From 23d4397e1ba5b703f1532411208ed3bc3fa069b0 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Mon, 25 May 2026 19:32:01 -0700
Subject: [PATCH 1/2] Extend CausalNodeTypeEnum with STATE/QUALITY/CAPACITY
 (+26 nodes retyped)
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Closes the v3 cohort's "Node-typing notes" follow-up. When v3
landed, four labels were mis-typed because the enum couldn't
represent their actual semantics:

  proton motive force  → BIOLOGICAL_PROCESS  (semantically a STATE)
  membrane fluidity    → BIOLOGICAL_PROCESS  (semantically a QUALITY)
  microbial biomass    → BIOLOGICAL_PROCESS  (closest fit: CHEMICAL)
  reducing power       → CHEMICAL            (semantically a CAPACITY)

PR #72 retyped biomass → CHEMICAL (the closest existing fit at
that time). This PR adds the three missing enum values
(STATE / QUALITY / CAPACITY) and retypes the remaining three
labels covering 26 nodes:

  proton motive force  BIOLOGICAL_PROCESS → STATE     16 nodes
  membrane fluidity    BIOLOGICAL_PROCESS → QUALITY    6 nodes
  reducing power       CHEMICAL           → CAPACITY   4 nodes

Schema (src/traitmech/schema/traitmech.yaml):
  CausalNodeTypeEnum gains STATE, QUALITY, CAPACITY permissible
  values with prose descriptions distinguishing each from the
  closest existing value (STATE vs BIOLOGICAL_PROCESS, QUALITY
  vs MOLECULAR_FUNCTION, CAPACITY vs CHEMICAL).

Migration (scripts/retype_causal_nodes.py):
  RETYPES dict extended from 1 to 4 entries; DEFERRED list now
  empty. Re-run produces 26 retypes across 25 files.

Mapping TSV (mappings/node_grounding.tsv):
  Three rows updated to use the new node_type keys so future
  seeded nodes ground correctly:
    proton motive force  BIOLOGICAL_PROCESS → STATE
    reducing power       CHEMICAL           → CAPACITY
    membrane fluidity    BIOLOGICAL_PROCESS → QUALITY
  All three still ground to their METPO:1007500/1007503/1007505
  cohort-v3 CURIEs.

v1 cohort (proposals/metpo_traitmech_v1/, Path B extend-in-place):
  Three new leaf rows under METPO:1007410 (trait causal node
  type):
    METPO:1007421  causal-graph state node
    METPO:1007422  causal-graph quality node    (xref PATO:0000001)
    METPO:1007423  causal-graph capacity node
  Subset tag unchanged (metpo_traitmech_2026_05).
  verify-proposal: all 13 CausalNodeTypeEnum values lifted, 0 failures.
  robot-validate-proposal: ELK +6, no UNSAT.

v3 cohort (proposals/metpo_traitmech_v3/proposal.md):
  "Node-typing notes" section rewritten to document the
  post-merge resolution (all four labels now correctly typed,
  pointing at PR #72 and PR_D).

Verified locally:
  - just validate-strict           → 0 ERROR rows / 357 files
  - just verify-proposal v1        → PASS (13 leaves lifted)
  - just verify-proposal v3        → PASS
  - just robot-validate-proposal v1 → PASS, ELK +6
  - retype-causal-nodes --apply (second pass) → 0 retypes (idempotent)
  - uv run pytest tests/           → 56 passed

