Predicate residual v5: rename 10 paraphrases + re-ground (−56 edges)

data/traits/ecology/biosafety_level.yaml

@@ -73,7 +73,7 @@ causal_graphs:
     description: Proposed enhanced classification beyond BSL-4.
   edges:
   - subject: pathogen_hazard_properties
-    predicate: determines
+    predicate: causes
     object: biosafety_level_trait
     description: Pathogen transmissibility, severity, and treatability jointly determine
       biosafety-level classification.
@@ -82,6 +82,7 @@ causal_graphs:
       snippet: virulence factors
       notes: Supports pathogen virulence properties as the biological inputs for hazard-level
         classification.
+    predicate_id: biolink:causes
   - subject: biosafety_level_trait
     predicate: mandates
     object: containment_requirements
@@ -161,3 +162,15 @@ curation_history:
   changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
     (rdfs:subClassOf×5).
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
+    determines → causes ×1.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:49Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (biolink:causes×1).
+  llm_assisted: true

data/traits/environment/aerobic.yaml

@@ -53,14 +53,15 @@ causal_graphs:
     grounding: METPO:1007504
   edges:
   - subject: aerobic_trait
-    predicate: requires
+    predicate: depends on
     object: molecular_oxygen
     description: Aerobic growth depends on molecular oxygen availability.
     evidence:
     - reference: DOI:10.1016/j.celrep.2023.112444
       snippet: obligate aerobe ... exposed to hypoxia, stops growing
       notes: Mycobacterium tuberculosis example supports oxygen dependence for aerobic
         growth.
+    predicate_id: RO:0002502
   - subject: aerobic_trait
     predicate: has mechanistic process
     object: aerobic_respiration
@@ -71,14 +72,15 @@ causal_graphs:
       notes: Review supports oxygen-reducing terminal oxidases as core aerobic respiratory
         enzymes.
   - subject: aerobic_respiration
-    predicate: requires
+    predicate: depends on
     object: molecular_oxygen
     description: Aerobic respiration requires oxygen.
     evidence:
     - reference: DOI:10.1016/j.celrep.2023.112444
       snippet: transfer electrons from the ETC to O2
       notes: Supports molecular oxygen as the terminal acceptor for bacterial respiratory
         electron transport.
+    predicate_id: RO:0002502
   - subject: molecular_oxygen
     predicate: acts as
     object: terminal_electron_acceptor
@@ -126,3 +128,15 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007504×1).
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings:
+    requires → depends on ×2.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:49Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (RO:0002502×2).
+  llm_assisted: true

data/traits/environment/halophily_preference.yaml

@@ -63,14 +63,15 @@ causal_graphs:
     description: Uptake systems importing osmoprotectants from the environment.
   edges:
   - subject: environmental_salinity
-    predicate: influences
+    predicate: regulates
     object: halophily_preference_trait
     description: Salt concentration determines whether growth requires, tolerates,
       or avoids salinity.
     evidence:
     - reference: DOI:10.1093/femsre/fuy009
       snippet: life at high salt concentrations
       notes: Review frames halophily as microbial life under high salt concentration.
+    predicate_id: RO:0002211
   - subject: environmental_salinity
     predicate: causes
     object: osmotic_stress
@@ -167,3 +168,15 @@ curation_history:
   changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
     (GO:0006970×1, CHEBI:65015×1).
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
+    influences → regulates ×1.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:49Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (RO:0002211×1).
+  llm_assisted: true

data/traits/environment/nacl_optimum.yaml

@@ -56,13 +56,14 @@ causal_graphs:
     description: Peak specific growth rate achieved at the optimal NaCl.
   edges:
   - subject: ambient_nacl
-    predicate: triggers
+    predicate: causes
     object: osmotic_balance
     description: External NaCl level engages the osmoadaptive balance machinery.
     evidence:
     - reference: DOI:10.1186/1746-1448-4-2
       snippet: cope with the high salt concentrations
       notes: Supports osmotic balance as the response to ambient NaCl.
+    predicate_id: biolink:causes
   - subject: compatible_solutes
     predicate: regulates
     object: osmotic_balance
@@ -146,3 +147,15 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (CHEBI:65015×1).
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
+    triggers → causes ×1.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:49Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (biolink:causes×1).
+  llm_assisted: true

data/traits/environment/nacl_range.yaml

@@ -58,22 +58,24 @@ causal_graphs:
       notes: Supports NaCl as the axis bounding the growth window.
     predicate_id: METPO:2007500
   - subject: low_salt_tolerance
-    predicate: sets
+    predicate: defines
     object: bounded_growth_window
     description: Tolerance to low salt sets the lower bound of the growth window.
     evidence:
     - reference: DOI:10.1186/1746-1448-4-2
       snippet: cope with the high salt concentrations
       notes: Saline-Systems review frames halophily around salt-tolerance mechanisms
         that span both the lower and upper limits of growth-supporting salinity.
+    predicate_id: METPO:2007500
   - subject: high_salt_tolerance
-    predicate: sets
+    predicate: defines
     object: bounded_growth_window
     description: Tolerance to high salt sets the upper bound of the growth window.
     evidence:
     - reference: DOI:10.1093/femsre/fuy009
       snippet: high salt concentrations
       notes: Supports tolerance to high salt as the upper-bound mechanism.
+    predicate_id: METPO:2007500
   - subject: bounded_growth_window
     predicate: manifests as
     object: nacl_range_trait
@@ -107,3 +109,15 @@ curation_history:
   changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
     (METPO:2007500×1).
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings:
+    sets → defines ×2.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:50Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (METPO:2007500×2).
+  llm_assisted: true

