_flagellar_number' label='polar flagellar number' type=QUALITY — in an island with no path to amphitrichous_trait data/traits/morphology/amphitrichous.yaml amphitrichous_bipolar_flagella FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 8, 3) — one record, several unrelated mechanisms +data/traits/morphology/axially_filamented.yaml axially_filamented_periplasmic_flagella INCONSISTENT_NODE_TYPE WARN node_id='periplasmic_flagella' type=CELLULAR_LOCALIZATION here — also ORGANELLE×2 elsewhere in the corpus data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation UNREACHABLE_FROM_TRAIT WARN node_id='rodA_pbp2_synthase' label='RodA-PBP2 synthase (Rod complex)' type=GENE_OR_PROTEIN — in an island with no path to bacillus_shaped_trait/spherical_morphology data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation UNREACHABLE_FROM_TRAIT WARN node_id='bacterial_elongation' label='bacterial cell elongation' type=BIOLOGICAL_PROCESS — in an island with no path to bacillus_shaped_trait/spherical_morphology data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation UNREACHABLE_FROM_TRAIT WARN node_id='moenomycin' label='moenomycin' type=CHEMICAL — in an island with no path to bacillus_shaped_trait/spherical_morphology data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation UNREACHABLE_FROM_TRAIT WARN node_id='class_a_pbps' label='class A penicillin-binding proteins' type=GENE_OR_PROTEIN — in an island with no path to bacillus_shaped_trait/spherical_morphology +data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=GENE_OR_PROTEIN here — also PATHWAY×2 elsewhere in the corpus data/traits/morphology/bacillus_shaped.yaml bacillus_shaped_rod_elongation FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 8, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/black_pigmented.yaml black_pigmented_melanin_polymer UNREACHABLE_FROM_TRAIT WARN node_id='dopaquinone' label='dopaquinone/dihydroxyindole intermediates' type=CHEMICAL — in an island with no path to black_pigmented_trait data/traits/morphology/black_pigmented.yaml black_pigmented_melanin_polymer UNREACHABLE_FROM_TRAIT WARN node_id='dhn_precursor' label='DHN (1,8-dihydroxynaphthalene)' type=CHEMICAL — in an island with no path to black_pigmented_trait @@ -1026,7 +1238,12 @@ data/traits/morphology/capsule.yaml capsule_polysaccharide_protection UNREACHABL data/traits/morphology/capsule.yaml capsule_polysaccharide_protection UNREACHABLE_FROM_TRAIT WARN node_id='lipid_linked_repeat_unit' label='lipid-linked capsule repeat unit' type=CHEMICAL — in an island with no path to capsule_trait data/traits/morphology/capsule.yaml capsule_polysaccharide_protection UNREACHABLE_FROM_TRAIT WARN node_id='wzb_phosphatase_cycle' label='Wzb phosphatase cycle' type=BIOLOGICAL_PROCESS — in an island with no path to capsule_trait data/traits/morphology/capsule.yaml capsule_polysaccharide_protection UNREACHABLE_FROM_TRAIT WARN node_id='wzc_capsule_assembly' label='Wzc-regulated capsule assembly' type=BIOLOGICAL_PROCESS — in an island with no path to capsule_trait +data/traits/morphology/capsule.yaml capsule_polysaccharide_protection INCONSISTENT_NODE_TYPE WARN node_id='immune_evasion' type=QUALITY here — also BIOLOGICAL_PROCESS×3 elsewhere in the corpus data/traits/morphology/capsule.yaml capsule_polysaccharide_protection FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms +data/traits/morphology/carboxysome.yaml carboxysome_co2_concentrating INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus +data/traits/morphology/carotenoid_pigmentation.yaml carotenoid_pigmentation_crt_pathway INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/morphology/cell_length.yaml cell_length_division_growth_control INCONSISTENT_NODE_TYPE WARN node_id='ftsz_ring' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×2 elsewhere in the corpus +data/traits/morphology/cell_length.yaml cell_length_division_growth_control INCONSISTENT_NODE_TYPE WARN node_id='elongasome' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus data/traits/morphology/cell_length_large.yaml cell_length_large_division_delay UNREACHABLE_FROM_TRAIT WARN node_id='sos_response' label='SOS response' type=BIOLOGICAL_PROCESS — in an island with no path to cell_length_large_trait/cell_length_trait data/traits/morphology/cell_length_large.yaml cell_length_large_division_delay UNREACHABLE_FROM_TRAIT WARN node_id='sula_division_inhibition' label='SulA-mediated division inhibition' type=BIOLOGICAL_PROCESS — in an island with no path to cell_length_large_trait/cell_length_trait data/traits/morphology/cell_length_large.yaml cell_length_large_division_delay UNREACHABLE_FROM_TRAIT WARN node_id='sula_protein' label='SulA' type=GENE_OR_PROTEIN — in an island with no path to cell_length_large_trait/cell_length_trait @@ -1040,6 +1257,8 @@ data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate UN data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate UNREACHABLE_FROM_TRAIT WARN node_id='pbp2_activity' label='PBP2 transpeptidase activity' type=MOLECULAR_FUNCTION — in an island with no path to cell_length_medium_trait/cell_length_trait/rod_shape data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate UNREACHABLE_FROM_TRAIT WARN node_id='membrane_synthesis' label='membrane synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to cell_length_medium_trait/cell_length_trait/rod_shape data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate UNREACHABLE_FROM_TRAIT WARN node_id='envelope_balance_state' label='PG-membrane envelope balance' type=STATE — in an island with no path to cell_length_medium_trait/cell_length_trait/rod_shape +data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=PATHWAY here — also GENE_OR_PROTEIN×3 elsewhere in the corpus +data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate INCONSISTENT_NODE_TYPE WARN node_id='rod_shape' type=TRAIT here — also QUALITY×1 elsewhere in the corpus data/traits/morphology/cell_length_medium.yaml cell_length_medium_growth_rate FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 4, 3, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/cell_length_small.yaml cell_length_small_size_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='ftsz_abundance' label='FtsZ abundance' type=GENE_OR_PROTEIN — in an island with no path to cell_length_small_trait/cell_length_trait data/traits/morphology/cell_length_small.yaml cell_length_small_size_setpoint UNREACHABLE_FROM_TRAIT WARN node_id='division_timing' label='cell division timing' type=BIOLOGICAL_PROCESS — in an island with no path to cell_length_small_trait/cell_length_trait @@ -1057,6 +1276,8 @@ data/traits/morphology/cell_length_very_small.yaml cell_length_very_small_stream data/traits/morphology/cell_length_very_small.yaml cell_length_very_small_streamlining FRAGMENTED_GRAPH WARN components=2 of 9 node(s) (sizes: 7, 2) — one record, several unrelated mechanisms data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton UNREACHABLE_FROM_TRAIT WARN node_id='flotillins' label='flotillins' type=GENE_OR_PROTEIN — in an island with no path to cell_shape_trait data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton UNREACHABLE_FROM_TRAIT WARN node_id='cell_wall_synthesis' label='cell wall synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to cell_shape_trait +data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=PATHWAY here — also GENE_OR_PROTEIN×3 elsewhere in the corpus +data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton INCONSISTENT_NODE_TYPE WARN node_id='rod_shape' type=QUALITY here — also TRAIT×1 elsewhere in the corpus data/traits/morphology/cell_shape.yaml cell_shape_peptidoglycan_cytoskeleton FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 12, 2) — one record, several unrelated mechanisms data/traits/morphology/cell_width_large.yaml cell_width_large_setpoint_increase UNREACHABLE_FROM_TRAIT WARN node_id='roda_pbp2_activation' label='RodA-PBP2 allosteric activation' type=BIOLOGICAL_PROCESS — in an island with no path to cell_width_large_trait/cell_width_trait data/traits/morphology/cell_width_large.yaml cell_width_large_setpoint_increase UNREACHABLE_FROM_TRAIT WARN node_id='pg_polymerization_crosslinking' label='peptidoglycan polymerization and crosslinking' type=BIOLOGICAL_PROCESS — in an island with no path to cell_width_large_trait/cell_width_trait @@ -1075,6 +1296,7 @@ data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamli data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining UNREACHABLE_FROM_TRAIT WARN node_id='nutrient_uptake_efficiency' label='nutrient uptake efficiency' type=CAPACITY — in an island with no path to cell_width_very_small_trait/cell_width_trait data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining UNREACHABLE_FROM_TRAIT WARN node_id='small_cell_bacteria' label='small-cell bacteria' type=STATE — in an island with no path to cell_width_very_small_trait/cell_width_trait data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining UNREACHABLE_FROM_TRAIT WARN node_id='oligotrophic_waters' label='oligotrophic waters' type=ENVIRONMENTAL_FACTOR — in an island with no path to cell_width_very_small_trait/cell_width_trait +data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=GENE_OR_PROTEIN here — also PATHWAY×2 elsewhere in the corpus data/traits/morphology/cell_width_very_small.yaml cell_width_very_small_streamlining FRAGMENTED_GRAPH WARN components=3 of 11 node(s) (sizes: 7, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/dumbbell_shaped.yaml dumbbell_shaped_snapping_division UNREACHABLE_FROM_TRAIT WARN node_id='septal_pg_hydrolysis' label='septal peptidoglycan hydrolysis' type=BIOLOGICAL_PROCESS — in an island with no path to dumbbell_shaped_trait data/traits/morphology/dumbbell_shaped.yaml dumbbell_shaped_snapping_division UNREACHABLE_FROM_TRAIT WARN node_id='daughter_cell_separation' label='daughter cell separation' type=BIOLOGICAL_PROCESS — in an island with no path to dumbbell_shaped_trait @@ -1087,6 +1309,7 @@ data/traits/morphology/dumbbell_shaped.yaml dumbbell_shaped_snapping_division FR data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation UNREACHABLE_FROM_TRAIT WARN node_id='divisome' label='divisome (FtsZ/PBP2x/FtsW)' type=GENE_OR_PROTEIN — in an island with no path to ellipsoidal_trait data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation UNREACHABLE_FROM_TRAIT WARN node_id='septal_pg_synthesis' label='septal peptidoglycan synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to ellipsoidal_trait data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation UNREACHABLE_FROM_TRAIT WARN node_id='undecaprenyl_phosphate' label='undecaprenyl phosphate (Und-P)' type=CHEMICAL — in an island with no path to ellipsoidal_trait +data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation INCONSISTENT_NODE_TYPE WARN node_id='elongasome' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus data/traits/morphology/ellipsoidal.yaml ellipsoidal_ovococcal_elongation FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 10, 3) — one record, several unrelated mechanisms data/traits/morphology/flagellar_arrangement.yaml flagellar_arrangement_flhf_flhg UNREACHABLE_FROM_TRAIT WARN node_id='flhf' label='FlhF' type=GENE_OR_PROTEIN — in an island with no path to flagellar_arrangement_trait data/traits/morphology/flagellar_arrangement.yaml flagellar_arrangement_flhf_flhg UNREACHABLE_FROM_TRAIT WARN node_id='flhg' label='FlhG' type=GENE_OR_PROTEIN — in an island with no path to flagellar_arrangement_trait @@ -1110,6 +1333,7 @@ data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth UN data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='cell_wall_biosynthesis' label='cell wall biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to flask_shaped_trait data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='bactofilin_cytoskeleton' label='bactofilin cytoskeleton' type=GENE_OR_PROTEIN — in an island with no path to flask_shaped_trait data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='asymmetric_compartment_growth' label='asymmetric compartment growth' type=BIOLOGICAL_PROCESS — in an island with no path to flask_shaped_trait +data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth INCONSISTENT_NODE_TYPE WARN node_id='bactofilin_lmdc_module' type=PATHWAY here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/morphology/flask_shaped.yaml flask_shaped_asymmetric_polar_growth FRAGMENTED_GRAPH WARN components=5 of 12 node(s) (sizes: 4, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='mreb' label='MreB' type=GENE_OR_PROTEIN — in an island with no path to fusiform_shaped_trait data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='lateral_pg_synthesis' label='lateral peptidoglycan synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to fusiform_shaped_trait @@ -1121,6 +1345,7 @@ data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='roda' label='RodA' type=GENE_OR_PROTEIN — in an island with no path to fusiform_shaped_trait data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='ftsw' label='FtsW' type=GENE_OR_PROTEIN — in an island with no path to fusiform_shaped_trait data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth UNREACHABLE_FROM_TRAIT WARN node_id='septal_pg_incorporation' label='septal peptidoglycan incorporation' type=BIOLOGICAL_PROCESS — in an island with no path to fusiform_shaped_trait +data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth INCONSISTENT_NODE_TYPE WARN node_id='elongasome' type=CELLULAR_LOCALIZATION here — also GENE_OR_PROTEIN×2 elsewhere in the corpus data/traits/morphology/fusiform_shaped.yaml fusiform_shaped_tapered_polar_growth FRAGMENTED_GRAPH WARN components=5 of 14 node(s) (sizes: 4, 3, 3, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TRAIT WARN node_id='gvpa_protein' label='GvpA' type=GENE_OR_PROTEIN — in an island with no path to gas_vesicle_trait/buoyancy data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TRAIT WARN node_id='gas_vesicle_shell' label='gas vesicle shell' type=CELLULAR_LOCALIZATION — in an island with no path to gas_vesicle_trait/buoyancy @@ -1133,6 +1358,7 @@ data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TR data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TRAIT WARN node_id='gas_vesicle_formation' label='gas vesicle formation' type=BIOLOGICAL_PROCESS — in an island with no path to gas_vesicle_trait/buoyancy data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy UNREACHABLE_FROM_TRAIT WARN node_id='ultrasound_scattering' label='ultrasound scattering' type=BIOLOGICAL_PROCESS — in an island with no path to gas_vesicle_trait/buoyancy data/traits/morphology/gas_vesicle.yaml gas_vesicle_buoyancy FRAGMENTED_GRAPH WARN components=5 of 13 node(s) (sizes: 4, 3, 2, 2, 2) — one record, several unrelated mechanisms +data/traits/morphology/gliding.yaml gliding_surface_motility INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/morphology/gram_negative.yaml gram_negative_outer_membrane_dye_loss UNREACHABLE_FROM_TRAIT WARN node_id='thin_peptidoglycan_layer' label='thin peptidoglycan layer' type=CELLULAR_LOCALIZATION — in an island with no path to gram_negative_trait data/traits/morphology/gram_negative.yaml gram_negative_outer_membrane_dye_loss UNREACHABLE_FROM_TRAIT WARN node_id='periplasmic_space' label='periplasmic space' type=CELLULAR_LOCALIZATION — in an island with no path to gram_negative_trait data/traits/morphology/gram_negative.yaml gram_negative_outer_membrane_dye_loss UNREACHABLE_FROM_TRAIT WARN node_id='crystal_violet_iodine_complex' label='crystal violet-iodine complex' type=CHEMICAL — in an island with no path to gram_negative_trait @@ -1149,6 +1375,7 @@ data/traits/morphology/gram_positive.yaml gram_positive_cell_wall_retention FRAG data/traits/morphology/gram_stain.yaml gram_stain_cell_envelope_retention UNREACHABLE_FROM_TRAIT WARN node_id='crystal_violet' label='crystal violet' type=CHEMICAL — in an island with no path to gram_stain_trait data/traits/morphology/gram_stain.yaml gram_stain_cell_envelope_retention UNREACHABLE_FROM_TRAIT WARN node_id='iodine_mordant' label='iodine mordant' type=CHEMICAL — in an island with no path to gram_stain_trait data/traits/morphology/gram_stain.yaml gram_stain_cell_envelope_retention FRAGMENTED_GRAPH WARN components=2 of 7 node(s) (sizes: 5, 2) — one record, several unrelated mechanisms +data/traits/morphology/green_pigmented.yaml green_pigmented_pyocyanin_phenazine INCONSISTENT_NODE_TYPE WARN node_id='phenazine_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='het_diff_process' label='heterocyst differentiation' type=BIOLOGICAL_PROCESS — in an island with no path to heterocyst_trait data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='hetr_regulator' label='HetR transcriptional regulator' type=GENE_OR_PROTEIN — in an island with no path to heterocyst_trait data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='furc_perr' label='FurC / PerR' type=GENE_OR_PROTEIN — in an island with no path to heterocyst_trait @@ -1158,6 +1385,7 @@ data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UN data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='oxygen' type=CHEMICAL — in an island with no path to heterocyst_trait data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='pats_peptide' label='PatS peptide' type=GENE_OR_PROTEIN — in an island with no path to heterocyst_trait data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation UNREACHABLE_FROM_TRAIT WARN node_id='hetn_regulator' label='HetN regulator' type=GENE_OR_PROTEIN — in an island with no path to heterocyst_trait +data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/morphology/heterocyst.yaml heterocyst_microoxic_nitrogen_fixation FRAGMENTED_GRAPH WARN components=4 of 14 node(s) (sizes: 5, 4, 3, 2) — one record, several unrelated mechanisms data/traits/morphology/intracellular_inclusion.yaml inclusion_compartmentalization UNREACHABLE_FROM_TRAIT WARN node_id='pha_synthase_pathway' label='PhaA/PhaB/PhaC pathway' type=PATHWAY — in an island with no path to inclusion_trait/buoyancy data/traits/morphology/intracellular_inclusion.yaml inclusion_compartmentalization UNREACHABLE_FROM_TRAIT WARN node_id='pha_granule' label='PHA granule' type=CELLULAR_LOCALIZATION — in an island with no path to inclusion_trait/buoyancy @@ -1189,6 +1417,10 @@ data/traits/morphology/monotrichous.yaml monotrichous_single_polar_flagellum UNR data/traits/morphology/monotrichous.yaml monotrichous_single_polar_flagellum UNREACHABLE_FROM_TRAIT WARN node_id='flif_msring' label='FliF MS-ring protein' type=GENE_OR_PROTEIN — in an island with no path to monotrichous_trait data/traits/morphology/monotrichous.yaml monotrichous_single_polar_flagellum UNREACHABLE_FROM_TRAIT WARN node_id='flim_flin' label='FliM/FliN C-ring partners' type=GENE_OR_PROTEIN — in an island with no path to monotrichous_trait data/traits/morphology/monotrichous.yaml monotrichous_single_polar_flagellum FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 7, 3) — one record, several unrelated mechanisms +data/traits/morphology/motile.yaml motile_energy_dependent_locomotion INCONSISTENT_NODE_TYPE WARN node_id='type_iv_pilus' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus +data/traits/morphology/motile.yaml motile_energy_dependent_locomotion INCONSISTENT_NODE_TYPE WARN node_id='twitching_motility' type=BIOLOGICAL_PROCESS here — also TRAIT×1 elsewhere in the corpus +data/traits/morphology/motility.yaml motility_locomotion_machinery INCONSISTENT_NODE_TYPE WARN node_id='type_iv_pilus' type=GENE_OR_PROTEIN here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus +data/traits/morphology/motility.yaml motility_locomotion_machinery INCONSISTENT_NODE_TYPE WARN node_id='twitching_motility' type=TRAIT