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---
 .../facultative_psychrophilic.yaml            |  8 +++-
 data/traits/environment/mesophilic.yaml       |  8 +++-
 data/traits/environment/neutrophilic.yaml     |  8 +++-
 .../environment/obligately_aerobic.yaml       |  8 +++-
 data/traits/environment/ph_optimum.yaml       |  8 +++-
 data/traits/environment/psychrophilic.yaml    |  8 +++-
 data/traits/environment/psychrotolerant.yaml  |  8 +++-
 .../environment/temperature_optimum.yaml      |  8 +++-
 .../environment/temperature_preference.yaml   |  8 +++-
 .../metabolism/aerobic_respiration.yaml       |  8 +++-
 .../metabolism/oxidative_phosphorylation.yaml |  8 +++-
 data/traits/metabolism/respiration.yaml       |  8 +++-
 data/traits/morphology/gliding.yaml           |  8 +++-
 data/traits/physiology/carboxydotrophic.yaml  |  8 +++-
 .../physiology/chemolithoautotrophic.yaml     | 11 +++++-
 .../physiology/chemolithoheterotrophic.yaml   |  8 +++-
 .../traits/physiology/chemoorganotrophic.yaml |  8 +++-
 data/traits/physiology/chemotrophic.yaml      |  8 +++-
 data/traits/physiology/hydrogenotrophic.yaml  |  8 +++-
 data/traits/physiology/lithoautotrophic.yaml  |  8 +++-
 data/traits/physiology/lithotrophic.yaml      |  8 +++-
 data/traits/physiology/organotrophic.yaml     |  8 +++-
 .../physiology/photolithoautotrophic.yaml     |  8 +++-
 .../physiology/photoorganoheterotrophic.yaml  |  8 +++-
 data/traits/physiology/phototrophic.yaml      |  8 +++-
 mappings/node_grounding.tsv                   |  6 +--
 .../metpo_proposal_classes_robot.tsv          |  3 ++
 proposals/metpo_traitmech_v3/proposal.md      | 38 ++++++++++++-------
 scripts/retype_causal_nodes.py                | 36 ++++++++++--------
 src/traitmech/schema/traitmech.yaml           | 18 +++++++++
 30 files changed, 246 insertions(+), 58 deletions(-)

