Extend CausalNodeTypeEnum with STATE/QUALITY/CAPACITY (+26 retyped)

data/traits/environment/facultative_psychrophilic.yaml

@@ -46,7 +46,7 @@ causal_graphs:
       growth.
   - node_id: membrane_fluidity
     label: membrane fluidity
-    node_type: BIOLOGICAL_PROCESS
+    node_type: QUALITY
     description: Physical state of the membrane needed for transport and growth.
     grounding: METPO:1007505
   - node_id: unsaturated_fatty_acids
@@ -143,3 +143,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007505×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:12Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
+    semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.'
+  llm_assisted: true

data/traits/environment/mesophilic.yaml

@@ -38,7 +38,7 @@ causal_graphs:
     description: Ambient temperature in the ~20–45 °C mesophilic range.
   - node_id: membrane_fluidity
     label: membrane fluidity
-    node_type: BIOLOGICAL_PROCESS
+    node_type: QUALITY
     description: Physical state of the cytoplasmic membrane supporting transport and
       bioenergetics.
     grounding: METPO:1007505
@@ -150,3 +150,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007505×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:12Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
+    semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.'
+  llm_assisted: true

data/traits/environment/neutrophilic.yaml

@@ -46,7 +46,7 @@ causal_graphs:
     grounding: GO:0030641
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Electrochemical proton gradient coupled to energy metabolism.
     grounding: METPO:1007500
   - node_id: cation_proton_antiporter
@@ -152,3 +152,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (PATO:0001432×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:12Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/environment/obligately_aerobic.yaml

@@ -49,7 +49,7 @@ causal_graphs:
     description: Oxygen-reducing terminal oxidase complexes.
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Electrochemical gradient powering ATP synthesis.
     grounding: METPO:1007500
   edges:
@@ -121,3 +121,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007500×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:12Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/environment/ph_optimum.yaml

@@ -46,7 +46,7 @@ causal_graphs:
     grounding: GO:0030641
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Electrochemical proton gradient powering ATP synthesis and transport.
     grounding: METPO:1007500
   - node_id: maximal_growth_rate
@@ -141,3 +141,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007500×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:12Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/environment/psychrophilic.yaml

@@ -37,7 +37,7 @@ causal_graphs:
     grounding: PATO:0000383
   - node_id: membrane_fluidity
     label: membrane fluidity
-    node_type: BIOLOGICAL_PROCESS
+    node_type: QUALITY
     description: Physical state of the membrane needed for transport and growth.
     grounding: METPO:1007505
   - node_id: unsaturated_fatty_acids
@@ -168,3 +168,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007505×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
+    semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.'
+  llm_assisted: true

data/traits/environment/psychrotolerant.yaml

@@ -38,7 +38,7 @@ causal_graphs:
     grounding: PATO:0000383
   - node_id: membrane_fluidity
     label: membrane fluidity
-    node_type: BIOLOGICAL_PROCESS
+    node_type: QUALITY
     description: Physical state of the cytoplasmic membrane supporting transport and
       bioenergetics.
     grounding: METPO:1007505
@@ -152,3 +152,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007505×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
+    semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.'
+  llm_assisted: true

data/traits/environment/temperature_optimum.yaml

@@ -38,7 +38,7 @@ causal_graphs:
     description: Ambient growth temperature imposed on the cell.
   - node_id: membrane_fluidity
     label: membrane fluidity
-    node_type: BIOLOGICAL_PROCESS
+    node_type: QUALITY
     description: Physical state of the cytoplasmic membrane supporting transport and
       bioenergetics.
     grounding: METPO:1007505
@@ -150,3 +150,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007505×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
+    semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.'
+  llm_assisted: true

data/traits/environment/temperature_preference.yaml

@@ -46,7 +46,7 @@ causal_graphs:
     description: Hot growth condition that challenges protein and membrane stability.
   - node_id: membrane_fluidity
     label: membrane fluidity
-    node_type: BIOLOGICAL_PROCESS
+    node_type: QUALITY
     description: Physical state of the membrane affecting transport and cell function.
     grounding: METPO:1007505
   - node_id: protein_stability
@@ -143,3 +143,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007505×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
+    semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.'
+  llm_assisted: true

data/traits/metabolism/aerobic_respiration.yaml

@@ -59,7 +59,7 @@ causal_graphs:
     description: Reduced product of oxygen reduction.
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Electrochemical ion gradient generated across the coupling membrane.
     grounding: METPO:1007500
   - node_id: atp_synthase
@@ -174,3 +174,9 @@ curation_history:
   changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
     (UniProtKB:A0A075NZN5×1, UniProtKB:A0A415TT77×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/metabolism/oxidative_phosphorylation.yaml