here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/morphology/mycelial_growth.yaml mycelial_branching_hyphal_growth UNREACHABLE_FROM_TRAIT WARN node_id='polarisome_splitting' label='polarisome splitting' type=BIOLOGICAL_PROCESS — in an island with no path to mycelial_growth_trait data/traits/morphology/mycelial_growth.yaml mycelial_branching_hyphal_growth UNREACHABLE_FROM_TRAIT WARN node_id='branch_emergence' label='new branch emergence' type=BIOLOGICAL_PROCESS — in an island with no path to mycelial_growth_trait data/traits/morphology/mycelial_growth.yaml mycelial_branching_hyphal_growth UNREACHABLE_FROM_TRAIT WARN node_id='cglA_ligase' label='CglA glycopolymer ligase' type=GENE_OR_PROTEIN — in an island with no path to mycelial_growth_trait @@ -1205,7 +1437,10 @@ data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumul data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation UNREACHABLE_FROM_TRAIT WARN node_id='zeaxanthin' label='zeaxanthin' type=CHEMICAL — in an island with no path to orange_pigmented_trait data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation UNREACHABLE_FROM_TRAIT WARN node_id='crt_w_ketolase' label='carotenoid ketolase (CrtW)' type=GENE_OR_PROTEIN — in an island with no path to orange_pigmented_trait data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation UNREACHABLE_FROM_TRAIT WARN node_id='ketocarotenoid_biosynthesis' label='ketocarotenoid biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to orange_pigmented_trait +data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=ENVIRONMENTAL_FACTOR here — also BIOLOGICAL_PROCESS×4 elsewhere in the corpus data/traits/morphology/orange_pigmented.yaml orange_pigmented_carotenoid_accumulation FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 8, 5, 2) — one record, several unrelated mechanisms +data/traits/morphology/ovoid_shaped.yaml ovoid_shaped_midcell_pg_assembly INCONSISTENT_NODE_TYPE WARN node_id='ftsz_ring' type=CELLULAR_LOCALIZATION here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/morphology/peritrichous.yaml peritrichous_surface_distributed_flagella UNREACHABLE_FROM_TRAIT WARN node_id='flhg_regulator' label='FlhG' type=GENE_OR_PROTEIN — in an island with no path to peritrichous_trait data/traits/morphology/peritrichous.yaml peritrichous_surface_distributed_flagella UNREACHABLE_FROM_TRAIT WARN node_id='flagellar_assembly_progression' label='progression of flagellar assembly' type=BIOLOGICAL_PROCESS — in an island with no path to peritrichous_trait data/traits/morphology/peritrichous.yaml peritrichous_surface_distributed_flagella UNREACHABLE_FROM_TRAIT WARN node_id='flagellar_filament_number' label='flagellar filament number' type=QUALITY — in an island with no path to peritrichous_trait @@ -1224,7 +1459,11 @@ data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants UNR data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants UNREACHABLE_FROM_TRAIT WARN node_id='homogentisate' label='homogentisate' type=CHEMICAL — in an island with no path to pigmentation_trait data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants UNREACHABLE_FROM_TRAIT WARN node_id='pyomelanin' label='pyomelanin' type=CHEMICAL — in an island with no path to pigmentation_trait data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants UNREACHABLE_FROM_TRAIT WARN node_id='hmga_gene' label='hmgA homogentisate 1,2-dioxygenase' type=GENE_OR_PROTEIN — in an island with no path to pigmentation_trait +data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×5 elsewhere in the corpus +data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants INCONSISTENT_NODE_TYPE WARN node_id='phenazine_biosynthesis' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/morphology/pigmentation.yaml pigmentation_biosynthetic_colorants FRAGMENTED_GRAPH WARN components=4 of 16 node(s) (sizes: 5, 5, 4, 2) — one record, several unrelated mechanisms +data/traits/morphology/pink_pigmented.yaml pink_pigmented_carotenoid_color INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus +data/traits/morphology/pink_pigmented.yaml pink_pigmented_carotenoid_color INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=ENVIRONMENTAL_FACTOR here — also CHEMICAL×11 elsewhere in the corpus data/traits/morphology/polyhydroxyalkanoate_granule.yaml pha_granule_carbon_energy_storage UNREACHABLE_FROM_TRAIT WARN node_id='nutrient_limitation_high_cn' label='nutrient limitation / high C:N ratio' type=ENVIRONMENTAL_FACTOR — in an island with no path to pha_granule_trait data/traits/morphology/polyhydroxyalkanoate_granule.yaml pha_granule_carbon_energy_storage UNREACHABLE_FROM_TRAIT WARN node_id='pha_accumulation' label='polyhydroxyalkanoate accumulation' type=BIOLOGICAL_PROCESS — in an island with no path to pha_granule_trait data/traits/morphology/polyhydroxyalkanoate_granule.yaml pha_granule_carbon_energy_storage UNREACHABLE_FROM_TRAIT WARN node_id='phar_regulator' label='PhaR regulator' type=GENE_OR_PROTEIN — in an island with no path to pha_granule_trait @@ -1240,6 +1479,7 @@ data/traits/morphology/prosthecate.yaml prosthecate_stalk_nutrient_uptake UNREAC data/traits/morphology/prosthecate.yaml prosthecate_stalk_nutrient_uptake UNREACHABLE_FROM_TRAIT WARN node_id='stpabcd_complex' label='StpABCD complex' type=GENE_OR_PROTEIN — in an island with no path to prosthecate_trait data/traits/morphology/prosthecate.yaml prosthecate_stalk_nutrient_uptake UNREACHABLE_FROM_TRAIT WARN node_id='stalk_diffusion' label='diffusion along stalk' type=BIOLOGICAL_PROCESS — in an island with no path to prosthecate_trait data/traits/morphology/prosthecate.yaml prosthecate_stalk_nutrient_uptake FRAGMENTED_GRAPH WARN components=3 of 10 node(s) (sizes: 5, 3, 2) — one record, several unrelated mechanisms +data/traits/morphology/red_pigmented.yaml red_pigmented_prodiginine_pathway INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='mreb_filaments' label='MreB filaments' type=GENE_OR_PROTEIN — in an island with no path to ring_shaped_trait data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='cell_wall_growth_rate' label='rate of cell wall growth' type=BIOLOGICAL_PROCESS — in an island with no path to ring_shaped_trait data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='pg_insertion_perpendicular' label='peptidoglycan insertion perpendicular to long axis' type=BIOLOGICAL_PROCESS — in an island with no path to ring_shaped_trait @@ -1251,12 +1491,14 @@ data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREAC data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='pg_synthesis_rate_skew' label='skewed peptidoglycan synthesis rates' type=BIOLOGICAL_PROCESS — in an island with no path to ring_shaped_trait data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='crescentin' label='crescentin' type=GENE_OR_PROTEIN — in an island with no path to ring_shaped_trait data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure UNREACHABLE_FROM_TRAIT WARN node_id='cell_curvature' label='cell curvature' type=QUALITY — in an island with no path to ring_shaped_trait +data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure INCONSISTENT_NODE_TYPE WARN node_id='bactofilin_lmdc_module' type=GENE_OR_PROTEIN here — also PATHWAY×1 elsewhere in the corpus data/traits/morphology/ring_shaped.yaml ring_shaped_curved_growth_closure FRAGMENTED_GRAPH WARN components=6 of 15 node(s) (sizes: 4, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='pbp2_structural_opening' label='PBP2 structural opening' type=MOLECULAR_FUNCTION — in an island with no path to rod_shaped_trait data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='rodA_polymerization' label='RodA polymerization activity' type=MOLECULAR_FUNCTION — in an island with no path to rod_shaped_trait data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='pg_crosslinking' label='peptidoglycan crosslinking' type=BIOLOGICAL_PROCESS — in an island with no path to rod_shaped_trait data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='elongasome_processivity' label='elongasome processivity' type=BIOLOGICAL_PROCESS — in an island with no path to rod_shaped_trait data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan UNREACHABLE_FROM_TRAIT WARN node_id='sidewall_reinforcement' label='rod-shaped sidewall reinforcement' type=BIOLOGICAL_PROCESS — in an island with no path to rod_shaped_trait +data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan INCONSISTENT_NODE_TYPE WARN node_id='rod_complex' type=GENE_OR_PROTEIN here — also PATHWAY×2 elsewhere in the corpus data/traits/morphology/rod_shaped.yaml rod_shaped_mreB_peptidoglycan FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 8, 5) — one record, several unrelated mechanisms data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet UNREACHABLE_FROM_TRAIT WARN node_id='ftsz_protein' label='FtsZ' type=GENE_OR_PROTEIN — in an island with no path to sarcina_trait data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet UNREACHABLE_FROM_TRAIT WARN node_id='z_ring' label='Z ring' type=CELLULAR_LOCALIZATION — in an island with no path to sarcina_trait @@ -1270,6 +1512,8 @@ data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_pac data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet UNREACHABLE_FROM_TRAIT WARN node_id='peripheral_pg_bridge' label='peripheral peptidoglycan bridge' type=CELLULAR_LOCALIZATION — in an island with no path to sarcina_trait data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet UNREACHABLE_FROM_TRAIT WARN node_id='daughter_cell_separation' label='daughter-cell separation' type=BIOLOGICAL_PROCESS — in an island with no path to sarcina_trait data/traits/morphology/sarcina_arrangement.yaml sarcina_three_plane_division_packet FRAGMENTED_GRAPH WARN components=5 of 14 node(s) (sizes: 4, 3, 3, 2, 2) — one record, several unrelated mechanisms +data/traits/morphology/spiral_shaped.yaml spiral_shaped_curvature_mechanisms INCONSISTENT_NODE_TYPE WARN