diff --git a/data/traits/environment/facultative_psychrophilic.yaml b/data/traits/environment/facultative_psychrophilic.yaml
index 5bdc0a9..4c2f5d0 100644
--- a/data/traits/environment/facultative_psychrophilic.yaml
+++ b/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
diff --git a/data/traits/environment/mesophilic.yaml b/data/traits/environment/mesophilic.yaml
index dbc705f..81f2d05 100644
--- a/data/traits/environment/mesophilic.yaml
+++ b/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
diff --git a/data/traits/environment/neutrophilic.yaml b/data/traits/environment/neutrophilic.yaml
index 687b799..b821d10 100644
--- a/data/traits/environment/neutrophilic.yaml
+++ b/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
diff --git a/data/traits/environment/obligately_aerobic.yaml b/data/traits/environment/obligately_aerobic.yaml
index 23890ed..93d5acb 100644
--- a/data/traits/environment/obligately_aerobic.yaml
+++ b/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
diff --git a/data/traits/environment/ph_optimum.yaml b/data/traits/environment/ph_optimum.yaml
index 929a748..d6c55ef 100644
--- a/data/traits/environment/ph_optimum.yaml
+++ b/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
diff --git a/data/traits/environment/psychrophilic.yaml b/data/traits/environment/psychrophilic.yaml
index 81bd2ec..d630709 100644
--- a/data/traits/environment/psychrophilic.yaml
+++ b/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
diff --git a/data/traits/environment/psychrotolerant.yaml b/data/traits/environment/psychrotolerant.yaml
index 3330981..9943025 100644
--- a/data/traits/environment/psychrotolerant.yaml
+++ b/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
diff --git a/data/traits/environment/temperature_optimum.yaml b/data/traits/environment/temperature_optimum.yaml
index 8c56ec6..ba06405 100644
--- a/data/traits/environment/temperature_optimum.yaml
+++ b/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
diff --git a/data/traits/environment/temperature_preference.yaml b/data/traits/environment/temperature_preference.yaml
index 6b54913..60049bf 100644
--- a/data/traits/environment/temperature_preference.yaml
+++ b/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
diff --git a/data/traits/metabolism/aerobic_respiration.yaml b/data/traits/metabolism/aerobic_respiration.yaml
index d04dcce..f9588ca 100644
--- a/data/traits/metabolism/aerobic_respiration.yaml
+++ b/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
diff --git a/data/traits/metabolism/oxidative_phosphorylation.yaml b/data/traits/metabolism/oxidative_phosphorylation.yaml
index 0314a19..d980604 100644
--- a/data/traits/metabolism/oxidative_phosphorylation.yaml
+++ b/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
diff --git a/data/traits/metabolism/respiration.yaml b/data/traits/metabolism/respiration.yaml
index 9794b69..b590215 100644
--- a/data/traits/metabolism/respiration.yaml
+++ b/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
diff --git a/data/traits/morphology/gliding.yaml b/data/traits/morphology/gliding.yaml
index 3cdd197..721e837 100644
--- a/data/traits/morphology/gliding.yaml
+++ b/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
diff --git a/data/traits/physiology/carboxydotrophic.yaml b/data/traits/physiology/carboxydotrophic.yaml
index 202ba30..9664055 100644
--- a/data/traits/physiology/carboxydotrophic.yaml
+++ b/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
diff --git a/data/traits/physiology/chemolithoautotrophic.yaml b/data/traits/physiology/chemolithoautotrophic.yaml
index 776bf4e..8a23a35 100644
--- a/data/traits/physiology/chemolithoautotrophic.yaml
+++ b/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
diff --git a/data/traits/physiology/chemolithoheterotrophic.yaml b/data/traits/physiology/chemolithoheterotrophic.yaml
index 6a91561..a0ac3ea 100644
--- a/data/traits/physiology/chemolithoheterotrophic.yaml
+++ b/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
diff --git a/data/traits/physiology/chemoorganotrophic.yaml b/data/traits/physiology/chemoorganotrophic.yaml
index bb85d6a..790dc75 100644
--- a/data/traits/physiology/chemoorganotrophic.yaml
+++ b/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
diff --git a/data/traits/physiology/chemotrophic.yaml b/data/traits/physiology/chemotrophic.yaml
index 87e62e9..c269496 100644
--- a/data/traits/physiology/chemotrophic.yaml
+++ b/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
diff --git a/data/traits/physiology/hydrogenotrophic.yaml b/data/traits/physiology/hydrogenotrophic.yaml
index d009ee1..23edff0 100644
--- a/data/traits/physiology/hydrogenotrophic.yaml
+++ b/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
diff --git a/data/traits/physiology/lithoautotrophic.yaml b/data/traits/physiology/lithoautotrophic.yaml
index 3d62d10..8341df9 100644
--- a/data/traits/physiology/lithoautotrophic.yaml
+++ b/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
diff --git a/data/traits/physiology/lithotrophic.yaml b/data/traits/physiology/lithotrophic.yaml
index cfefff4..34188f4 100644
--- a/data/traits/physiology/lithotrophic.yaml
+++ b/data/traits/physiology/lithotrophic.yaml
@@ -57,7 +57,7 @@ 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 used for energy conservation.
     grounding: METPO:1007500
   - node_id: atp
@@ -158,3 +158,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (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
diff --git a/data/traits/physiology/organotrophic.yaml b/data/traits/physiology/organotrophic.yaml
index 3ac4941..d984f12 100644
--- a/data/traits/physiology/organotrophic.yaml
+++ b/data/traits/physiology/organotrophic.yaml
@@ -56,7 +56,7 @@ 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 respiration.
     grounding: METPO:1007500
   - node_id: atp
@@ -178,3 +178,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (CHEBI:50860×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:14Z'
+  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
diff --git a/data/traits/physiology/photolithoautotrophic.yaml b/data/traits/physiology/photolithoautotrophic.yaml
index c571c54..ed8efd3 100644
--- a/data/traits/physiology/photolithoautotrophic.yaml
+++ b/data/traits/physiology/photolithoautotrophic.yaml
@@ -61,7 +61,7 @@ causal_graphs:
     description: Oxidation of reduced sulfur compounds during phototrophic metabolism.
   - node_id: reducing_power
     label: reducing power
-    node_type: CHEMICAL
+    node_type: CAPACITY
     description: Reduced electron carriers used for biosynthesis.
     grounding: METPO:1007503
   - node_id: carbon_dioxide
@@ -221,3 +221,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (GO:0015977×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:14Z'
+  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
diff --git a/data/traits/physiology/photoorganoheterotrophic.yaml b/data/traits/physiology/photoorganoheterotrophic.yaml
index af1511e..1a8a3ab 100644
--- a/data/traits/physiology/photoorganoheterotrophic.yaml
+++ b/data/traits/physiology/photoorganoheterotrophic.yaml
@@ -53,7 +53,7 @@ causal_graphs:
     grounding: GO:0009767
   - node_id: proton_motive_force
     label: proton motive force
-    node_type: BIOLOGICAL_PROCESS
+    node_type: STATE
     description: Ion gradient generated by electron transport.
     grounding: METPO:1007500
   - node_id: atp
@@ -185,3 +185,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (CHEBI:50860×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:14Z'
+  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
diff --git a/data/traits/physiology/phototrophic.yaml b/data/traits/physiology/phototrophic.yaml
index 961d39e..311002c 100644
--- a/data/traits/physiology/phototrophic.yaml
+++ b/data/traits/physiology/phototrophic.yaml
