ground-or-propose-metpo: residual worklist + Tier-0 env-factor groundings

kb/communities/AMD_Acidophile_Heterotroph_Network.yaml

@@ -327,10 +327,6 @@ 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
@@ -400,10 +396,6 @@ 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
@@ -469,10 +461,6 @@ 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
@@ -600,10 +588,6 @@ 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
@@ -654,10 +638,6 @@ 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

kb/communities/AMD_Nitrososphaerota_Archaeal.yaml

@@ -411,15 +411,6 @@ 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

kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml

@@ -220,11 +220,6 @@ 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

kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml

@@ -150,10 +150,6 @@ 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

kb/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.yaml

@@ -65,11 +65,6 @@ 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

kb/communities/At_RSPHERE_SynCom.yaml

@@ -271,10 +271,6 @@ 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

kb/communities/Australian_Lead_Zinc_Polymetallic.yaml

@@ -399,10 +399,6 @@ 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
@@ -475,10 +471,6 @@ 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
@@ -616,10 +608,6 @@ 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
@@ -680,10 +668,6 @@ 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
@@ -748,15 +732,6 @@ 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

kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml

@@ -212,10 +212,6 @@ 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

kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml

@@ -96,10 +96,6 @@ 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
@@ -134,10 +130,6 @@ 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

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

kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml

@@ -252,10 +252,6 @@ 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
@@ -339,10 +335,6 @@ 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

kb/communities/Cinnamate_Degradation_Consortium.yaml

@@ -110,10 +110,6 @@ 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:

kb/communities/Copper_Biomining_Heap_Leach.yaml

@@ -275,10 +275,6 @@ 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
@@ -337,10 +333,6 @@ 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
@@ -389,10 +381,6 @@ 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
@@ -453,11 +441,6 @@ 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
@@ -500,11 +483,6 @@ 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

kb/communities/East_River_Floodplain_Core_Microbiome.yaml

@@ -137,10 +137,6 @@ 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
@@ -181,10 +177,6 @@ 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

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

kb/communities/Ewaste_Bioleaching_Consortium.yaml

@@ -269,10 +269,6 @@ 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
@@ -345,11 +341,6 @@ 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
@@ -390,10 +381,6 @@ 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
@@ -492,10 +479,6 @@ 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