node_id='periplasmic_flagella' type=ORGANELLE here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus +data/traits/morphology/spirochete_shaped.yaml spirochete_shaped_periplasmic_flagella INCONSISTENT_NODE_TYPE WARN node_id='periplasmic_flagella' type=ORGANELLE here — also CELLULAR_LOCALIZATION×1 elsewhere in the corpus data/traits/morphology/spore_forming.yaml spore_forming_endospore_assembly UNREACHABLE_FROM_TRAIT WARN node_id='spoIID' label='SpoIID' type=GENE_OR_PROTEIN — in an island with no path to spore_forming_trait data/traits/morphology/spore_forming.yaml spore_forming_endospore_assembly UNREACHABLE_FROM_TRAIT WARN node_id='spoIIM' label='SpoIIM' type=GENE_OR_PROTEIN — in an island with no path to spore_forming_trait data/traits/morphology/spore_forming.yaml spore_forming_endospore_assembly UNREACHABLE_FROM_TRAIT WARN node_id='spoIIP' label='SpoIIP' type=GENE_OR_PROTEIN — in an island with no path to spore_forming_trait @@ -1300,6 +1544,7 @@ data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis UN data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis UNREACHABLE_FROM_TRAIT WARN node_id='spore_dna_protection' label='spore DNA protection' type=BIOLOGICAL_PROCESS — in an island with no path to sporulation_trait data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis UNREACHABLE_FROM_TRAIT WARN node_id='spore_coat_cortex' label='spore coat and cortex' type=CELLULAR_LOCALIZATION — in an island with no path to sporulation_trait data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis UNREACHABLE_FROM_TRAIT WARN node_id='stress_resistance' label='heat and chemical resistance' type=QUALITY — in an island with no path to sporulation_trait +data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis INCONSISTENT_NODE_TYPE WARN node_id='stress_resistance' type=QUALITY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/morphology/sporulation.yaml sporulation_spo0a_sigma_morphogenesis FRAGMENTED_GRAPH WARN components=6 of 19 node(s) (sizes: 8, 3, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/square_shaped.yaml square_shaped_planar_anisotropic_growth UNREACHABLE_FROM_TRAIT WARN node_id='archaeal_slayer' label='archaeal S-layer' type=ORGANELLE — in an island with no path to square_shaped_trait data/traits/morphology/square_shaped.yaml square_shaped_planar_anisotropic_growth UNREACHABLE_FROM_TRAIT WARN node_id='cell_shape' label='cell shape' type=QUALITY — in an island with no path to square_shaped_trait @@ -1312,6 +1557,7 @@ data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_ data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster UNREACHABLE_FROM_TRAIT WARN node_id='ftsz' label='FtsZ' type=GENE_OR_PROTEIN — in an island with no path to staphylococcus_trait data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster UNREACHABLE_FROM_TRAIT WARN node_id='ftsz_ring' label='FtsZ Z-ring' type=CELLULAR_LOCALIZATION — in an island with no path to staphylococcus_trait data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster UNREACHABLE_FROM_TRAIT WARN node_id='divisome_pg_synthesis' label='divisome peptidoglycan synthesis at division site' type=BIOLOGICAL_PROCESS — in an island with no path to staphylococcus_trait +data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster INCONSISTENT_NODE_TYPE WARN node_id='ftsz_ring' type=CELLULAR_LOCALIZATION here — also GENE_OR_PROTEIN×1 elsewhere in the corpus data/traits/morphology/staphylococcus_arrangement.yaml staphylococcus_irregular_division_cluster FRAGMENTED_GRAPH WARN components=2 of 8 node(s) (sizes: 5, 3) — one record, several unrelated mechanisms data/traits/morphology/star_shaped.yaml star_shaped_multiple_prosthecae UNREACHABLE_FROM_TRAIT WARN node_id='baca_lmdc_module' label='BacA-LmdC morphogenesis module' type=GENE_OR_PROTEIN — in an island with no path to star_shaped_trait data/traits/morphology/star_shaped.yaml star_shaped_multiple_prosthecae UNREACHABLE_FROM_TRAIT WARN node_id='local_pg_remodeling' label='local peptidoglycan remodeling' type=BIOLOGICAL_PROCESS — in an island with no path to star_shaped_trait @@ -1325,6 +1571,7 @@ data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retractio data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction UNREACHABLE_FROM_TRAIT WARN node_id='pilus_filament_surface_exposure' label='type IV pilus surface exposure' type=BIOLOGICAL_PROCESS — in an island with no path to twitching_trait data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction UNREACHABLE_FROM_TRAIT WARN node_id='pilmnop_alignment_complex' label='PilM/N/O/P alignment complex' type=CELLULAR_LOCALIZATION — in an island with no path to twitching_trait data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction UNREACHABLE_FROM_TRAIT WARN node_id='t4p_machine' label='type IV pilus machine' type=CELLULAR_LOCALIZATION — in an island with no path to twitching_trait +data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction INCONSISTENT_NODE_TYPE WARN node_id='type_iv_pilus' type=CELLULAR_LOCALIZATION here — also GENE_OR_PROTEIN×2 elsewhere in the corpus data/traits/morphology/twitching_motility.yaml twitching_type_iv_pilus_retraction FRAGMENTED_GRAPH WARN components=4 of 11 node(s) (sizes: 5, 2, 2, 2) — one record, several unrelated mechanisms data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='ipp_dmapp' label='IPP/DMAPP' type=CHEMICAL — in an island with no path to yellow_pigmented_trait data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='ggpp' label='geranylgeranyl diphosphate (GGPP)' type=CHEMICAL — in an island with no path to yellow_pigmented_trait @@ -1332,6 +1579,7 @@ data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color U data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='lycopene' label='lycopene' type=CHEMICAL — in an island with no path to yellow_pigmented_trait data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='crti' label='CrtI (phytoene desaturase)' type=GENE_OR_PROTEIN — in an island with no path to yellow_pigmented_trait data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color UNREACHABLE_FROM_TRAIT WARN node_id='lycopene_biosynthesis' label='lycopene biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to yellow_pigmented_trait +data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color INCONSISTENT_NODE_TYPE WARN node_id='carotenoid_biosynthesis' type=BIOLOGICAL_PROCESS here — also PATHWAY×1 elsewhere in the corpus data/traits/morphology/yellow_pigmented.yaml yellow_pigmented_carotenoid_color FRAGMENTED_GRAPH WARN components=2 of 15 node(s) (sizes: 9, 6) — one record, several unrelated mechanisms data/traits/physiology/antibiotic_resistance.yaml antibiotic_resistance_mechanisms UNREACHABLE_FROM_TRAIT WARN node_id='outer_membrane_porin' label='outer membrane porin' type=GENE_OR_PROTEIN — in an island with no path to antibiotic_resistance_trait data/traits/physiology/antibiotic_resistance.yaml antibiotic_resistance_mechanisms UNREACHABLE_FROM_TRAIT WARN node_id='antibiotic_influx' label='antibiotic influx' type=BIOLOGICAL_PROCESS — in an island with no path to antibiotic_resistance_trait @@ -1345,19 +1593,28 @@ data/traits/physiology/antibiotic_resistance.yaml antibiotic_resistance_mechanis data/traits/physiology/autotrophic.yaml autotrophic_inorganic_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='environmental_ph' label='environmental pH' type=ENVIRONMENTAL_FACTOR — in an island with no path to autotrophic_trait data/traits/physiology/autotrophic.yaml autotrophic_inorganic_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='dissolved_inorganic_carbon' label='dissolved inorganic carbon' type=CHEMICAL — in an island with no path to autotrophic_trait data/traits/physiology/autotrophic.yaml autotrophic_inorganic_carbon_fixation FRAGMENTED_GRAPH WARN components=2 of 18 node(s) (sizes: 16, 2) — one record, several unrelated mechanisms +data/traits/physiology/bioluminescence.yaml bioluminescence_luciferase INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='nife_codh' label='Ni,Fe-carbon monoxide dehydrogenase' type=GENE_OR_PROTEIN — in an island with no path to carboxydotrophic_trait data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='oxygen_sensitivity' label='oxygen sensitivity' type=QUALITY — in an island with no path to carboxydotrophic_trait data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='coo_operon' label='coo operon' type=GENE_OR_PROTEIN — in an island with no path to carboxydotrophic_trait data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='cooa_regulator' label='CooA' type=GENE_OR_PROTEIN — in an island with no path to carboxydotrophic_trait +data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/carboxydotrophic.yaml carboxydotrophic_co_oxidation FRAGMENTED_GRAPH WARN components=2 of 18 node(s) (sizes: 14, 4) — one record, several unrelated mechanisms +data/traits/physiology/catalase_activity.yaml catalase_activity_h2o2_detoxification INCONSISTENT_NODE_TYPE WARN node_id='catalase' type=GENE_OR_PROTEIN here — also MOLECULAR_FUNCTION×1 elsewhere in the corpus +data/traits/physiology/catalase_activity.yaml catalase_activity_h2o2_detoxification INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/physiology/chemoheterotrophic.yaml chemoheterotrophic_organic_energy_carbon UNREACHABLE_FROM_TRAIT WARN node_id='mannitol_pts' label='PEP-dependent phosphotransferase system (mannitol PTS)' type=GENE_OR_PROTEIN — in an island with no path to chemoheterotrophic_trait data/traits/physiology/chemoheterotrophic.yaml chemoheterotrophic_organic_energy_carbon UNREACHABLE_FROM_TRAIT WARN node_id='mannitol' label='mannitol' type=CHEMICAL — in an island with no path to chemoheterotrophic_trait +data/traits/physiology/chemoheterotrophic.yaml chemoheterotrophic_organic_energy_carbon INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=PATHWAY here — also BIOLOGICAL_PROCESS×3 elsewhere in the corpus