From 718bdddcd5b351c9d9ee4da55c02127b6cb772cf Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Fri, 3 Jul 2026 12:52:57 -0700 Subject: [PATCH 1/2] ground-or-propose-metpo: worklist + Tier-0 env-factor groundings MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Scan of all communities → reports/ungrounded_community_terms.tsv (60 recurring concepts, freq>=2; freq-1 tail skipped). biological_processes are all GO-grounded already (prior id-label cleanup), so that surface is empty. Tier-0 grounded the clear environmental-factor condition qualities/referents to PATO/CHEBI (Temperature→PATO:0000146, pH→PATO:0001842, Light→PATO:0015013, O2→CHEBI:15379, H2→CHEBI:18276, sulfate→CHEBI:16189, iron→CHEBI:24875) in mappings/community_term_grounding.tsv; skipped 3 non-ontological design/provenance labels. env_factor/downstream_target have no binding slot yet — groundings recorded in the TSV with an "add EnvironmentalFactor.term slot" follow-up. Deferred (scoped in reports/ground_or_propose_metpo_run.md): the ambiguous interaction-predicate middle + a possible METPO v2 proposal cohort. Co-Authored-By: Claude Fable 5 --- mappings/community_term_grounding.tsv | 14 ++++++ reports/ground_or_propose_metpo_run.md | 33 ++++++++++++++ reports/ungrounded_community_terms.tsv | 61 ++++++++++++++++++++++++++ 3 files changed, 108 insertions(+) create mode 100644 mappings/community_term_grounding.tsv create mode 100644 reports/ground_or_propose_metpo_run.md create mode 100644 reports/ungrounded_community_terms.tsv diff --git a/mappings/community_term_grounding.tsv b/mappings/community_term_grounding.tsv new file mode 100644 index 00000000..9487958c --- /dev/null +++ b/mappings/community_term_grounding.tsv @@ -0,0 +1,14 @@ +surface label target_curie target_label predicate source confidence notes +env_factor Temperature PATO:0000146 temperature skos:exactMatch PATO high condition quality +env_factor pH PATO:0001842 acidity skos:closeMatch PATO high pH is the operational measure of acidity +env_factor Extreme Acidity PATO:0001842 acidity skos:broadMatch PATO high acidophile habitats (AMD etc.) +env_factor Light PATO:0015013 degree of illumination skos:closeMatch PATO high phototroph light regime +env_factor Oxygen Availability CHEBI:15379 dioxygen skos:relatedMatch CHEBI high factor referent is O2; availability is a PATO quality of it (needs schema slot) +env_factor Oxygen gradient CHEBI:15379 dioxygen skos:relatedMatch CHEBI medium spatial O2 gradient +env_factor Anaerobic conditions CHEBI:15379 dioxygen skos:relatedMatch CHEBI medium absence of O2; no clean ENVO/PATO "anoxic condition" quality (proposal candidate) +env_factor Hydrogen Partial Pressure CHEBI:18276 dihydrogen skos:relatedMatch CHEBI high factor referent is H2 partial pressure +env_factor Sulfate Concentration CHEBI:16189 sulfate skos:relatedMatch CHEBI high factor referent is sulfate +env_factor Iron Concentration CHEBI:24875 iron cation skos:relatedMatch CHEBI medium verify exact iron species per record +env_factor defined synthetic community design - - - - - skipped: non-ontological (design descriptor, not an environmental factor) +env_factor Source environment - - - - - skipped: non-ontological (provenance note) +env_factor Agricultural application - - - - - skipped: non-ontological (use-case note) diff --git a/reports/ground_or_propose_metpo_run.md b/reports/ground_or_propose_metpo_run.md new file mode 100644 index 00000000..de04f7e8 --- /dev/null +++ b/reports/ground_or_propose_metpo_run.md @@ -0,0 +1,33 @@ +# ground-or-propose-metpo — run summary + +## Worklist (reports/ungrounded_community_terms.tsv, freq>=2) +- interaction_name: 15 recurring (803 distinct incl. freq-1 tail, skipped) +- downstream_target: 13 recurring (76 distinct) +- env_factor: 32 recurring (537 distinct) +- bioprocess_no_go: 0 — all `biological_processes` already carry GO ids (prior id-label cleanup) + +## Tier-0 grounded this run (mappings/community_term_grounding.tsv) +Environmental-factor condition qualities / referents (the clear mechanical head): +Temperature→PATO:0000146, pH & Extreme Acidity→PATO:0001842 acidity, Light→PATO:0015013, +Oxygen (availability/gradient/anaerobic)→CHEBI:15379 dioxygen, Hydrogen Partial +Pressure→CHEBI:18276 dihydrogen, Sulfate→CHEBI:16189, Iron→CHEBI:24875. +Skipped as non-ontological: "defined synthetic community design" (35×), "Source +environment", "Agricultural application" — narrative/design descriptors, not factors. + +NB: `environmental_factors[].name` and `ecological_interactions[].downstream[].target` +have **no ontology binding slot** in the schema today, so these groundings are recorded +in the mapping TSV only. **Follow-up: add a `term` slot to EnvironmentalFactor** (and +optionally to InteractionDownstream) so the groundings can be written into the YAMLs and +enforced by the id↔label gate. + +## Deferred (ambiguous middle — needs deep-research + possibly a METPO proposal cohort) +- Interaction `name` head (interspecies electron/hydrogen transfer, chain elongation, + DIET+methanogenesis, plant growth promotion, …): mostly **compound narrative labels**; + their primary semantics already live in `interaction_type` (grounded to the v1 METPO + cohort). Reusable primitives worth a METPO/RO/GO decision: "interspecies electron + transfer", "interspecies hydrogen transfer", "cross-feeding" (already METPO v1), + "plant growth promotion". +- downstream_target mineral-dissolution/redox nodes (pyrite/chalcopyrite/bastnaesite + dissolution, iron oxidation): GO/CHEBI-adjacent, no slot. +These are a bounded next batch (≈10–15 `deep-research-community` cluster queries + one +`proposals/metpo_communitymech_v2/` cohort), not run here. diff --git a/reports/ungrounded_community_terms.tsv b/reports/ungrounded_community_terms.tsv new file mode 100644 index 00000000..b31bac81 --- /dev/null +++ b/reports/ungrounded_community_terms.tsv @@ -0,0 +1,61 @@ +surface label count example_community +interaction_name Sulcia Essential Amino Acid Provisioning 3 BioModels_MODEL1806250003_Spittlebug_Sulcia_Sodalis +interaction_name Interspecies Hydrogen Transfer and Methanogenesis 3 Desulfovibrio_Methanococcus_Syntrophy +interaction_name CO2 Fixation and Sucrose Production 3 Synechococcus_Bacillus_SPC +interaction_name Stratified Iron Redox Cycling 2 Australian_Lead_Zinc_Polymetallic +interaction_name Ethanol-Driven Chain Elongation 2 Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture +interaction_name Cross-Feeding with Rhizobium 2 EcoFAB_Ring_Trial_SynCom17 +interaction_name Ethanol Oxidation and Direct Electron Transfer 2 Geobacter_Methanosaeta_DIET +interaction_name Direct Electron Acceptance and Methanogenesis 2 Geobacter_Methanosaeta_DIET +interaction_name Plant Growth Promotion 2 Lotus_LjSC3 +interaction_name Synergistic Lignocellulose Degradation 2 MAMC_M48_Lignocellulose +interaction_name Complementary Iron and Sulfur Oxidation 2 PGM_Spent_Catalyst_Bioleaching +interaction_name Ferrous Iron Oxidation by Leptospirillum 2 Richmond_Mine_AMD_Biofilm +interaction_name Sucrose Uptake and Heterotrophic Growth 2 Synechococcus_Bacillus_SPC +interaction_name Propionate Oxidation and H2/Formate Production 2 Syntrophobacter_Methanobacterium_Syntrophy +interaction_name Interspecies Electron Transfer and Methanogenesis 2 Syntrophobacter_Methanobacterium_Syntrophy +downstream_target REE Dissolution from Bastnaesite and Monazite 3 Bayan_Obo_REE_Tailings_Consortium +downstream_target Interspecies Hydrogen Transfer and Methanogenesis 3 Desulfovibrio_Methanococcus_Syntrophy +downstream_target Copper Sulfide Dissolution 2 Copper_Biomining_Heap_Leach +downstream_target Direct Electron Acceptance and Methanogenesis 2 Geobacter_Methanosaeta_DIET +downstream_target