@@ -40,7 +40,7 @@ causal_graphs:
     description: Membrane across which ions are translocated.
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Transmembrane electrochemical proton gradient.
     grounding: METPO:1007500
   - node_id: atp_synthase
@@ -141,3 +141,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007500×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/metabolism/respiration.yaml

@@ -62,7 +62,7 @@ causal_graphs:
     grounding: GO:0022900
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Electrochemical ion gradient generated across a coupling membrane.
     grounding: METPO:1007500
   - node_id: atp_synthase
@@ -197,3 +197,9 @@ curation_history:
   changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
     (CHEBI:17499×1, GO:0022900×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/morphology/gliding.yaml

@@ -45,7 +45,7 @@ causal_graphs:
     description: Secretion-associated machinery linked to Flavobacterium gliding.
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Electrochemical gradient powering some gliding motors.
     grounding: METPO:1007500
   edges:
@@ -116,3 +116,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007500×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/physiology/carboxydotrophic.yaml

@@ -58,7 +58,7 @@ causal_graphs:
     description: Terminal oxidase enabling respiration during CO oxidation.
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Ion gradient used for energy conservation.
     grounding: METPO:1007500
   - node_id: reduced_pyridine_nucleotides
@@ -182,3 +182,9 @@ curation_history:
   changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
     (UniProtKB:A0A061JSS8×1, UniProtKB:A0A099I9V3×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/physiology/chemolithoautotrophic.yaml

@@ -43,7 +43,7 @@ causal_graphs:
     grounding: GO:0022900
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Electrochemical gradient generated by energy-conserving electron
       transfer.
     grounding: METPO:1007500
@@ -54,7 +54,7 @@ causal_graphs:
     description: Energy carrier supporting biosynthesis.
   - node_id: reducing_power
     label: reducing power
-    node_type: CHEMICAL
+    node_type: CAPACITY
     description: NAD(P)H or related reductants supporting CO2 reduction.
     grounding: METPO:1007503
   - node_id: carbon_dioxide
@@ -215,3 +215,10 @@ curation_history:
   changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
     (GO:0022900×1, GO:0015977×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  changes: 'Re-typed 2 causal-node node_type field(s) to align with CausalNodeTypeEnum
+    semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1; reducing power:
+    CHEMICAL → CAPACITY ×1.'
+  llm_assisted: true

data/traits/physiology/chemolithoheterotrophic.yaml

@@ -61,7 +61,7 @@ causal_graphs:
     grounding: GO:0022904
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Electrochemical ion gradient generated by respiratory electron transport.
     grounding: METPO:1007500
   - node_id: atp
@@ -214,3 +214,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (CHEBI:50860×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/physiology/chemoorganotrophic.yaml

@@ -55,7 +55,7 @@ causal_graphs:
     grounding: METPO:1007504
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Ion gradient generated by respiratory electron transport.
     grounding: METPO:1007500
   - node_id: atp
@@ -177,3 +177,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (CHEBI:50860×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/physiology/chemotrophic.yaml

@@ -65,7 +65,7 @@ causal_graphs:
     grounding: METPO:1007504
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Electrochemical ion gradient generated by electron transport.
     grounding: METPO:1007500
   - node_id: atp
@@ -192,3 +192,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (CHEBI:50860×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/physiology/hydrogenotrophic.yaml

@@ -48,7 +48,7 @@ causal_graphs:
     grounding: GO:0022900
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Ion gradient used for energy conservation.
     grounding: METPO:1007500
   - node_id: carbon_dioxide
@@ -185,3 +185,9 @@ curation_history:
   changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
     (GO:0022900×1, GO:0015977×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  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

data/traits/physiology/lithoautotrophic.yaml

@@ -41,7 +41,7 @@ causal_graphs:
     description: Conversion of redox energy into ion gradients and ATP.
   - node_id: reducing_power
     label: reducing power
-    node_type: CHEMICAL
+    node_type: CAPACITY
     description: Reduced electron carriers used in biosynthesis.
     grounding: METPO:1007503
   - node_id: carbon_dioxide
@@ -169,3 +169,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (GO:0015977×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:13Z'
+  curator: claude
+  action: RETYPE_CAUSAL_NODES
+  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
+    semantics: reducing power: CHEMICAL → CAPACITY ×1.'
+  llm_assisted: true