data/traits/environment/obligately_aerobic.yaml

@@ -54,14 +54,15 @@ causal_graphs:
     grounding: METPO:1007500
   edges:
   - subject: obligate_aerobic_trait
-    predicate: requires
+    predicate: depends on
     object: molecular_oxygen
     description: Obligate aerobic growth depends on oxygen availability.
     evidence:
     - reference: DOI:10.1016/j.celrep.2023.112444
       snippet: obligate aerobe ... exposed to hypoxia, stops growing
       notes: Mycobacterium tuberculosis example supports oxygen requirement in an
         obligately aerobic bacterium.
+    predicate_id: RO:0002502
   - subject: terminal_oxidases
     predicate: reduces
     object: molecular_oxygen
@@ -127,3 +128,15 @@ curation_history:
   changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
     semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.'
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
+    requires → depends on ×1.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:50Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (RO:0002502×1).
+  llm_assisted: true

data/traits/environment/obligately_alkaphilic.yaml

@@ -103,14 +103,15 @@ causal_graphs:
       snippet: achieve net H+ accumulation
       notes: Supports proton accumulation by antiporters in alkaliphiles.
   - subject: proton_coupled_atp_synthase
-    predicate: constrains
+    predicate: regulates
     object: obligately_alkaphilic_trait
     description: Proton-coupled ATP synthesis at very high pH creates a bioenergetic
       constraint requiring alkaliphile-specific adaptations.
     evidence:
     - reference: DOI:10.1016/j.bbabio.2010.02.028
       snippet: robust H+-coupled ATP synthesis at external pH values > 10
       notes: Supports the proton-coupled ATP synthesis challenge in alkaliphiles.
+    predicate_id: RO:0002211
   - subject: cytoplasmic_ph_homeostasis
     predicate: enables
     object: obligately_alkaphilic_trait
@@ -164,3 +165,15 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (PATO:0001429×1).
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
+    constrains → regulates ×1.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:50Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (RO:0002211×1).
+  llm_assisted: true

data/traits/environment/ph_growth_preference.yaml

@@ -49,14 +49,15 @@ causal_graphs:
     grounding: GO:0030641
   edges:
   - subject: environmental_ph
-    predicate: influences
+    predicate: regulates
     object: ph_growth_preference_trait
     description: Environmental pH determines which pH conditions support growth.
     evidence:
     - reference: DOI:10.1038/nrmicro2549
       snippet: tolerate or grow at external pH values
       notes: Review frames pH growth as a response to external pH outside the cytoplasmic
         range.
+    predicate_id: RO:0002211
   - subject: acidic_external_ph
     predicate: challenges
     object: cytoplasmic_ph_homeostasis
@@ -133,3 +134,15 @@ curation_history:
   changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
     (PATO:0001428×1, PATO:0001429×1).
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
+    influences → regulates ×1.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:50Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (RO:0002211×1).
+  llm_assisted: true

data/traits/environment/ph_range.yaml

@@ -60,23 +60,25 @@ causal_graphs:
       notes: Supports external pH as the axis bounding the growth window.
     predicate_id: METPO:2007500
   - subject: acid_tolerance
-    predicate: sets
+    predicate: defines
     object: bounded_growth_window
     description: Acid tolerance sets the lower bound of the pH growth window.
     evidence:
     - reference: DOI:10.1016/j.tim.2007.02.005
       snippet: highly impermeable cell membranes
       notes: Supports envelope proton barriers as the lower-bound mechanism for low-pH
         growth.
+    predicate_id: METPO:2007500
   - subject: alkaline_tolerance
-    predicate: sets
+    predicate: defines
     object: bounded_growth_window
     description: Alkaline tolerance sets the upper bound of the pH growth window.
     evidence:
     - reference: DOI:10.1038/nrmicro2549
       snippet: alkaliphiles
       notes: Supports alkaline-tolerance physiology as the upper-bound mechanism for
         high-pH growth.
+    predicate_id: METPO:2007500
   - subject: bounded_growth_window
     predicate: manifests as
     object: ph_range_trait
@@ -110,3 +112,15 @@ curation_history:
   changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
     (METPO:2007500×1).
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings:
+    sets → defines ×2.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:50Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (METPO:2007500×2).
+  llm_assisted: true

data/traits/environment/stenohaline.yaml

@@ -81,7 +81,7 @@ causal_graphs:
       notes: Supports water flux during osmotic imbalance.
     predicate_id: RO:0002211
   - subject: salinity_adaptation_genes
-    predicate: constrains
+    predicate: regulates
     object: stenohaline_trait
     description: Salinity adaptation gene repertoires help determine salinity niche
       breadth; limited repertoires can correspond to narrow tolerance.
@@ -90,6 +90,7 @@ causal_graphs:
       snippet: genes associated with microbial salinity adaptation
       notes: The constraint direction is inferred from the study's salinity adaptation
         analysis; kept broad because organism-specific gene sets vary.
+    predicate_id: RO:0002211
   - subject: salinity_shift
     predicate: exceeds tolerance of
     object: stenohaline_trait
@@ -137,3 +138,15 @@ curation_history:
   changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
     (METPO:2007500×1).
   llm_assisted: true
+- timestamp: '2026-05-26T05:00:47Z'
+  curator: claude
+  action: RENAME_PREDICATE_LABELS
+  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
+    constrains → regulates ×1.'
+  llm_assisted: true
+- timestamp: '2026-05-26T05:00:50Z'
+  curator: claude
+  action: GROUND_CAUSAL_PREDICATES
+  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
+    (RO:0002211×1).
+  llm_assisted: true