@@ -64,7 +64,7 @@ causal_graphs:
     description: Energy carrier generated by phototrophic electron transport.
   - node_id: reducing_power
     label: reducing power
-    node_type: CHEMICAL
+    node_type: CAPACITY
     description: NAD(P)H or reduced ferredoxin generated by photosynthetic electron
       transport.
     grounding: METPO:1007503
@@ -158,3 +158,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (METPO:1007503×1).
   llm_assisted: true
+- timestamp: '2026-05-26T02:30:14Z'
+  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
diff --git a/mappings/node_grounding.tsv b/mappings/node_grounding.tsv
index 0d3e365..1e8bf14 100644
--- a/mappings/node_grounding.tsv
+++ b/mappings/node_grounding.tsv
@@ -39,13 +39,13 @@ low temperature	ENVIRONMENTAL_FACTOR	PATO:0000383	decreased temperature	PATO	hig
 anaerobic condition	ENVIRONMENTAL_FACTOR	ENVO:01001057	anaerobic environment	ENVO	high	exact ENVO term
 anoxic condition	ENVIRONMENTAL_FACTOR	ENVO:01001057	anaerobic environment	ENVO	high	ENVO collapses anoxic and anaerobic into one environment class
 carotenoid biosynthesis	BIOLOGICAL_PROCESS	GO:0016117	carotenoid biosynthetic process	GO	high	exact GO term; pigmentation contexts
-proton motive force	BIOLOGICAL_PROCESS	METPO:1007500	proton motive force	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 16 nodes (mistyped as BIOLOGICAL_PROCESS in corpus — semantically a bioenergetic state)
+proton motive force	STATE	METPO:1007500	proton motive force	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 16 nodes — re-typed BIOLOGICAL_PROCESS → STATE in PR_D after CausalNodeTypeEnum gained the STATE permissible value (bioenergetic gradient, not a process)
 biomass	CHEMICAL	METPO:1007501	microbial biomass	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 16 nodes — re-typed BIOLOGICAL_PROCESS → CHEMICAL via scripts/retype_causal_nodes.py (closest existing CausalNodeTypeEnum fit for aggregate biochemistry)
 inorganic electron donor	CHEMICAL	METPO:1007502	inorganic electron donor	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 7 nodes — class-of-chemicals abstraction for lithotrophy
-reducing power	CHEMICAL	METPO:1007503	reducing power	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 4 nodes — electron-pool capacity
+reducing power	CAPACITY	METPO:1007503	reducing power	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 4 nodes — re-typed CHEMICAL → CAPACITY in PR_D after CausalNodeTypeEnum gained the CAPACITY permissible value (electron-donating pool, not a single chemical)
 terminal electron acceptor	CHEMICAL	METPO:1007504	terminal electron acceptor	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 3 nodes as CHEMICAL (also 2 as MOLECULAR_FUNCTION below)
 terminal electron acceptor	MOLECULAR_FUNCTION	METPO:1007504	terminal electron acceptor	METPO	high	same proposed METPO class covers both senses; MOLECULAR_FUNCTION typing surfaces the role-of interpretation
-membrane fluidity	BIOLOGICAL_PROCESS	METPO:1007505	membrane fluidity	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 6 nodes (mistyped as BIOLOGICAL_PROCESS — semantically a membrane quality)
+membrane fluidity	QUALITY	METPO:1007505	membrane fluidity	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 6 nodes — re-typed BIOLOGICAL_PROCESS → QUALITY in PR_D after CausalNodeTypeEnum gained the QUALITY permissible value (PATO-style attribute, not a process)
 mreb	GENE_OR_PROTEIN	UniProtKB:A0A1B1UYY2	MreB	UniProt	high	representative UniProt entry selected via kg-microbe merged-kg_uniprot_nodes.tsv (name-ends-with-label + alphabetic-first CURIE)
 na+/h+ antiporter	GENE_OR_PROTEIN	UniProtKB:A0A068T423	Na+/H+ antiporter	UniProt	high	representative UniProt entry selected via kg-microbe merged-kg_uniprot_nodes.tsv (name-ends-with-label + alphabetic-first CURIE)
 ftsz	GENE_OR_PROTEIN	UniProtKB:C0LUM8	FtsZ	UniProt	high	representative UniProt entry selected via kg-microbe merged-kg_uniprot_nodes.tsv (name-ends-with-label + alphabetic-first CURIE)
diff --git a/proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv b/proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv
index 5623d37..e92d554 100644
--- a/proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv
+++ b/proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv
@@ -14,3 +14,6 @@ METPO:1007417	causal-graph organelle node	A trait causal node that denotes a mic
 METPO:1007418	causal-graph cellular localization node	A trait causal node that denotes a cellular component or subcellular localization (cytoplasm, membrane, periplasm, cell wall, etc.) at which a trait mechanism is realized.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.CELLULAR_LOCALIZATION	METPO:1007410	cellular component node|localization node	GO:0005575	metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.CELLULAR_LOCALIZATION
 METPO:1007419	causal-graph molecular function node	A trait causal node that denotes a molecular activity or function (catalysis, transport, binding) contributing to the trait mechanism.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.MOLECULAR_FUNCTION	METPO:1007410	molecular function node|molecular activity node	GO:0003674	metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.MOLECULAR_FUNCTION
 METPO:1007420	causal-graph biological process node	A trait causal node that denotes a biological process (e.g. respiration, nitrogen fixation, biofilm formation) that is part of, or causally upstream of, the trait mechanism.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.BIOLOGICAL_PROCESS	METPO:1007410	biological process node	GO:0008150	metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.BIOLOGICAL_PROCESS
+METPO:1007421	causal-graph state node	A trait causal node that denotes a bioenergetic or molecular state of the cell — a gradient or steady-value (e.g. proton motive force, redox state of the quinone pool) that mediates the trait mechanism. Distinct from a process: the state is the thing maintained, not its establishment.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.STATE	METPO:1007410	state node|bioenergetic state node		metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.STATE (extended in PR_D)
+METPO:1007422	causal-graph quality node	A trait causal node that denotes a quality or measurable attribute of a cellular component (PATO-style axis attached to a microbial entity) — e.g. membrane fluidity, GC content, motility speed — that modulates the trait mechanism.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.QUALITY	METPO:1007410	quality node|attribute node	PATO:0000001	metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.QUALITY (extended in PR_D)
+METPO:1007423	causal-graph capacity node	A trait causal node that denotes a metabolic or functional capacity — an electron-donating pool, ATP charge, or other reservoir-of-X notion that is neither a single chemical species nor a process (e.g. reducing power, energy charge).	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.CAPACITY	METPO:1007410	capacity node|reservoir node		metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.CAPACITY (extended in PR_D)
diff --git a/proposals/metpo_traitmech_v3/proposal.md b/proposals/metpo_traitmech_v3/proposal.md
index aa7fa5a..ad22ce0 100644
--- a/proposals/metpo_traitmech_v3/proposal.md
+++ b/proposals/metpo_traitmech_v3/proposal.md
@@ -73,20 +73,30 @@ them under a richer parent (e.g. *bioenergetic state*,
 | `terminal electron acceptor` | individual CHEBIs (O₂, NO₃⁻, SO₄²⁻) | role-of class is missing upstream; corpus mixes CHEMICAL + MOLECULAR_FUNCTION node-typings of the same concept |
 | `membrane fluidity` | PATO:0001985 (viscosity) | viscosity is closely related but is a generic physical quality; membrane-specific lipid-mobility sense has no exact upstream term |
 