Chalcopyrite Dissolution by Ferric Iron 2 Industrial_Bioreactor_Consortium +downstream_target Teichoic Acid-Mediated HREE Selective Biosorption 2 Ion_Adsorption_REE_Indigenous_Community +downstream_target Vanadium Immobilization via V(IV) Precipitation 2 Panzhihua_Vanadium_Titanium_Tailings +downstream_target Iron Oxidation and Ferric Iron Generation 2 Rammelsberg_Cobalt_Nickel_Tailings +downstream_target Pyrite Dissolution 2 Richmond_Mine_AMD_Biofilm +downstream_target Ferrous Iron Oxidation by Leptospirillum 2 Richmond_Mine_AMD_Biofilm +downstream_target Enhanced Root Colonization and Nodulation 2 Soybean_N_Fixation_sfSynCom +downstream_target Sucrose Uptake and Heterotrophic Growth 2 Synechococcus_Bacillus_SPC +downstream_target Interspecies Electron Transfer and Methanogenesis 2 Syntrophobacter_Methanobacterium_Syntrophy +env_factor defined synthetic community design 35 Aerobic_Denitrification_Disturbance_SynCom +env_factor Temperature 22 AMD_Acidophile_Heterotroph_Network +env_factor pH 14 Bayan_Obo_REE_Tailings_Consortium +env_factor Anaerobic conditions 12 Chlamydomonas_Bacterial_H2_Consortium +env_factor Oxygen Availability 7 AMD_Acidophile_Heterotroph_Network +env_factor Light 5 Chlamydomonas_Bacterial_H2_Consortium +env_factor Substrate 5 Cinnamate_Degradation_Consortium +env_factor Hydrogen Partial Pressure 5 DVM_Triculture +env_factor Cellulose substrate 4 Caldibacillus_Clostridium_Aerotolerant_Cellulose_Coculture +env_factor Metal Concentrations 3 AMD_Acidophile_Heterotroph_Network +env_factor Source environment 3 Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community +env_factor germ-free mouse host 3 Bacteroides_Eubacterium_Gnotobiotic_Gut_Model +env_factor Extreme Acidity 3 Ewaste_Bioleaching_Consortium +env_factor Sulfate Concentration 3 Iberian_Pit_Lake_Stratified_Community +env_factor Oxygen gradient 3 Lac_Pavin_Stratified_Lake_Community +env_factor Target pathogen 3 Maize_Root_Simplified_Community +env_factor Agricultural application 3 Maize_Root_Simplified_Community +env_factor Gas substrate 2 Acetobacterium_Clostridium_CO2_Electrolysis_Coculture +env_factor Application 2 At_RSPHERE_SynCom +env_factor Iron Concentration 2 Australian_Lead_Zinc_Polymetallic +env_factor Oxygen Stratification 2 Australian_Lead_Zinc_Polymetallic +env_factor Redox Potential 2 Chromium_Sulfur_Reduction_Enrichment +env_factor Growth Conditions 2 Dangl_SynComm_35 +env_factor light-dark cycle 2 Emiliania_Phaeobacter_Dynamic_Interaction +env_factor Pili Expression 2 Geobacter_Methanosaeta_DIET +env_factor Birth status 2 Infant_Gut_DNA_Phage_Succession_Community +env_factor Total Vanadium Concentration 2 Panzhihua_Vanadium_Titanium_Tailings +env_factor Methane emissions 2 Prairie_Pothole_Wetland_Sulfur_Carbon_Virus_Community +env_factor Illumination 2 Synechococcus_Azotobacter_Photoproduction_Mutualism +env_factor Hydrogen and Formate Partial Pressure 2 Syntrophobacter_Methanobacterium_Syntrophy +env_factor Ecological Relevance 2 Syntrophobacter_Methanobacterium_Syntrophy +env_factor Anaerobic methanogenic condition 2 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture From 4a8fea41793d863f1ef273eebc538ba1e0a441a0 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Fri, 3 Jul 2026 13:03:11 -0700 Subject: [PATCH 2/2] #182: drop generic obsolete-GO annotations + mint term-requests for the rest MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Per the #182 decision (drop-generic + mint-rest): DROP — remove the low-value generic obsolete-GO biological_process annotations that the id-label cleanup had remapped to broad/mismatched terms: redox process (-> the MF oxidoreductase activity), organic-substance metabolic/catabolic (-> broad parents). 131 entries across 48 files (removal-only; empty biological_processes headers cleaned). KEEP the meaningful remaps (multi-organism -> interspecies interaction GO:0044419, metal-ion sequestering GO:0140487, anion transporter GO:0008509). scripts/drop_obsolete_go_bp.py matches on both the remapped id AND the obsolete-origin preferred_term so legitimate uses are safe. MINT — proposals/term_requests_communitymech.md: CHEBI requests (lead/zinc sulfide, chromium(III) hydroxide, 3-OH-C14-HSL) + an ENVO request (phyllosphere) for the concepts with no exact existing term (currently on nearest-valid stopgaps), with definitions/parents and the source communities. Co-Authored-By: Claude Fable 5 --- .../AMD_Acidophile_Heterotroph_Network.yaml | 20 ----- .../AMD_Nitrososphaerota_Archaeal.yaml | 9 -- ...alborg_East_Full_Scale_EBPR_Community.yaml | 5 -- ...undra_Permafrost_Iron_Redox_Community.yaml | 4 - ...lasmata_CuMMO_Soil_Sediment_Community.yaml | 5 -- kb/communities/At_RSPHERE_SynCom.yaml | 4 - .../Australian_Lead_Zinc_Polymetallic.yaml | 25 ------ .../Bayan_Obo_REE_Tailings_Consortium.yaml | 4 - ...teria_Photosynthetic_Biofilm_Sediment.yaml | 8 -- ...d_Precipitation_Legacy_Soil_Community.yaml | 4 - .../Chromium_Sulfur_Reduction_Enrichment.yaml | 8 -- .../Cinnamate_Degradation_Consortium.yaml | 4 - .../Copper_Biomining_Heap_Leach.yaml | 22 ----- ...East_River_Floodplain_Core_Microbiome.yaml | 8 -- ...Hillslope_Riparian_Transect_Community.yaml | 5 -- .../Ewaste_Bioleaching_Consortium.yaml | 17 ---- .../Ferroplasma_Leptospirillum_Syntrophy.yaml | 22 ----- .../GOM_Oil_Degrading_Consortium.yaml | 5 -- ...ter_Elusimicrobia_Diverse_Metabolisms.yaml | 5 -- ...300_Area_Unconfined_Aquifer_Community.yaml | 9 -- ...Iberian_Pit_Lake_Stratified_Community.yaml | 8 -- .../Industrial_Bioreactor_Consortium.yaml | 45 ---------- ...n_Adsorption_REE_Indigenous_Community.yaml | 15 ---- ...Mixed_Gallium_LED_Recovery_Consortium.yaml | 17 ---- .../Naica_Deep_Subsurface_Thermophilic.yaml | 18 ---- ...Desulfovibrio_Geobacter_Trophic_Model.yaml | 10 --- ...Uranium_Nitrate_Groundwater_Community.yaml | 4 - ...al_FourSpecies_Degradation_Consortium.yaml | 13 --- .../PGM_Spent_Catalyst_Bioleaching.yaml | 21 ----- .../Panzhihua_Vanadium_Titanium_Tailings.yaml | 12 --- .../Phenol_Carboxylation_Consortium.yaml | 9 -- .../Phormidium_Alkaline_Consortium.yaml | 5 -- ...aromonas_Vanadium_Reduction_Community.yaml | 16 ---- ...inated_Ethene_Cometabolism_Enrichment.yaml | 4 - ...dococcus_Chloronitrobenzene_Coculture.yaml | 13 --- .../Rammelsberg_Cobalt_Nickel_Tailings.yaml | 13 --- ...s_Geobacter_Magnetite_Redox_Coculture.yaml | 17 ---- kb/communities/Richmond_Mine_AMD_Biofilm.yaml | 21 ----- .../Rifle_Uranium_Reducing_Community.yaml | 27 ------ ...ch_Inlet_OMZ_Redox_Gradient_Community.yaml | 12 --- ...Salar_Atacama_Lithium_Brine_Community.yaml | 8 -- ...ter_Exoelectrogenic_Biofilm_Community.yaml | 10 --- ...s_Lignin_Dimer_Valorization_Coculture.yaml | 10 --- ...e_Carboxydocella_CO_Aquifer_Community.yaml | 5 -- .../Syntrophus_Benzoate_Degrader.yaml | 4 - .../Thermophilic_Pyrite_QS_Consortium.yaml | 16 ---- .../Tinto_River_Iron_Cycling_Community.yaml | 19 ---- ...desmium_Alteromonas_Marine_Consortium.yaml | 5 -- proposals/term_requests_communitymech.md | 41 +++++++++ scripts/drop_obsolete_go_bp.py | 90 +++++++++++++++++++ 50 files changed, 131 insertions(+), 570 deletions(-) create mode 100644 proposals/term_requests_communitymech.md create mode 100644 scripts/drop_obsolete_go_bp.py diff --git a/kb/communities/AMD_Acidophile_Heterotroph_Network.yaml b/kb/communities/AMD_Acidophile_Heterotroph_Network.yaml index 5353656c..7949d80f 100644 --- a/kb/communities/AMD_Acidophile_Heterotroph_Network.yaml +++ b/kb/communities/AMD_Acidophile_Heterotroph_Network.yaml @@ -287,10 +287,6 @@ ecological_interactions: label: phosphate(3-) notes: Released from nucleic acid and phospholipid degradation biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: aerobic respiration term: id: GO:0009060 @@ -360,10 +356,6 @@ ecological_interactions: label: organic acid notes: Organic acids (malate, citrate, succinate) as electron donors biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -429,10 +421,6 @@ ecological_interactions: label: organic molecular entity notes: Organic carbon required for heterotrophic growth biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -560,10 +548,6 @@ ecological_interactions: term: id: GO:0015979 label: photosynthesis - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: PMID:10939661 supports: SUPPORT @@ -614,10 +598,6 @@ ecological_interactions: term: id: GO:0000272 label: polysaccharide catabolic process - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: doi:10.1007/BF02106205 supports: SUPPORT diff --git a/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml b/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml index e382c688..3eeaa452 100644 --- a/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml +++ b/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml @@ -387,15 +387,6 @@ ecological_interactions: id: CHEBI:29033 label: iron(2+) notes: Also oxidized by Ferroplasma for energy - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:33388792 supports: SUPPORT diff --git a/kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml b/kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml index 93c62b6a..ffdfb0ef 100644 --- a/kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml +++ b/kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml @@ -196,11 +196,6 @@ ecological_interactions: term: id: CHEBI:30089 label: acetate - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:22170425 supports: SUPPORT diff --git a/kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml b/kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml index 93e0dbc0..abbec2b3 100644 --- a/kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml +++ b/kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml @@ -126,10 +126,6 @@ ecological_interactions: term: id: GO:0006826 label: iron ion transport - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:37996661 supports: SUPPORT diff --git a/kb/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.yaml b/kb/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.yaml index 4678232e..e169f9a9 100644 --- a/kb/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.yaml +++ b/kb/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.yaml @@ -57,11 +57,6 @@ ecological_interactions: abstract. interaction_type: COMMENSALISM scope: COMMUNITY_LEVEL - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:34987183 supports: SUPPORT diff --git a/kb/communities/At_RSPHERE_SynCom.yaml b/kb/communities/At_RSPHERE_SynCom.yaml index e0bbf5cf..14a1449f 100644 --- a/kb/communities/At_RSPHERE_SynCom.yaml +++ b/kb/communities/At_RSPHERE_SynCom.yaml @@ -263,10 +263,6 @@ ecological_interactions: id: NCBITaxon:3702 label: Arabidopsis thaliana biological_processes: - - preferred_term: organic substance metabolic process - term: - id: GO:0008152 - label: metabolic process - preferred_term: plant-bacterium mutualism term: id: GO:0044403 diff --git a/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml b/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml index f6d006e4..96c1758b 100644 --- a/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml +++ b/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml @@ -351,10 +351,6 @@ ecological_interactions: label: sulfuric acid notes: Maintains pH 1.5-3.0 for metal solubility biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -427,10 +423,6 @@ ecological_interactions: label: ferrihydrite notes: Fe(III) oxyhydroxide mineral phase biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -568,10 +560,6 @@ ecological_interactions: term: id: GO:0046688 label: response to copper ion - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.3390/min14030255 supports: SUPPORT @@ -632,10 +620,6 @@ ecological_interactions: label: sulfuric acid notes: Produced from sulfur oxidation biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -700,15 +684,6 @@ ecological_interactions: id: CHEBI:29033 label: iron(2+) notes: Product providing substrate for autotrophs - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.1128/aem.02883-07 supports: SUPPORT diff --git a/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml b/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml index bcdfb072..4cb957a5 100644 --- a/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml +++ b/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml @@ -188,10 +188,6 @@ ecological_interactions: label: iron(3+) notes: Product of iron oxidation biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 diff --git a/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml b/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml index 06ee2e5d..7dcffe56 100644 --- a/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml +++ b/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml @@ -88,10 +88,6 @@ ecological_interactions: term: id: GO:0015979 label: photosynthesis - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:25416774 supports: SUPPORT @@ -126,10 +122,6 @@ ecological_interactions: term: id: GO:0019420 label: dissimilatory sulfate reduction - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:25416774 supports: SUPPORT diff --git a/kb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml b/kb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml index fcf7bfed..f4b3ec88 100644 --- a/kb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml +++ b/kb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml @@ -68,10 +68,6 @@ ecological_interactions: id: CHEBI:8005 label: peptidoglycan biological_processes: - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: amino acid biosynthetic process term: id: GO:0008652 diff --git a/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml b/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml index dcbda6e8..428b64e6 100644 --- a/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml +++ b/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml @@ -228,10 +228,6 @@ ecological_interactions: label: chromium(3+) notes: Precipitated Cr(III) product biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: cellular detoxification term: id: GO:1990748 @@ -315,10 +311,6 @@ ecological_interactions: term: id: GO:0019417 label: sulfur oxidation - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.1021/acs.est.8b05053 supports: SUPPORT diff --git a/kb/communities/Cinnamate_Degradation_Consortium.yaml b/kb/communities/Cinnamate_Degradation_Consortium.yaml index 19f29aba..e27ffcf3 100644 --- a/kb/communities/Cinnamate_Degradation_Consortium.yaml +++ b/kb/communities/Cinnamate_Degradation_Consortium.yaml @@ -86,10 +86,6 @@ ecological_interactions: term: id: GO:0006635 label: fatty acid beta-oxidation - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process downstream: - target: Syntrophic Benzoate Degradation evidence: diff --git a/kb/communities/Copper_Biomining_Heap_Leach.yaml b/kb/communities/Copper_Biomining_Heap_Leach.yaml index 3c661889..f6722041 100644 --- a/kb/communities/Copper_Biomining_Heap_Leach.yaml +++ b/kb/communities/Copper_Biomining_Heap_Leach.yaml @@ -235,10 +235,6 @@ ecological_interactions: label: iron(3+) concentration: Generated product; reaches 1.86-1.9 g/L in aged heaps biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -297,10 +293,6 @@ ecological_interactions: label: iron(3+) concentration: 1.86-1.9 g/L in aged heaps biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -349,10 +341,6 @@ ecological_interactions: label: sulfuric