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..d917d665 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 +279,43 @@ 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 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 + 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 +381,34 @@ 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..32a16598 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 +739,114 @@ 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_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}