-### Node-typing notes
-
-Four of these are *mis-typed* in the corpus (a separate cleanup):
-- `proton motive force` and `membrane fluidity` appear under
-  `node_type: BIOLOGICAL_PROCESS` but are semantically a
-  bioenergetic state and a membrane quality respectively.
-- `microbial biomass` and `reducing power` are typed as
-  `BIOLOGICAL_PROCESS` / `CHEMICAL` but are aggregate matter and
-  capacity respectively.
-
-Lifting them to METPO with proper classification gives downstream
-re-typing migrations a target. The mapping TSV in this PR grounds
-them via the corpus's current (mis-)typing so the corpus-side fix
-can land separately.
+### Node-typing notes (resolved post-merge)
+
+When v3 first landed, four of these classes were *mis-typed* in
+the corpus because the `CausalNodeTypeEnum` lacked appropriate
+values:
+- `proton motive force` and `membrane fluidity` appeared under
+  `node_type: BIOLOGICAL_PROCESS` (semantically a bioenergetic
+  state and a membrane quality).
+- `microbial biomass` and `reducing power` were typed as
+  `BIOLOGICAL_PROCESS` / `CHEMICAL` (aggregate matter and capacity).
+
+All four are now correctly typed:
+- `biomass` → `CHEMICAL` (PR #72, the closest existing fit at
+  the time).
+- `proton motive force` → `STATE` (PR_D, after the enum was
+  extended with `STATE`/`QUALITY`/`CAPACITY`).
+- `membrane fluidity` → `QUALITY` (PR_D).
+- `reducing power` → `CAPACITY` (PR_D).
+
+The v1 cohort's `CausalNodeTypeEnum` lift was extended in-place
+(Path B per the metpo-proposal skill) to mint three new leaf
+classes — `METPO:1007421` (state node), `METPO:1007422` (quality
+node), `METPO:1007423` (capacity node) — keeping the subset tag
+`metpo_traitmech_2026_05`.
 