data/traits/physiology/chemoheterotrophic.yaml chemoheterotrophic_organic_energy_carbon FRAGMENTED_GRAPH WARN components=2 of 14 node(s) (sizes: 12, 2) — one record, several unrelated mechanisms +data/traits/physiology/chemolithoautotrophic.yaml chemolithoautotrophic_energy_and_fixation INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/physiology/chemolithoautotrophic.yaml chemolithoautotrophic_energy_and_fixation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/physiology/chemolithoautotrophic.yaml chemolithoautotrophic_energy_and_fixation INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CAPACITY here — also CHEMICAL×1 elsewhere in the corpus data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='sox_pathway' label='Sox sulfur-oxidation pathway' type=PATHWAY — in an island with no path to chemolithoheterotrophic_trait data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='thiosulfate' label='thiosulfate' type=CHEMICAL — in an island with no path to chemolithoheterotrophic_trait data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='sulfate' label='sulfate' type=CHEMICAL — in an island with no path to chemolithoheterotrophic_trait data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='branched_thiosulfate_oxidation' label='branched thiosulfate oxidation pathway' type=PATHWAY — in an island with no path to chemolithoheterotrophic_trait data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='elemental_sulfur' label='elemental sulfur' type=CHEMICAL — in an island with no path to chemolithoheterotrophic_trait +data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/chemolithoheterotrophic.yaml chemolithoheterotrophic_inorganic_energy_organic_carbon FRAGMENTED_GRAPH WARN components=3 of 16 node(s) (sizes: 11, 3, 2) — one record, several unrelated mechanisms data/traits/physiology/chemolithotrophic.yaml chemolithotrophic_inorganic_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='ammonia' label='ammonia' type=CHEMICAL — in an island with no path to chemolithotrophic_trait data/traits/physiology/chemolithotrophic.yaml chemolithotrophic_inorganic_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='ammonia_monooxygenase' label='ammonia monooxygenase' type=GENE_OR_PROTEIN — in an island with no path to chemolithotrophic_trait @@ -1373,11 +1630,16 @@ data/traits/physiology/chemolithotrophic.yaml chemolithotrophic_inorganic_oxidat data/traits/physiology/chemolithotrophic.yaml chemolithotrophic_inorganic_oxidation FRAGMENTED_GRAPH WARN components=5 of 15 node(s) (sizes: 4, 4, 3, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/chemoorganoheterotrophic.yaml chemoorganoheterotrophic_organic_energy_carbon UNREACHABLE_FROM_TRAIT WARN node_id='extracellular_cazymes' label='extracellular carbohydrate-active enzymes' type=MOLECULAR_FUNCTION — in an island with no path to chemoorganoheterotrophic_trait data/traits/physiology/chemoorganoheterotrophic.yaml chemoorganoheterotrophic_organic_energy_carbon UNREACHABLE_FROM_TRAIT WARN node_id='complex_polysaccharides' label='complex polysaccharides' type=CHEMICAL — in an island with no path to chemoorganoheterotrophic_trait +data/traits/physiology/chemoorganoheterotrophic.yaml chemoorganoheterotrophic_organic_energy_carbon INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=PATHWAY here — also BIOLOGICAL_PROCESS×3 elsewhere in the corpus data/traits/physiology/chemoorganoheterotrophic.yaml chemoorganoheterotrophic_organic_energy_carbon FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy UNREACHABLE_FROM_TRAIT WARN node_id='aerobic_respiration' label='aerobic respiration' type=BIOLOGICAL_PROCESS — in an island with no path to chemoorganotrophic_trait data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy UNREACHABLE_FROM_TRAIT WARN node_id='anaerobic_respiration' label='anaerobic respiration' type=BIOLOGICAL_PROCESS — in an island with no path to chemoorganotrophic_trait data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='oxygen' type=ENVIRONMENTAL_FACTOR — in an island with no path to chemoorganotrophic_trait data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy UNREACHABLE_FROM_TRAIT WARN node_id='nitrate_nitrite' label='nitrate/nitrite' type=ENVIRONMENTAL_FACTOR — in an island with no path to chemoorganotrophic_trait +data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=CHEMICAL here — also MOLECULAR_FUNCTION×2 elsewhere in the corpus +data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=ENVIRONMENTAL_FACTOR here — also CHEMICAL×11 elsewhere in the corpus +data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus data/traits/physiology/chemoorganotrophic.yaml chemoorganotrophic_organic_oxidation_energy FRAGMENTED_GRAPH WARN components=3 of 17 node(s) (sizes: 13, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_FROM_TRAIT WARN node_id='chemoreceptor_mcp' label='chemoreceptor (MCP)' type=GENE_OR_PROTEIN — in an island with no path to chemotaxis_trait data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_FROM_TRAIT WARN node_id='chea_kinase' label='CheA histidine kinase' type=GENE_OR_PROTEIN — in an island with no path to chemotaxis_trait @@ -1389,6 +1651,8 @@ data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_ data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_FROM_TRAIT WARN node_id='chew' label='CheW coupling protein' type=GENE_OR_PROTEIN — in an island with no path to chemotaxis_trait data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response UNREACHABLE_FROM_TRAIT WARN node_id='cw_flagellar_rotation' label='clockwise flagellar rotation' type=BIOLOGICAL_PROCESS — in an island with no path to chemotaxis_trait data/traits/physiology/chemotaxis.yaml chemotaxis_gradient_response FRAGMENTED_GRAPH WARN components=2 of 12 node(s) (sizes: 9, 3) — one record, several unrelated mechanisms +data/traits/physiology/chemotrophic.yaml chemotrophic_chemical_redox_energy INCONSISTENT_NODE_TYPE WARN node_id='terminal_electron_acceptor' type=CHEMICAL here — also MOLECULAR_FUNCTION×2 elsewhere in the corpus +data/traits/physiology/chemotrophic.yaml chemotrophic_chemical_redox_energy INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/copiotrophic.yaml copiotrophic_high_nutrient_fast_growth UNREACHABLE_FROM_TRAIT WARN node_id='catabolite_repression' label='catabolite repression / dynamic transcriptional regulation' type=BIOLOGICAL_PROCESS — in an island with no path to copiotrophic_trait data/traits/physiology/copiotrophic.yaml copiotrophic_high_nutrient_fast_growth UNREACHABLE_FROM_TRAIT WARN node_id='proteome_reallocation' label='proteome reallocation' type=BIOLOGICAL_PROCESS — in an island with no path to copiotrophic_trait data/traits/physiology/copiotrophic.yaml copiotrophic_high_nutrient_fast_growth FRAGMENTED_GRAPH WARN components=2 of 15 node(s) (sizes: 13, 2) — one record, several unrelated mechanisms @@ -1396,6 +1660,9 @@ data/traits/physiology/dormancy.yaml dormancy_seed_bank UNREACHABLE_FROM_TRAIT W data/traits/physiology/dormancy.yaml dormancy_seed_bank UNREACHABLE_FROM_TRAIT WARN node_id='protein_synthesis' label='protein synthesis' type=BIOLOGICAL_PROCESS — in an island with no path to dormancy_trait data/traits/physiology/dormancy.yaml dormancy_seed_bank UNREACHABLE_FROM_TRAIT WARN node_id='ribosome' label='ribosome' type=ORGANELLE — in an island with no path to dormancy_trait data/traits/physiology/dormancy.yaml dormancy_seed_bank FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 7, 3) — one record, several unrelated mechanisms +data/traits/physiology/heterotrophic.yaml heterotrophic_organic_carbon_assimilation INCONSISTENT_NODE_TYPE WARN node_id='fermentation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/physiology/hydrogenotrophic.yaml hydrogenotrophic_hydrogen_oxidation_fixation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/physiology/hydrogenotrophic.yaml hydrogenotrophic_hydrogen_oxidation_fixation INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='membrane_dehydrogenase' label='membrane-bound (de)hydrogenase' type=GENE_OR_PROTEIN — in an island with no path to lithoautotrophic_trait data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='electron_transport_chain' label='electron transport chain' type=BIOLOGICAL_PROCESS — in an island with no path to lithoautotrophic_trait data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='proton_motive_force' label='proton motive force' type=CAPACITY — in an island with no path to lithoautotrophic_trait @@ -1403,9 +1670,13 @@ data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='reverse_electron_flow' label='reverse electron flow' type=BIOLOGICAL_PROCESS — in an island with no path to lithoautotrophic_trait data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='nadh_reducing_equivalents' label='NAD(H) reducing equivalents' type=CHEMICAL — in an island with no path to lithoautotrophic_trait data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation UNREACHABLE_FROM_TRAIT WARN node_id='cytbc1_nadh_dehydrogenase' label='cytochrome bc1 and NADH dehydrogenase' type=GENE_OR_PROTEIN — in an island with no path to lithoautotrophic_trait +data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CAPACITY here — also CHEMICAL×1 elsewhere in the corpus +data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=BIOLOGICAL_PROCESS here — also PATHWAY×4 elsewhere in the corpus +data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=CAPACITY here — also BIOLOGICAL_PROCESS×13, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/physiology/lithoautotrophic.yaml lithoautotrophic_inorganic_donor_co2_fixation FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 8, 4, 3) — one record, several unrelated mechanisms data/traits/physiology/lithoheterotrophic.yaml lithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='conductive_pili_cytochromes' label='conductive pili and c-type cytochromes' type=GENE_OR_PROTEIN — in an island