ground-or-propose-metpo: residual worklist + Tier-0 env-factor groundings (#187)

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

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 <noreply@anthropic.com>

* #182: drop generic obsolete-GO annotations + mint term-requests for the rest

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 <noreply@anthropic.com>

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

Author: realmarcin

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