acid concentration: Maintains pH 1.5-2.5 biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -413,11 +401,6 @@ ecological_interactions: id: CHEBI:29033 label: iron(2+) notes: Regenerated substrate - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity downstream: - target: Ferrous Iron Oxidation in Early Heaps description: Released Fe²⁺ is re-oxidized to regenerate Fe³⁺ oxidant @@ -460,11 +443,6 @@ ecological_interactions: term: id: CHEBI:26833 label: sulfur atom - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.1111/j.1751-7915.2009.00112.x supports: SUPPORT diff --git a/kb/communities/East_River_Floodplain_Core_Microbiome.yaml b/kb/communities/East_River_Floodplain_Core_Microbiome.yaml index f67f6d92..6097c146 100644 --- a/kb/communities/East_River_Floodplain_Core_Microbiome.yaml +++ b/kb/communities/East_River_Floodplain_Core_Microbiome.yaml @@ -113,10 +113,6 @@ ecological_interactions: term: id: GO:0009060 label: aerobic respiration - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -157,10 +153,6 @@ ecological_interactions: term: id: GO:0015977 label: carbon fixation - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:34022966 supports: SUPPORT diff --git a/kb/communities/East_River_Hillslope_Riparian_Transect_Community.yaml b/kb/communities/East_River_Hillslope_Riparian_Transect_Community.yaml index 8281a96d..5ab7b7d2 100644 --- a/kb/communities/East_River_Hillslope_Riparian_Transect_Community.yaml +++ b/kb/communities/East_River_Hillslope_Riparian_Transect_Community.yaml @@ -320,11 +320,6 @@ ecological_interactions: function associated with the deeper transect microbiome. interaction_type: NICHE_PARTITIONING scope: COMMUNITY_LEVEL - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:31380022 supports: SUPPORT diff --git a/kb/communities/Ewaste_Bioleaching_Consortium.yaml b/kb/communities/Ewaste_Bioleaching_Consortium.yaml index 648710fc..1334a88f 100644 --- a/kb/communities/Ewaste_Bioleaching_Consortium.yaml +++ b/kb/communities/Ewaste_Bioleaching_Consortium.yaml @@ -229,10 +229,6 @@ ecological_interactions: label: copper(2+) concentration: 2.6-4.2 g/L (100% dissolution yield) biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -305,11 +301,6 @@ ecological_interactions: id: CHEBI:30512 label: silver atom notes: Mobilized from traces and solder - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.3389/fmicb.2021.669738 supports: SUPPORT @@ -350,10 +341,6 @@ ecological_interactions: label: sulfuric acid concentration: Maintains pH 1.2 ± 0.1 biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -452,10 +439,6 @@ ecological_interactions: label: sulfuric acid notes: Generated by A. thiooxidans for pH control biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: nitrogen fixation term: id: GO:0009399 diff --git a/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml b/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml index 97aeb5f0..552ad91c 100644 --- a/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml +++ b/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml @@ -146,10 +146,6 @@ ecological_interactions: label: organic molecular entity notes: Secreted organic matter consumed by Ferroplasma biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -213,15 +209,6 @@ ecological_interactions: id: CHEBI:29033 label: iron(2+) notes: Also oxidized by Ferroplasma for energy - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity downstream: - target: Enhanced Chalcopyrite Bioleaching description: Detoxification and enhanced growth improve mineral dissolution @@ -267,10 +254,6 @@ ecological_interactions: id: CHEBI:29034 label: iron(3+) biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -335,11 +318,6 @@ ecological_interactions: id: CHEBI:86471 label: pyrite notes: FeS₂ mineral substrate - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:27535541 supports: SUPPORT diff --git a/kb/communities/GOM_Oil_Degrading_Consortium.yaml b/kb/communities/GOM_Oil_Degrading_Consortium.yaml index 665363be..9b64d4f7 100644 --- a/kb/communities/GOM_Oil_Degrading_Consortium.yaml +++ b/kb/communities/GOM_Oil_Degrading_Consortium.yaml @@ -138,11 +138,6 @@ ecological_interactions: term: id: CHEBI:39106 label: pyrene - biological_processes: - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: doi:10.3389/fmars.2022.962071 supports: SUPPORT diff --git a/kb/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.yaml b/kb/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.yaml index 4ced0d74..ae96436e 100644 --- a/kb/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.yaml +++ b/kb/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.yaml @@ -83,11 +83,6 @@ ecological_interactions: term: id: CHEBI:15379 label: dioxygen - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:32681159 supports: SUPPORT diff --git a/kb/communities/Hanford_300_Area_Unconfined_Aquifer_Community.yaml b/kb/communities/Hanford_300_Area_Unconfined_Aquifer_Community.yaml index 92f65209..eb579f24 100644 --- a/kb/communities/Hanford_300_Area_Unconfined_Aquifer_Community.yaml +++ b/kb/communities/Hanford_300_Area_Unconfined_Aquifer_Community.yaml @@ -110,11 +110,6 @@ ecological_interactions: term: id: CHEBI:17632 label: nitrate - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:22456444 supports: SUPPORT @@ -159,10 +154,6 @@ ecological_interactions: term: id: GO:0019329 label: ammonia oxidation - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:22456444 supports: SUPPORT diff --git a/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml b/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml index 087fa00f..df85c957 100644 --- a/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml +++ b/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml @@ -336,10 +336,6 @@ ecological_interactions: id: CHEBI:29034 label: iron(3+) biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -511,10 +507,6 @@ ecological_interactions: id: NCBITaxon:2301 label: Thermoplasmatales biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: tricarboxylic acid cycle term: id: GO:0006099 diff --git a/kb/communities/Industrial_Bioreactor_Consortium.yaml b/kb/communities/Industrial_Bioreactor_Consortium.yaml index e56dc13d..660088b1 100644 --- a/kb/communities/Industrial_Bioreactor_Consortium.yaml +++ b/kb/communities/Industrial_Bioreactor_Consortium.yaml @@ -373,10 +373,6 @@ ecological_interactions: label: iron(3+) concentration: Generated oxidant; increases to >15 g/L in late stages biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -435,10 +431,6 @@ ecological_interactions: label: sulfuric acid concentration: Maintains pH 1.5-2.0 biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -486,15 +478,6 @@ ecological_interactions: id: CHEBI:50860 label: organic molecular entity notes: Yeast extract, molasses, cell lysate for mixotrophic growth - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - - preferred_term: organic substance metabolic process - term: - id: GO:0008152 - label: metabolic process evidence: - reference: PMID:24242252 supports: SUPPORT @@ -538,10 +521,6 @@ ecological_interactions: label: iron(3+) concentration: '>15 g/L in late stages' biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -603,11 +582,6 @@ ecological_interactions: id: CHEBI:29033 label: iron(2+) notes: Regenerated substrate for iron oxidizers - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity downstream: - target: Thermophilic Ferrous Iron Oxidation in Early Reactor Stages description: Released Fe²⁺ is re-oxidized to regenerate Fe³⁺ oxidant @@ -657,10 +631,6 @@ ecological_interactions: label: peptide notes: From cell lysis; required due to amino acid auxotrophy biological_processes: - - preferred_term: organic substance metabolic process - term: - id: GO:0008152 - label: metabolic process - preferred_term: heterotrophic metabolism term: id: GO:0019319 @@ -703,11 +673,6 @@ ecological_interactions: id: CHEBI:29034 label: iron(3+) notes: Product for chalcopyrite oxidation - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:24242252 supports: SUPPORT @@ -740,11 +705,6 @@ ecological_interactions: id: CHEBI:29033 label: iron(2+) notes: Shared substrate - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.3390/biology12111411 supports: PARTIAL @@ -768,11 +728,6 @@ ecological_interactions: term: id: NCBITaxon:1872114 label: Acidiplasma sp. - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.3390/biology12111411 supports: PARTIAL diff --git a/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml b/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml index 0ddc9663..a84122d5 100644 --- a/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml +++ b/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml @@ -372,11 +372,6 @@ ecological_interactions: id: CHEBI:50860 label: organic molecular entity notes: Diverse organic metabolites driving bioweathering - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process downstream: - target: Teichoic Acid-Mediated HREE Selective Biosorption description: Dissolved REE become available for selective bacterial biosorption @@ -484,11 +479,6 @@ ecological_interactions: id: CHEBI:16995 label: oxalic acid notes: Strong chelator for mineral dissolution - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process downstream: - target: Teichoic Acid-Mediated HREE Selective Biosorption description: Fungal dissolution releases REE for bacterial biosorption @@ -537,11 +527,6 @@ ecological_interactions: id: CHEBI:50860 label: organic molecular entity notes: Exopolysaccharides and organic ligands for REE binding - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: PMID:35708325 supports: PARTIAL diff --git a/kb/communities/Mixed_Gallium_LED_Recovery_Consortium.yaml b/kb/communities/Mixed_Gallium_LED_Recovery_Consortium.yaml index 26eec081..b99645cd 100644 --- a/kb/communities/Mixed_Gallium_LED_Recovery_Consortium.yaml +++ b/kb/communities/Mixed_Gallium_LED_Recovery_Consortium.yaml @@ -204,10 +204,6 @@ ecological_interactions: label: gallium atom concentration: 99.5% leaching efficiency at 15 g/L pulp density in 3 days biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -275,10 +271,6 @@ ecological_interactions: label: nickel(2+) notes: Recovered from LED nickel plating biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -338,10 +330,6 @@ ecological_interactions: label: gallium atom concentration: 99.5% recovery efficiency in 3 days biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -395,11 +383,6 @@ ecological_interactions: id: CHEBI:29034 label: iron(3+) notes: Biogenic oxidant in lixiviant - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:31203122 supports: SUPPORT diff --git a/kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml b/kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml index 79ee9533..cb294c05 100644 --- a/kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml +++ b/kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml @@ -248,10 +248,6 @@ ecological_interactions: term: id: GO:0015977 label: carbon fixation - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity downstream: - target: Denitrification by Betaproteobacteria description: Nitrite from ammonia oxidation supports denitrification @@ -297,11 +293,6 @@ ecological_interactions: id: CHEBI:50860 label: organic molecular entity concentration: Trace (<1 mg/L DOC typical) - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: doi:10.3389/fmicb.2013.00037 supports: SUPPORT @@ -389,15 +380,6 @@ ecological_interactions: id: CHEBI:18276 label: dihydrogen notes: Potential electron donor - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.3389/fmicb.2013.00037 supports: SUPPORT diff --git a/kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml b/kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml index 76ddabe1..5886e52e 100644 --- a/kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml +++ b/kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml @@ -207,11 +207,6 @@ ecological_interactions: term: id: CHEBI:18012 label: fumaric acid - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.1186/1471-2180-10-149 supports: SUPPORT @@ -238,11 +233,6 @@ ecological_interactions: term: id: NCBITaxon:2 label: Bacteria - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.1186/1471-2180-10-149 supports: SUPPORT diff --git a/kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml b/kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml index 93457a35..8451b28a 100644 --- a/kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml +++ b/kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml @@ -154,10 +154,6 @@ ecological_interactions: id: CHEBI:29034 label: iron(3+) biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: denitrification term: id: GO:0019333 diff --git a/kb/communities/PET_Artificial_FourSpecies_Degradation_Consortium.yaml b/kb/communities/PET_Artificial_FourSpecies_Degradation_Consortium.yaml index df586748..ba0ecf1c 100644 --- a/kb/communities/PET_Artificial_FourSpecies_Degradation_Consortium.yaml +++ b/kb/communities/PET_Artificial_FourSpecies_Degradation_Consortium.yaml @@ -146,11 +146,6 @@ ecological_interactions: term: id: CHEBI:53259 label: poly(ethylene terephthalate) macromolecule - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: PMID:35003008 supports: SUPPORT @@ -182,10 +177,6 @@ ecological_interactions: id: CHEBI:15702 label: terephthalic acid biological_processes: - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: biological process involved in interspecies interaction between organisms term: id: GO:0044419 @@ -221,10 +212,6 @@ ecological_interactions: id: CHEBI:30742 label: ethylene glycol biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: biological process involved in interspecies interaction between organisms term: id: GO:0044419 diff --git a/kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml b/kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml index d94bcc42..e4fde633 100644 --- a/kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml +++ b/kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml @@ -262,10 +262,6 @@ ecological_interactions: label: sulfuric acid notes: Complementary acid generation biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -395,10 +391,6 @@ ecological_interactions: label: aluminium oxide notes: γ-Al₂O₃ catalyst support (substrate) biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -477,10 +469,6 @@ ecological_interactions: label: rhodium atom notes: Target PGM from automotive TWC catalysts biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -555,11 +543,6 @@ ecological_interactions: id: CHEBI:33359 label: rhodium atom notes: Target from automotive catalysts - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.1016/j.jenvman.2019.04.081 supports: SUPPORT @@ -622,10 +605,6 @@ ecological_interactions: term: id: GO:0006790 label: sulfur compound metabolic process - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:31059950 supports: SUPPORT diff --git a/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml b/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml index f6449310..e3b64a3e 100644 --- a/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml +++ b/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml @@ -444,10 +444,6 @@ ecological_interactions: label: acetate notes: Electron donor from fermentation and root exudates biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: dissimilatory reduction term: id: GO:0019645 @@ -518,10 +514,6 @@ ecological_interactions: term: id: GO:0015976 label: carbon utilization - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: cellular carbohydrate metabolic process term: id: GO:0005975 @@ -649,10 +641,6 @@ ecological_interactions: label: copper(2+) notes: Tolerated through efflux and sequestration biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: cellular response to metal ion term: id: GO:0071248 diff --git a/kb/communities/Phenol_Carboxylation_Consortium.yaml b/kb/communities/Phenol_Carboxylation_Consortium.yaml index 2c01c210..807a8860 100644 --- a/kb/communities/Phenol_Carboxylation_Consortium.yaml +++ b/kb/communities/Phenol_Carboxylation_Consortium.yaml @@ -103,10 +103,6 @@ ecological_interactions: term: id: GO:0018958 label: phenol-containing compound metabolic process - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process downstream: - target: Benzoate Degradation to Acetate and Methane evidence: @@ -183,11 +179,6 @@ ecological_interactions: id: CHEBI:18276 label: dihydrogen notes: Potential electron carrier - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:18281436 supports: SUPPORT diff --git a/kb/communities/Phormidium_Alkaline_Consortium.yaml b/kb/communities/Phormidium_Alkaline_Consortium.yaml index e7758a7a..ec055d90 100644 --- a/kb/communities/Phormidium_Alkaline_Consortium.yaml +++ b/kb/communities/Phormidium_Alkaline_Consortium.yaml @@ -245,11 +245,6 @@ ecological_interactions: term: id: CHEBI:18276 label: dihydrogen - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process downstream: - target: Nutrient Remineralization description: Heterotrophs remineralize nutrients for cyanobacterial reuse diff --git a/kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml b/kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml index 3548120c..077d93d7 100644 --- a/kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml +++ b/kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml @@ -231,10 +231,6 @@ ecological_interactions: label: acetate concentration: 2-10 mM supplied or produced from lactate biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: dissimilatory reduction term: id: GO:0019645 @@ -294,10 +290,6 @@ ecological_interactions: label: vanadium dioxide notes: VO₂ and hydrated forms as precipitates biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: metal ion sequestration term: id: GO:0140487 @@ -365,10 +357,6 @@ ecological_interactions: term: id: GO:0019420 label: dissimilatory sulfate reduction - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:33125214 supports: SUPPORT @@ -426,10 +414,6 @@ ecological_interactions: label: vanadate(3-) notes: Secondary electron acceptor after Fe(III) depletion biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 diff --git a/kb/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml b/kb/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml index f66f61d7..295e12ad 100644 --- a/kb/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml +++ b/kb/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml @@ -250,10 +250,6 @@ ecological_interactions: term: id: GO:0071466 label: cellular response to xenobiotic stimulus - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: doi:10.1016/j.jenvman.2026.129957 supports: SUPPORT diff --git a/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml b/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml index 33d8e5c0..d750a460 100644 --- a/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml +++ b/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml @@ -117,10 +117,6 @@ ecological_interactions: id: CHEBI:34399 label: 4-Chloronitrobenzene biological_processes: - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: interspecies interaction between organisms term: id: GO:0044419 @@ -151,10 +147,6 @@ ecological_interactions: id: NCBITaxon:303 label: Pseudomonas putida biological_processes: - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: interspecies interaction between organisms term: id: GO:0044419 @@ -188,11 +180,6 @@ ecological_interactions: term: id: CHEBI:34399 label: 4-Chloronitrobenzene - biological_processes: - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: PMID:10049867 supports: SUPPORT diff --git a/kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml b/kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml index 0412d966..584bbfdf 100644 --- a/kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml +++ b/kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml @@ -160,10 +160,6 @@ ecological_interactions: term: id: GO:0006826 label: iron ion transport - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity downstream: - target: Cobalt and Copper Mobilization from Sulfide Minerals description: Ferric iron oxidizes sulfide minerals releasing cobalt and copper @@ -220,11 +216,6 @@ ecological_interactions: id: CHEBI:16189 label: sulfate notes: Product of sulfide mineral oxidation - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity downstream: - target: Iron Oxidation and Ferric Iron Generation description: Fe²⁺ released from mineral oxidation is recycled to At. ferrooxidans @@ -283,10 +274,6 @@ ecological_interactions: label: sulfate notes: Final oxidation product biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 diff --git a/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml b/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml index af9e103e..49de4831 100644 --- a/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml +++ b/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml @@ -123,10 +123,6 @@ ecological_interactions: id: CHEBI:29034 label: iron(3+) biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -166,10 +162,6 @@ ecological_interactions: term: id: GO:0015979 label: photosynthesis - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:25814583 supports: SUPPORT @@ -201,10 +193,6 @@ ecological_interactions: id: CHEBI:29033 label: iron(2+) biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -226,11 +214,6 @@ ecological_interactions: term: id: CHEBI:50821 label: ferrosoferric oxide - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:25814583 supports: SUPPORT diff --git a/kb/communities/Richmond_Mine_AMD_Biofilm.yaml b/kb/communities/Richmond_Mine_AMD_Biofilm.yaml index 245e3c33..07312336 100644 --- a/kb/communities/Richmond_Mine_AMD_Biofilm.yaml +++ b/kb/communities/Richmond_Mine_AMD_Biofilm.yaml @@ -258,10 +258,6 @@ ecological_interactions: label: iron(3+) concentration: Generated continuously to oxidize pyrite biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -314,10 +310,6 @@ ecological_interactions: id: CHEBI:29034 label: iron(3+) biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: carbon fixation term: id: GO:0015977 @@ -381,11 +373,6 @@ ecological_interactions: id: CHEBI:26836 label: sulfuric acid concentration: Generates pH 0.5-1.0 - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity downstream: - target: Ferrous Iron Oxidation by Leptospirillum description: Released Fe(II) is re-oxidized by iron-oxidizing community @@ -480,10 +467,6 @@ ecological_interactions: label: organic molecular entity notes: Lysed cell components and fermentation products biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: tricarboxylic acid cycle term: id: GO:0006099 @@ -537,10 +520,6 @@ ecological_interactions: id: CHEBI:26833 label: sulfur atom biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 diff --git a/kb/communities/Rifle_Uranium_Reducing_Community.yaml b/kb/communities/Rifle_Uranium_Reducing_Community.yaml index e6c612a2..8e6f8ec9 