with no path to lithoheterotrophic_trait data/traits/physiology/lithoheterotrophic.yaml lithoheterotrophic_inorganic_energy_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='diet' label='direct interspecies electron transfer' type=BIOLOGICAL_PROCESS — in an island with no path to lithoheterotrophic_trait +data/traits/physiology/lithoheterotrophic.yaml lithoheterotrophic_inorganic_energy_organic_carbon INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/physiology/lithoheterotrophic.yaml lithoheterotrophic_inorganic_energy_organic_carbon FRAGMENTED_GRAPH WARN components=2 of 18 node(s) (sizes: 16, 2) — one record, several unrelated mechanisms data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='thiosulfate' label='thiosulfate' type=CHEMICAL — in an island with no path to lithotrophic_trait data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='sox_multienzyme_system' label='Sox multienzyme system' type=GENE_OR_PROTEIN — in an island with no path to lithotrophic_trait @@ -1419,6 +1690,8 @@ data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNR data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='nitrite_oxidoreductase' label='nitrite oxidoreductase (NXR)' type=GENE_OR_PROTEIN — in an island with no path to lithotrophic_trait data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='oxygen' label='molecular oxygen' type=CHEMICAL — in an island with no path to lithotrophic_trait data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy UNREACHABLE_FROM_TRAIT WARN node_id='sulfur_oxidation_process' label='sulfur oxidation' type=BIOLOGICAL_PROCESS — in an island with no path to lithotrophic_trait +data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus +data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy INCONSISTENT_NODE_TYPE WARN node_id='oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×2 elsewhere in the corpus data/traits/physiology/lithotrophic.yaml lithotrophic_inorganic_donor_energy FRAGMENTED_GRAPH WARN components=7 of 19 node(s) (sizes: 7, 2, 2, 2, 2, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='formaldehyde' label='formaldehyde' type=CHEMICAL — in an island with no path to methanotrophic_trait data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='formaldehyde_assimilation' label='formaldehyde assimilation' type=PATHWAY — in an island with no path to methanotrophic_trait @@ -1432,6 +1705,7 @@ data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNRE data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='methanobactin' label='methanobactin' type=CHEMICAL — in an island with no path to methanotrophic_trait data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='cuprous_ion' label='Cu(I)' type=CHEMICAL — in an island with no path to methanotrophic_trait data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation UNREACHABLE_FROM_TRAIT WARN node_id='copper_acquisition' label='copper acquisition' type=BIOLOGICAL_PROCESS — in an island with no path to methanotrophic_trait +data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/physiology/methanotrophic.yaml methanotrophic_methane_oxidation FRAGMENTED_GRAPH WARN components=5 of 20 node(s) (sizes: 8, 6, 2, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation UNREACHABLE_FROM_TRAIT WARN node_id='formaldehyde_dehydrogenase' label='formaldehyde dehydrogenase (Fld/FDH)' type=GENE_OR_PROTEIN — in an island with no path to methylotrophic_trait data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation UNREACHABLE_FROM_TRAIT WARN node_id='formate' label='formate' type=CHEMICAL — in an island with no path to methylotrophic_trait @@ -1441,6 +1715,8 @@ data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation UNREACHABLE_FROM_TRAIT WARN node_id='pqq' label='pyrroloquinoline quinone (PQQ)' type=CHEMICAL — in an island with no path to methylotrophic_trait data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation UNREACHABLE_FROM_TRAIT WARN node_id='calcium_ion' label='calcium ion (Ca2+)' type=CHEMICAL — in an island with no path to methylotrophic_trait data/traits/physiology/methylotrophic.yaml methylotrophic_methanol_assimilation FRAGMENTED_GRAPH WARN components=4 of 19 node(s) (sizes: 12, 3, 2, 2) — one record, several unrelated mechanisms +data/traits/physiology/mixotrophic.yaml mixotrophic_dual_carbon_energy_use INCONSISTENT_NODE_TYPE WARN node_id='electron_transport_chain' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/physiology/mixotrophic.yaml mixotrophic_dual_carbon_energy_use INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/physiology/natural_competence.yaml natural_competence_dna_uptake UNREACHABLE_FROM_TRAIT WARN node_id='pilus_retraction' label='competence pilus retraction' type=BIOLOGICAL_PROCESS — in an island with no path to natural_competence_trait data/traits/physiology/natural_competence.yaml natural_competence_dna_uptake UNREACHABLE_FROM_TRAIT WARN node_id='dna_uptake' label='extracellular DNA uptake' type=BIOLOGICAL_PROCESS — in an island with no path to natural_competence_trait data/traits/physiology/natural_competence.yaml natural_competence_dna_uptake UNREACHABLE_FROM_TRAIT WARN node_id='comec' label='ComEC' type=GENE_OR_PROTEIN — in an island with no path to natural_competence_trait @@ -1456,14 +1732,19 @@ data/traits/physiology/nutrient_adaptation.yaml nutrient_adaptation_life_history data/traits/physiology/nutrient_adaptation.yaml nutrient_adaptation_life_history_axis UNREACHABLE_FROM_TRAIT WARN node_id='maximum_growth_potential' label='maximum growth potential' type=CAPACITY — in an island with no path to nutrient_adaptation_trait/copiotrophic_phenotype/oligotrophic_phenotype data/traits/physiology/nutrient_adaptation.yaml nutrient_adaptation_life_history_axis UNREACHABLE_FROM_TRAIT WARN node_id='carbohydrate_acquisition_genes' label='carbohydrate acquisition gene abundance' type=GENE_OR_PROTEIN — in an island with no path to nutrient_adaptation_trait/copiotrophic_phenotype/oligotrophic_phenotype data/traits/physiology/nutrient_adaptation.yaml nutrient_adaptation_life_history_axis FRAGMENTED_GRAPH WARN components=3 of 13 node(s) (sizes: 8, 3, 2) — one record, several unrelated mechanisms +data/traits/physiology/organoheterotrophic.yaml organoheterotrophic_organic_donor_carbon INCONSISTENT_NODE_TYPE WARN node_id='oxidative_phosphorylation' type=PATHWAY here — also BIOLOGICAL_PROCESS×2 elsewhere in the corpus +data/traits/physiology/organotrophic.yaml organotrophic_organic_compound_oxidation INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='family_a_cytochrome_c_oxidase' label='family A cytochrome c oxidase' type=GENE_OR_PROTEIN — in an island with no path to oxidase_activity_trait data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='reduced_cytochrome_c' label='reduced cytochrome c' type=CHEMICAL — in an island with no path to oxidase_activity_trait data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='cua_center' label='CuA center' type=CHEMICAL — in an island with no path to oxidase_activity_trait data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='heme_a' label='heme a' type=CHEMICAL — in an island with no path to oxidase_activity_trait data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase UNREACHABLE_FROM_TRAIT WARN node_id='cua_cub_copper_centers' label='CuA/CuB copper centers' type=CHEMICAL — in an island with no path to oxidase_activity_trait +data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus data/traits/physiology/oxidase_activity.yaml oxidase_activity_terminal_oxidase FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='antibiotic_resistance' label='antibiotic resistance' type=BIOLOGICAL_PROCESS — in an island with no path to persister_trait data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance UNREACHABLE_FROM_TRAIT WARN node_id='elevated_mic' label='elevated minimum inhibitory concentration' type=QUALITY — in an island with no path to persister_trait +data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance INCONSISTENT_NODE_TYPE WARN node_id='oxidative_phosphorylation' type=BIOLOGICAL_PROCESS here — also PATHWAY×2 elsewhere in the corpus +data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=BIOLOGICAL_PROCESS here — also CAPACITY×2, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/physiology/persister_cell_formation.yaml persister_dormancy_tolerance FRAGMENTED_GRAPH WARN components=2 of 10 node(s) (sizes: 8, 2) — one record, several unrelated mechanisms data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='photosystem_ii' label='photosystem II' type=GENE_OR_PROTEIN — in an island with no path to photoautotrophic_trait data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='water' label='water' type=CHEMICAL — in an island with no path to photoautotrophic_trait @@ -1479,15 +1760,21 @@ data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_car data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='carboxysome' label='carboxysome' type=ORGANELLE — in an island with no path to photoautotrophic_trait data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='carboxysomal_carbonic_anhydrase' label='carboxysomal carbonic anhydrase' type=GENE_OR_PROTEIN — in an island with no path to photoautotrophic_trait data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation UNREACHABLE_FROM_TRAIT WARN node_id='bicarbonate' label='bicarbonate' type=CHEMICAL — in an island with no path to photoautotrophic_trait +data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation INCONSISTENT_NODE_TYPE WARN node_id='molecular_oxygen' type=CHEMICAL here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus data/traits/physiology/photoautotrophic.yaml photoautotrophic_cyanobacterial_carbon_fixation FRAGMENTED_GRAPH WARN components=4 of 16 node(s) (sizes: 9, 3, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='proteorhodopsin' label='proteorhodopsin' type=GENE_OR_PROTEIN — in an