 ## Hierarchy decisions
 
diff --git a/scripts/retype_causal_nodes.py b/scripts/retype_causal_nodes.py
index 84c057c..f78261a 100644
--- a/scripts/retype_causal_nodes.py
+++ b/scripts/retype_causal_nodes.py
@@ -45,27 +45,33 @@
 # (label_lower, current_node_type) → new_node_type.
 #
 # Scope rule: only re-type when an existing CausalNodeTypeEnum value
-# is a clean semantic fit. For mis-typed nodes whose proper category
-# is missing from the enum (bioenergetic STATE, membrane QUALITY,
-# metabolic CAPACITY), defer to a follow-up that extends the enum.
+# is a clean semantic fit. The first entry (biomass) landed in
+# PR #72; the next three landed in PR_D after the enum was extended
+# with STATE / QUALITY / CAPACITY values.
 RETYPES: dict[tuple[str, str], str] = {
     # Microbial biomass is aggregate biochemistry — best existing fit
     # in CausalNodeTypeEnum is CHEMICAL (a chemical entity / mixture).
-    # Currently mis-typed as BIOLOGICAL_PROCESS in the v3 proposal
-    # (proposals/metpo_traitmech_v3/proposal.md, "Node-typing notes").
     ("biomass", "BIOLOGICAL_PROCESS"): "CHEMICAL",
+
+    # Proton motive force is a bioenergetic state (electrochemical
+    # gradient), not a process. STATE was added to the enum in PR_D.
+    ("proton motive force", "BIOLOGICAL_PROCESS"): "STATE",
+
+    # Membrane fluidity is a PATO-style quality of the membrane, not
+    # a process. QUALITY was added to the enum in PR_D.
+    ("membrane fluidity", "BIOLOGICAL_PROCESS"): "QUALITY",
+
+    # Reducing power is a metabolic capacity (electron-donating
+    # pool), not a single chemical species. CAPACITY was added to
+    # the enum in PR_D.
+    ("reducing power", "CHEMICAL"): "CAPACITY",
 }
 