100644 --- a/kb/communities/Rifle_Uranium_Reducing_Community.yaml +++ b/kb/communities/Rifle_Uranium_Reducing_Community.yaml @@ -224,10 +224,6 @@ ecological_interactions: label: iron(2+) notes: Product of Fe(III) reduction biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: acetate catabolic process term: id: GO:0045733 @@ -278,11 +274,6 @@ ecological_interactions: id: CHEBI:32995 label: uranium(4+) notes: As uraninite (UO₂) nanoparticles - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:14532040 supports: SUPPORT @@ -320,11 +311,6 @@ ecological_interactions: term: id: CHEBI:32995 label: uranium(4+) - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:18843300 supports: SUPPORT @@ -378,10 +364,6 @@ ecological_interactions: term: id: GO:0019420 label: dissimilatory sulfate reduction - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:14532040 supports: SUPPORT @@ -422,11 +404,6 @@ ecological_interactions: id: CHEBI:16189 label: sulfate notes: Becomes dominant electron acceptor after Fe(III) depletion - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:14532040 supports: SUPPORT @@ -484,10 +461,6 @@ ecological_interactions: term: id: GO:0019420 label: dissimilatory sulfate reduction - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:12788780 supports: SUPPORT diff --git a/kb/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.yaml b/kb/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.yaml index ec76cc59..7327212f 100644 --- a/kb/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.yaml +++ b/kb/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.yaml @@ -181,10 +181,6 @@ ecological_interactions: term: id: GO:0019333 label: denitrification pathway - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:27655888 supports: SUPPORT @@ -227,10 +223,6 @@ ecological_interactions: term: id: GO:0019333 label: denitrification pathway - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:27655888 supports: SUPPORT @@ -272,10 +264,6 @@ ecological_interactions: term: id: GO:0019333 label: denitrification pathway - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:27655888 supports: SUPPORT diff --git a/kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml b/kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml index 54a24f9d..70078ea1 100644 --- a/kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml +++ b/kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml @@ -264,10 +264,6 @@ ecological_interactions: label: organic molecular entity notes: Diverse organic carbon sources including polysaccharides, proteins, amino acids biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: aerobic respiration term: id: GO:0009060 @@ -387,10 +383,6 @@ ecological_interactions: label: organic molecular entity notes: Diverse organic carbon sources biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process - preferred_term: aerobic respiration term: id: GO:0009060 diff --git a/kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml b/kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml index ce9cce47..d764bb53 100644 --- a/kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml +++ b/kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml @@ -156,11 +156,6 @@ ecological_interactions: term: id: NCBITaxon:35554 label: Geobacter sulfurreducens - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:28087529 supports: SUPPORT @@ -187,11 +182,6 @@ ecological_interactions: term: id: NCBITaxon:2 label: Bacteria - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:28087529 supports: SUPPORT diff --git a/kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml b/kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml index 0a898508..a90ac73b 100644 --- a/kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml +++ b/kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml @@ -119,11 +119,6 @@ ecological_interactions: id: CHEBI:53650 label: guaiacylglycerol-beta-guaiacyl ether notes: Representative beta-O-4 lignin-derived dimer substrate tested in the study. - biological_processes: - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: PMID:36030484 supports: SUPPORT @@ -151,11 +146,6 @@ ecological_interactions: id: CHEBI:30778 label: gallic acid notes: The publication reports gallate as a target product. - biological_processes: - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: PMID:36030484 supports: SUPPORT diff --git a/kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml b/kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml index 3e7b1746..3d2e5ebc 100644 --- a/kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml +++ b/kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml @@ -45,11 +45,6 @@ ecological_interactions: switching after the scCO2 injection experiment. interaction_type: CROSS_FEEDING scope: COMMUNITY_LEVEL - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity evidence: - reference: PMID:32633030 supports: SUPPORT diff --git a/kb/communities/Syntrophus_Benzoate_Degrader.yaml b/kb/communities/Syntrophus_Benzoate_Degrader.yaml index a1e5a2d0..38ec8f78 100644 --- a/kb/communities/Syntrophus_Benzoate_Degrader.yaml +++ b/kb/communities/Syntrophus_Benzoate_Degrader.yaml @@ -110,10 +110,6 @@ ecological_interactions: term: id: GO:0018874 label: benzoate metabolic process - - preferred_term: aromatic compound catabolic process - term: - id: GO:0009056 - label: catabolic process downstream: - target: Interspecies Hydrogen Transfer and Methanogenesis description: H2 and formate produced by S. aciditrophicus are consumed by M. hungatei for methanogenesis diff --git a/kb/communities/Thermophilic_Pyrite_QS_Consortium.yaml b/kb/communities/Thermophilic_Pyrite_QS_Consortium.yaml index 8ca65038..827ad12e 100644 --- a/kb/communities/Thermophilic_Pyrite_QS_Consortium.yaml +++ b/kb/communities/Thermophilic_Pyrite_QS_Consortium.yaml @@ -241,10 +241,6 @@ ecological_interactions: label: iron(3+) concentration: Product for mineral oxidation; regulated by QS biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -313,10 +309,6 @@ ecological_interactions: label: sulfuric acid concentration: Maintains pH 2.0-2.5 biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: sulfur compound metabolic process term: id: GO:0006790 @@ -377,10 +369,6 @@ ecological_interactions: id: CHEBI:26836 label: sulfuric acid biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -467,10 +455,6 @@ ecological_interactions: label: sulfuric acid notes: From sulfur oxidation biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: biofilm formation term: id: GO:0042710 diff --git a/kb/communities/Tinto_River_Iron_Cycling_Community.yaml b/kb/communities/Tinto_River_Iron_Cycling_Community.yaml index 8a98a52e..dec968b3 100644 --- a/kb/communities/Tinto_River_Iron_Cycling_Community.yaml +++ b/kb/communities/Tinto_River_Iron_Cycling_Community.yaml @@ -195,11 +195,6 @@ ecological_interactions: term: id: CHEBI:29034 label: iron(3+) - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity downstream: - target: Heterotrophic Carbon-Iron Coupling description: Autotrophic production supports heterotrophs @@ -222,11 +217,6 @@ ecological_interactions: term: id: NCBITaxon:522 label: Acidiphilium - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: doi:10.1128/aem.69.8.4853-4865.2003 supports: PARTIAL @@ -305,10 +295,6 @@ ecological_interactions: id: CHEBI:26836 label: sulfuric acid biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity - preferred_term: iron ion transport term: id: GO:0006826 @@ -353,11 +339,6 @@ ecological_interactions: id: CHEBI:50860 label: organic molecular entity notes: Complex organic polymers from algae and microbial biomass - biological_processes: - - preferred_term: organic substance catabolic process - term: - id: GO:0009056 - label: catabolic process evidence: - reference: PMID:25369810 supports: SUPPORT diff --git a/kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml b/kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml index b390a6f0..43cb43ec 100644 --- a/kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml +++ b/kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml @@ -115,11 +115,6 @@ ecological_interactions: label: iron(2+) notes: Iron acquisition was one inferred interaction axis; ferrous iron is used as a conservative CHEBI grounding for iron availability. - biological_processes: - - preferred_term: oxidation-reduction process - term: - id: GO:0016491 - label: oxidoreductase activity notes: Reactive oxygen species detoxification is an inferred interaction process. evidence: - reference: PMID:28440800 diff --git a/proposals/term_requests_communitymech.md b/proposals/term_requests_communitymech.md new file mode 100644 index 00000000..613b9bf0 --- /dev/null +++ b/proposals/term_requests_communitymech.md @@ -0,0 +1,41 @@ +# Ontology term requests — CommunityMech (#182 "mint") + +Concepts used in `kb/communities/` whose intended term does not exist in the target +ontology. Each is currently grounded to the **nearest valid** existing term (so the +id↔label gate stays green and `preferred_term` keeps the specific meaning); this file +requests the proper terms so the groundings can be tightened once minted. Verified +absent via OAK (sqlite:obo:*) + live OLS/NCBI. + +## CHEBI term requests (submit at https://github.com/ebi-teams/chebi-submissions) + +| Requested term | Formula | Proposed parent (CHEBI) | Current stopgap grounding | Source community | +|---|---|---|---|---| +| lead(II) sulfide (galena) | PbS | metal sulfide / sulfide salt (CHEBI:46718); cf. lead(2+) CHEBI:49807 | CHEBI:46718 sulfide salt | Australian_Lead_Zinc_Polymetallic | +| zinc sulfide (sphalerite) | ZnS | metal sulfide / sulfide salt (CHEBI:46718); cf. zinc(2+) CHEBI:29105 | CHEBI:46718 sulfide salt | Australian_Lead_Zinc_Polymetallic | +| chromium(III) hydroxide | Cr(OH)3 | transition-element hydroxide; cf. chromium(3+) CHEBI:49544 | CHEBI:49544 chromium(3+) | Chromium_Sulfur_Reduction_Enrichment | +| N-(3-hydroxytetradecanoyl)-L-homoserine lactone (3-OH-C14-HSL) | C18H33NO4 | N-acyl-L-homoserine lactone (CHEBI:55474) | CHEBI:55474 N-acyl-L-homoserine lactone | Thermophilic_Pyrite_QS_Consortium | + +Definitions (Aristotelian, for the submission): +- **lead(II) sulfide** — a metal sulfide that is the lead(2+) salt of sulfide; the mineral galena. +- **zinc sulfide** — a metal sulfide that is the zinc(2+) salt of sulfide; the mineral sphalerite/wurtzite. +- **chromium(III) hydroxide** — a chromium hydroxide in which chromium is in the +3 oxidation state. +- **N-(3-hydroxytetradecanoyl)-L-homoserine lactone** — an N-acyl-L-homoserine lactone in which the acyl group is 3-hydroxytetradecanoyl (a saturated 3-OH C14 AHL quorum-sensing signal). + +## ENVO term request (submit at https://github.com/EnvironmentOntology/envo/issues) + +| Requested term | Proposed parent (ENVO) | Current stopgap grounding | Source community | +|---|---|---|---| +| phyllosphere | plant-associated environment (ENVO:01001001) | ENVO:01001001 plant-associated environment | Arabidopsis_Phyllosphere_SynCom7 | + +- **phyllosphere** — a plant-associated environment comprising the aerial surfaces of a plant (leaves and stems) and their resident microbiota. + +## Regrounding notes (no new term needed) +- **organic matter** — reground from `CHEBI:50860` (organic molecular entity) to **`ENVO:01000155` organic material** (already exists; better fit for a material/factor). Affects Avena_Rhizosphere_Detritusphere_Niche_Succession, Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community. +- **humic acid**, **yeast extract** — complex undefined mixtures; CHEBI does not mint undefined mixtures. Better handled as a MediaIngredientMech / FoodOn ingredient term (yeast extract) or ENVO material (humic substance). Kept at the current broad CHEBI grounding for now. +- **Stenotrophomonas goyi** — a validly published 2023 species not yet in the pinned NCBITaxon snapshot; grounded at genus `NCBITaxon:40323`. No proposal — it will resolve when NCBITaxon is refreshed. + +## Companion: dropped terms +The generic obsolete-GO annotations (redox process, organic-substance metabolic/catabolic) +were **dropped** rather than kept (131 entries, 48 files) — see `scripts/drop_obsolete_go_bp.py`. +Meaningful obsolete-GO remaps were kept (multi-organism → interspecies interaction +`GO:0044419`, metal-ion sequestering `GO:0140487`, anion transporter `GO:0008509`). diff --git a/scripts/drop_obsolete_go_bp.py b/scripts/drop_obsolete_go_bp.py new file mode 100644 index 00000000..11b95330 --- /dev/null +++ b/scripts/drop_obsolete_go_bp.py @@ -0,0 +1,90 @@ +#!/usr/bin/env python3 +"""Drop the low-value generic obsolete-GO biological_process annotations (#182). + +The id-label cleanup remapped obsolete generic GO terms to the nearest valid +current term. Per the #182 decision, the *generic* ones (redox process -> the MF +oxidoreductase activity; organic-substance metabolic/catabolic -> broad parents) +add little and are dropped here. Meaningful remaps are KEPT (multi-organism -> +interspecies interaction GO:0044419, metal-ion sequestering GO:0140487, anion +transporter GO:0008509). + +Matches a biological_process entry only when BOTH the remapped id AND the +obsolete-origin preferred_term match, so legitimate uses of the target terms are +untouched. Removes the 4-line entry; if that empties a biological_processes list, +removes the header line too. Text-only (no reflow). + +Usage: uv run python scripts/drop_obsolete_go_bp.py [--dry-run] +""" + +from __future__ import annotations + +import re +import sys +from pathlib import Path + +DRY = "--dry-run" in sys.argv +COMMUNITIES = Path("kb/communities") + +# (preferred_term, remapped_id) pairs to drop. +DROP = { + ("oxidation-reduction process", "GO:0016491"), + ("organic substance metabolic process", "GO:0008152"), + ("organic substance catabolic process", "GO:0009056"), + ("aromatic compound catabolic process", "GO:0009056"), +} + + +def drop_file(path: Path) -> int: + lines = path.read_text().splitlines() + out: list[str] = [] + i, removed = 0, 0 + while i < len(lines): + m = re.match(r"^(\s*)- preferred_term: (.+?)\s*$", lines[i]) + if m and i + 3 < len(lines): + indent, pt = m.group(1), m.group(2) + term_ok = re.match(rf"^{indent} term:\s*$", lines[i + 1]) + idm = re.match(rf"^{indent} id: (\S+)\s*$", lines[i + 2]) + label_ok = re.match(rf"^{indent} label:", lines[i + 3]) + if term_ok and idm and label_ok and (pt, idm.group(1)) in DROP: + i += 4 # skip the whole entry + removed += 1 + continue + out.append(lines[i]) + i += 1 + + if not removed: + return 0 + + # Remove any biological_processes: header that no longer has list items. + cleaned: list[str] = [] + j = 0 + while j < len(out): + hm = re.match(r"^(\s*)biological_processes:\s*$", out[j]) + if hm: + nxt = out[j + 1] if j + 1 < len(out) else "" + if not re.match(rf"^{hm.group(1)}- ", nxt): # no remaining list items + j += 1 + continue + cleaned.append(out[j]) + j += 1 + + if not DRY: + path.write_text("\n".join(cleaned) + "\n") + return removed + + +def main() -> int: + total, files = 0, 0 + for f in sorted(COMMUNITIES.glob("*.yaml")): + n = drop_file(f) + if n: + files += 1 + total += n + print(f" -{n:2d} {f.name}") + tag = "[DRY] " if DRY else "" + print(f"\n{tag}dropped {total} generic obsolete-GO entries across {files} files") + return 0 + + +if __name__ == "__main__": + raise SystemExit(main())