island with no path to photoheterotrophic_trait/aerobic_anoxygenic_phototrophs data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon UNREACHABLE_FROM_TRAIT WARN node_id='nadph_anabolic' label='NAD(P)H for anabolic metabolism' type=CHEMICAL — in an island with no path to photoheterotrophic_trait/aerobic_anoxygenic_phototrophs +data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon INCONSISTENT_NODE_TYPE WARN node_id='membrane_potential' type=STATE here — also BIOLOGICAL_PROCESS×1, CHEMICAL×1, QUALITY×1 elsewhere in the corpus data/traits/physiology/photoheterotrophic.yaml photoheterotrophic_light_organic_carbon FRAGMENTED_GRAPH WARN components=2 of 16 node(s) (sizes: 14, 2) — one record, several unrelated mechanisms data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='sulfide' label='sulfide' type=CHEMICAL — in an island with no path to photolithoautotrophic_trait data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='sulfur_oxidation' label='sulfur oxidation' type=BIOLOGICAL_PROCESS — in an island with no path to photolithoautotrophic_trait data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='carbonic_anhydrase' label='carbonic anhydrase' type=GENE_OR_PROTEIN — in an island with no path to photolithoautotrophic_trait data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='bicarbonate' label='bicarbonate' type=CHEMICAL — in an island with no path to photolithoautotrophic_trait data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation UNREACHABLE_FROM_TRAIT WARN node_id='dic_transporter' label='inorganic carbon transporter' type=GENE_OR_PROTEIN — in an island with no path to photolithoautotrophic_trait +data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CAPACITY here — also CHEMICAL×1 elsewhere in the corpus data/traits/physiology/photolithoautotrophic.yaml photolithoautotrophic_light_inorganic_donor_fixation FRAGMENTED_GRAPH WARN components=3 of 15 node(s) (sizes: 10, 3, 2) — one record, several unrelated mechanisms data/traits/physiology/photolithotrophic.yaml photolithotrophic_inorganic_electron_donors UNREACHABLE_FROM_TRAIT WARN node_id='hydrogen_sulfide_oxidation' label='hydrogen sulfide oxidation' type=BIOLOGICAL_PROCESS — in an island with no path to photolithotrophic_trait/photoferrotrophy data/traits/physiology/photolithotrophic.yaml photolithotrophic_inorganic_electron_donors UNREACHABLE_FROM_TRAIT WARN node_id='elemental_sulfur' label='elemental sulfur' type=CHEMICAL — in an island with no path to photolithotrophic_trait/photoferrotrophy @@ -1498,15 +1785,22 @@ data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_li data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons UNREACHABLE_FROM_TRAIT WARN node_id='bchl_photoheterotrophy' label='bacteriochlorophyll-based anoxygenic photoheterotrophy' type=PATHWAY — in an island with no path to photoorganoheterotrophic_trait data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons UNREACHABLE_FROM_TRAIT WARN node_id='diurnal_cycle' label='diurnal dark-light cycle' type=ENVIRONMENTAL_FACTOR — in an island with no path to photoorganoheterotrophic_trait data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons UNREACHABLE_FROM_TRAIT WARN node_id='rhythmic_transcription' label='rhythmic transcription' type=BIOLOGICAL_PROCESS — in an island with no path to photoorganoheterotrophic_trait +data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=STATE here — also BIOLOGICAL_PROCESS×13, CAPACITY×2, CHEMICAL×2 elsewhere in the corpus data/traits/physiology/photoorganoheterotrophic.yaml photoorganoheterotrophic_light_organic_electrons FRAGMENTED_GRAPH WARN components=4 of 16 node(s) (sizes: 10, 2, 2, 2) — one record, several unrelated mechanisms data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='rhodopsin' label='rhodopsin' type=GENE_OR_PROTEIN — in an island with no path to phototrophic_trait data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture UNREACHABLE_FROM_TRAIT WARN node_id='ion_transport' label='ion transport across membrane' type=BIOLOGICAL_PROCESS — in an island with no path to phototrophic_trait +data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='photosynthetic_electron_transport' type=PATHWAY here — also BIOLOGICAL_PROCESS×1 elsewhere in the corpus +data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='reducing_power' type=CAPACITY here — also CHEMICAL×1 elsewhere in the corpus +data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture INCONSISTENT_NODE_TYPE WARN node_id='proton_motive_force' type=CAPACITY here — also BIOLOGICAL_PROCESS×13, CHEMICAL×2, STATE×18 elsewhere in the corpus data/traits/physiology/phototrophic.yaml phototrophic_light_energy_capture FRAGMENTED_GRAPH WARN components=2 of 13 node(s) (sizes: 11, 2) — one record, several unrelated mechanisms data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='rpos' label='RpoS sigma factor' type=GENE_OR_PROTEIN — in an island with no path to vbnc_trait data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='resuscitation' label='resuscitation from VBNC' type=BIOLOGICAL_PROCESS — in an island with no path to vbnc_trait data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='atp' label='ATP' type=CHEMICAL — in an island with no path to vbnc_trait data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='nad_synthesis' label='NAD+ biosynthesis' type=BIOLOGICAL_PROCESS — in an island with no path to vbnc_trait data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy UNREACHABLE_FROM_TRAIT WARN node_id='tca_oxphos' label='TCA cycle flux and oxidative phosphorylation' type=BIOLOGICAL_PROCESS — in an island with no path to vbnc_trait +data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy INCONSISTENT_NODE_TYPE WARN node_id='oxidative_stress' type=BIOLOGICAL_PROCESS here — also ENVIRONMENTAL_FACTOR×1 elsewhere in the corpus +data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy INCONSISTENT_NODE_TYPE WARN node_id='stress_resistance' type=BIOLOGICAL_PROCESS here — also QUALITY×1 elsewhere in the corpus data/traits/physiology/viable_but_nonculturable_state.yaml vbnc_stress_induced_dormancy FRAGMENTED_GRAPH WARN components=2 of 11 node(s) (sizes: 6, 5) — one record, several unrelated mechanisms data/traits/upper/observation.yaml observation_measurement_upper_context UNREACHABLE_FROM_TRAIT WARN node_id='metadata' label='metadata' type=EXPERIMENTAL_FACTOR — in an island with no path to measured_quality/material_entity/material_entity_evaluant/sample data/traits/upper/observation.yaml observation_measurement_upper_context UNREACHABLE_FROM_TRAIT WARN node_id='mixs_standard' label='MIxS reporting standard' type=EXPERIMENTAL_FACTOR — in an island with no path to measured_quality/material_entity/material_entity_evaluant/sample diff --git a/scripts/audit_causal_graphs.py b/scripts/audit_causal_graphs.py index 9f7f7f47..dbb835f2 100644 --- a/scripts/audit_causal_graphs.py +++ b/scripts/audit_causal_graphs.py @@ -42,6 +42,30 @@ IS organism-scoped and is flagged. Widening to QUALITY would need the organism/enzyme distinction, which this heuristic does not make (#353 review). [WARN] + INCONSISTENT_NODE_TYPE one ``node_id`` carrying different ``node_type``s in + different records. The only CROSS-RECORD check here — + neither record is wrong read alone, which is why + nothing caught it. `proton_motive_force` is typed four + ways across 35 records; 63 node_ids disagree with + themselves corpus-wide. #355 made it consequential by + minting `powers` (METPO:2007900) gated on + ``subject_types``, so two byte-identical assertions now + ground or not purely by how the subject is typed + (#356). + + NOT EVERY HIT IS A DEFECT, and the baseline is where + that gets decided rather than here. `terminal + electron acceptor` is typed both CHEMICAL and + MOLECULAR_FUNCTION on purpose — mappings/node_grounding.tsv + carries a row for each, saying "same proposed METPO + class covers both senses; MOLECULAR_FUNCTION typing + surfaces the role-of interpretation". Same two-senses + shape as `reduces` (#330/#333) and the CAPACITY table + in the playbook. Where a family really does mean two + things, the fix is TWO node_ids, not one type: this + check asks whether one id means one thing, and a + curator answering "no, two" resolves it by splitting. + [WARN] UNREACHABLE_FROM_TRAIT a node that IS referenced by some edge, but sits in an island with no undirected path back to any TRAIT node. The graph is several disjoint fragments rather @@ -113,6 +137,7 @@ SEVERITY = { "DUPLICATE_GROUNDING": WARN, "DISPOSITION_MISTYPED": WARN, + "INCONSISTENT_NODE_TYPE": WARN, "DANGLING_EDGE": ERROR, "ORPHAN_NODE": ERROR, "NO_TRAIT_NODE": ERROR, @@ -254,8 +279,36 @@ def connectivity_rows(traits_dir: Path) -> list[dict[str, str]]: re.IGNORECASE) +def node_type_index(traits_dir: Path) -> dict[str, dict[str, int]]: + """``node_id`` → ``{node_type: number of records using it}``, corpus-wide. + + Every other check in this file is scoped to one graph. This one cannot be: + the defect is that two RECORDS disagree, and neither record is wrong when + read alone. #355 is what made it consequential — it minted `METPO:2007900` + (`powers`) gated to ``subject_types = BIOLOGICAL_PROCESS|STATE``, so two + byte-identical assertions now ground or not purely by how their subject is + typed: `carboxydotrophic.yaml`'s `proton_motive_force` (STATE) grounds, + `phototrophic.yaml`'s (CAPACITY) is `blocked_by_node_type` (#356). + """ + index: dict[str, dict[str, int]] = defaultdict(lambda: defaultdict(int)) + for path in sorted(traits_dir.rglob("*.yaml")): + try: + doc = yaml.safe_load(path.read_text()) + except yaml.YAMLError: + continue + if not isinstance(doc, dict): + continue + for graph in (doc.get("causal_graphs") or []): + for node in (graph.get("nodes") or []): + nid, ntype = node.get("node_id"), node.get("node_type") + if nid and ntype: + index[nid][ntype] += 1 + return {k: dict(v) for k, v in index.items()} + + def audit(traits_dir: Path) -> list[dict[str, str]]: findings: list[dict[str, str]] = [] + type_index = node_type_index(traits_dir) for path in sorted(traits_dir.rglob("*.yaml")): try: doc = yaml.safe_load(path.read_text()) @@ -321,6 +374,34 @@ def audit(traits_dir: Path) -> list[dict[str, str]]: f"{'/'.join(trait_nodes)}"), }) + # One node_id, several node_types across the corpus (#356). Reported + # on EVERY occurrence rather than on a presumed-wrong minority, + # because nothing here knows which type is right — `proton_motive_force` + # splits 18 STATE / 13 BIOLOGICAL_PROCESS and the gradient genuinely + # is a state while generating it is a process, so the majority is an + # observation, not a verdict. Per-occurrence rows also mean a family + # clears together the moment it is normalised. + # + # The detail leads with node_id, so `_key` discriminates by node + # within a graph. Deliberately NOT led with the type set: a family + # part-way through a burn-down would re-key on every step and + # un-suppress rows nobody has reached yet, which is the failure + # FRAGMENTED_GRAPH's comment describes from the other direction. + for n in nodes: + nid = n.get("node_id") + ntype = n.get("node_type") + types = type_index.get(nid or "", {}) + if not nid or not ntype or len(types) < 2: + continue + others = ", ".join(f"{t}×{c}" for t, c in sorted(types.items()) + if t != ntype) + findings.append({ + "file": rel, "graph_id": gid, "defect": "INCONSISTENT_NODE_TYPE", + "severity": SEVERITY["INCONSISTENT_NODE_TYPE"], + "detail": (f"node_id={nid!r} type={ntype} here — also {others} " + f"elsewhere in the corpus"), + }) + # Two nodes with the same grounding are one concept modelled twice. by_grounding: dict[str, list[str]] = defaultdict(list) for n in nodes: diff --git a/tests/test_audit_causal_graphs.py b/tests/test_audit_causal_graphs.py index 65b5ccf2..2b024aca 100644 --- a/tests/test_audit_causal_graphs.py +++ b/tests/test_audit_causal_graphs.py @@ -28,6 +28,7 @@ _key, audit, connectivity_rows, + node_type_index, partition, ) @@ -738,3 +739,84 @@ def test_connectivity_out_defaults_next_to_out_not_into_the_repo(tmp_path): assert (out.parent / "causal_graph_connectivity.tsv").exists() assert not (REPO_ROOT / "reports" / "causal_graph_connectivity.tsv").samefile( out.parent / "causal_graph_connectivity.tsv") + + +# --------------------------------------------- INCONSISTENT_NODE_TYPE (#356) + +TYPED_STATE = """\ +identifier: traitmech:000910 +label: a +causal_graphs: +- graph_id: ga + nodes: + - {node_id: trait_a, label: a, node_type: TRAIT} + - {node_id: proton_motive_force, label: pmf, node_type: STATE} + edges: + - {subject: proton_motive_force, object: trait_a, predicate: confers} +""" + +TYPED_CAPACITY = TYPED_STATE.replace("traitmech:000910", "traitmech:000911") \ + .replace("graph_id: ga", "graph_id: gb") \ + .replace("node_type: STATE", "node_type: CAPACITY") + + +def _multi_record(tmp_path: Path, *bodies: str) -> Path: + d = tmp_path / "traits" + d.mkdir(exist_ok=True) + for i, body in enumerate(bodies): + (d / f"rec{i}.yaml").write_text(textwrap.dedent(body)) + return d + + +def test_inconsistent_node_type_is_cross_record(tmp_path): + """Neither record is wrong read alone — which is why nothing caught this + before. Each occurrence is reported, so the family clears together.""" + d = _multi_record(tmp_path, TYPED_STATE, TYPED_CAPACITY) + hits = [f for f in audit(d) if f["defect"] == "INCONSISTENT_NODE_TYPE"] + + assert len(hits) == 2 + assert {f["file"].split("/")[-1] for f in hits} == {"rec0.yaml", "rec1.yaml"} + for f in hits: + assert f["detail"].startswith("node_id='proton_motive_force'") + assert f["severity"] == SEVERITY["INCONSISTENT_NODE_TYPE"] + # Each row names the OTHER typing, so a row is actionable on its own. + assert "CAPACITY×1" in next(f["detail"] for f in hits if f["file"].endswith("rec0.yaml")) + assert "STATE×1" in next(f["detail"] for f in hits if f["file"].endswith("rec1.yaml")) + + +def test_consistent_node_type_across_records_is_silent(tmp_path): + """One id used in twenty records with one type is not a finding — the + check is about disagreement, not about reuse.""" + d = _multi_record(tmp_path, TYPED_STATE, + TYPED_STATE.replace("traitmech:000910", "traitmech:000912") + .replace("graph_id: ga", "graph_id: gc")) + assert [f for f in audit(d) if f["defect"] == "INCONSISTENT_NODE_TYPE"] == [] + + +def test_inconsistent_node_type_keys_on_node_id_not_the_type_set(tmp_path): + """The baseline discriminator must be the node_id. + + Leading with the type set would re-key every row of a family each time one + member is fixed, un-suppressing rows nobody has reached yet — a burn-down + that fights itself. + """ + d = _multi_record(tmp_path, TYPED_STATE, TYPED_CAPACITY) + before = {_key(f) for f in audit(d) if f["defect"] == "INCONSISTENT_NODE_TYPE"} + + # A third record joins with yet another type: the type SET changes, so the + # detail text changes, but the existing rows must keep their identity. + third = TYPED_STATE.replace("traitmech:000910", "traitmech:000913") \ + .replace("graph_id: ga", "graph_id: gd") \ + .replace("node_type: STATE", "node_type: CHEMICAL") + (tmp_path / "traits" / "rec2.yaml").write_text(textwrap.dedent(third)) + after = {_key(f) for f in audit(d) if f["defect"] == "INCONSISTENT_NODE_TYPE"} + + assert before < after # old keys survive verbatim + assert len(after) == len(before) + 1 + + +def test_node_type_index_counts_records_per_type(tmp_path): + d = _multi_record(tmp_path, TYPED_STATE, TYPED_CAPACITY) + idx = node_type_index(d) + assert idx["proton_motive_force"] == {"STATE": 1, "CAPACITY": 1} + assert idx["trait_a"] == {"TRAIT": 2} From abf15edf12d1ab13ca60fb7dba213d66d6abd3fd Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Wed, 12 Aug 2026 20:05:03 -0700 Subject: [PATCH 2/2] Say occurrences, and pin the distinction with a test (#374) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit From review of this PR. node_type_index() was documented as counting "records" and counts node OCCURRENCES. The two are equal everywhere in the corpus today — checked rather than assumed: no node_id appears twice in one graph, and none appears in two graphs of one record (0 and 0). So the docstring was accidentally true, by coincidence rather than construction, and nothing forbids the shape that breaks it. It matters because the count is quoted straight into the finding text — "also STATE×18 elsewhere in the corpus" — whose whole job is to size the disagreement. A record with one node_id in two graphs would silently inflate it. Docstring now says occurrences and says why the distinction is currently invisible. The old test could not see it either (one graph per record, so both readings pass), so there is now a fixture with one node_id in two graphs of one record asserting {"STATE": 2} — one record, two occurrences. 47 tests in this file, 535 total. Co-Authored-By: Claude Opus 5 --- scripts/audit_causal_graphs.py | 9 ++++++++- tests/test_audit_causal_graphs.py | 32 ++++++++++++++++++++++++++++++- 2 files changed, 39 insertions(+), 2 deletions(-) diff --git a/scripts/audit_causal_graphs.py b/scripts/audit_causal_graphs.py index dbb835f2..d917d665 100644 --- a/scripts/audit_causal_graphs.py +++ b/scripts/audit_causal_graphs.py @@ -280,7 +280,14 @@ def connectivity_rows(traits_dir: Path) -> list[dict[str, str]]: def node_type_index(traits_dir: Path) -> dict[str, dict[str, int]]: - """``node_id`` → ``{node_type: number of records using it}``, corpus-wide. + """``node_id`` → ``{node_type: number of NODE OCCURRENCES}``, corpus-wide. + + Occurrences, not records, and the distinction is currently invisible: no + ``node_id`` appears twice in one graph, and none appears in two graphs of + one record, so the two counts are equal everywhere today. Nothing enforces + that, though, and the count is quoted straight into the finding text + ("STATE×18") whose whole job is to size the disagreement — so it says which + it means rather than relying on the corpus staying shaped this way (#374). Every other check in this file is scoped to one graph. This one cannot be: the defect is that two RECORDS disagree, and neither record is wrong when diff --git a/tests/test_audit_causal_graphs.py b/tests/test_audit_causal_graphs.py index 2b024aca..32a16598 100644 --- a/tests/test_audit_causal_graphs.py +++ b/tests/test_audit_causal_graphs.py @@ -815,8 +815,38 @@ def test_inconsistent_node_type_keys_on_node_id_not_the_type_set(tmp_path): assert len(after) == len(before) + 1 -def test_node_type_index_counts_records_per_type(tmp_path): +def test_node_type_index_counts_occurrences_per_type(tmp_path): d = _multi_record(tmp_path, TYPED_STATE, TYPED_CAPACITY) idx = node_type_index(d) assert idx["proton_motive_force"] == {"STATE": 1, "CAPACITY": 1} assert idx["trait_a"] == {"TRAIT": 2} + + +def test_node_type_index_counts_occurrences_not_records(tmp_path): + """Pins the distinction the old fixtures could not see (#374). + + Every fixture above has one graph per record, so occurrence-counting and + record-counting agree and either implementation passes. This record carries + the same node_id in TWO graphs, which is where they diverge — and the count + is quoted into the finding text, so it has to mean what it says. + """ + two_graphs = """\ + identifier: traitmech:000920 + label: a + causal_graphs: + - graph_id: g1 + nodes: + - {node_id: t1, label: t1, node_type: TRAIT} + - {node_id: pmf, label: pmf, node_type: STATE} + edges: + - {subject: pmf, object: t1, predicate: confers} + - graph_id: g2 + nodes: + - {node_id: t2, label: t2, node_type: TRAIT} + - {node_id: pmf, label: pmf, node_type: STATE} + edges: + - {subject: pmf, object: t2, predicate: confers} + """ + idx = node_type_index(_isolated(tmp_path, "two_graphs", two_graphs)) + # One RECORD, two OCCURRENCES. + assert idx["pmf"] == {"STATE": 2}