-# Mis-typed labels that the current enum can't represent cleanly.
-# Listed here so the PR description and proposal.md stay in sync.
-DEFERRED = [
-    ("proton motive force", "BIOLOGICAL_PROCESS",
-     "needs a bioenergetic-STATE enum value"),
-    ("membrane fluidity", "BIOLOGICAL_PROCESS",
-     "needs a QUALITY enum value (PATO axis)"),
-    ("reducing power", "CHEMICAL",
-     "needs a metabolic-CAPACITY enum value"),
-]
+# All mis-typed labels surfaced in the v3 proposal are now resolved
+# (PR #72 for biomass; PR_D for the other three). New mis-typings
+# discovered post-PR_D should be appended above with a comment
+# pointing at where the new enum value (if needed) was added.
+DEFERRED: list[tuple[str, str, str]] = []
 
 
 def retype_nodes_in_doc(doc: dict[str, Any]) -> tuple[int, Counter]:
diff --git a/src/traitmech/schema/traitmech.yaml b/src/traitmech/schema/traitmech.yaml
index b8ad7d8..5020f8f 100644
--- a/src/traitmech/schema/traitmech.yaml
+++ b/src/traitmech/schema/traitmech.yaml
@@ -440,3 +440,21 @@ enums:
         description: A molecular activity or function.
       BIOLOGICAL_PROCESS:
         description: A biological process.
+      STATE:
+        description: >-
+          A bioenergetic or molecular state of the cell (e.g. proton
+          motive force, redox state of the quinone pool) that
+          mediates a trait mechanism. Distinct from a process: the
+          state is the gradient / steady-value, not its establishment.
+      QUALITY:
+        description: >-
+          A quality or measurable attribute of a cellular component
+          (e.g. membrane fluidity, GC content, motility speed) —
+          a PATO-style axis attached to a microbial entity that
+          modulates the trait mechanism.
+      CAPACITY:
+        description: >-
+          A metabolic or functional capacity — an electron-donating
+          pool, ATP charge, or other reservoir-of-X notion that is
+          neither a single chemical species nor a process. Examples
+          include reducing power (NADH/NADPH pool) and energy charge.

From 959e1a79f2763fc4c22aa93d4ae6fe9eec331a5a Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Mon, 25 May 2026 21:56:49 -0700
Subject: [PATCH 2/2] Address Copilot review on PR #81
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

All six Copilot inline comments were the same finding: the inline
references to "PR_D" are placeholders, not real PR identifiers, so
they'll be meaningless once the PR is merged.

Replaced across all four affected files:
  - scripts/retype_causal_nodes.py        (5 occurrences)
  - mappings/node_grounding.tsv           (3 occurrences in notes)
  - proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv
                                          (3 occurrences in row obs)
  - proposals/metpo_traitmech_v3/proposal.md  (3 occurrences)

Replacement phrasing depends on context:
  - "extended in PR_D"
      → "extended via the STATE/QUALITY/CAPACITY enum extension"
  - "added to the enum in PR_D"
      → "added to the enum in the same batch"
  - "PR_D for the other three"
      → "the STATE/QUALITY/CAPACITY batch for the other three"
  - "STATE in PR_D after CausalNodeTypeEnum"
      → "STATE after CausalNodeTypeEnum"
  - "PR_D, after the enum was"
      → "after the enum was"
  - "(PR_D)" → "(same enum-extension batch)"

The references to PR #72 (biomass retype, already merged) are
kept verbatim — that PR number is stable.

Verified:
  - just verify-proposal metpo_traitmech_v1 → PASS
  - just verify-proposal metpo_traitmech_v3 → PASS
  - just validate-strict                    → 0 ERROR rows
  - grep -r "PR_D" scripts mappings proposals → 0 hits

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---
 mappings/node_grounding.tsv                          |  6 +++---
 .../metpo_proposal_classes_robot.tsv                 |  6 +++---
 proposals/metpo_traitmech_v3/proposal.md             |  6 +++---
 scripts/retype_causal_nodes.py                       | 12 ++++++------
 4 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/mappings/node_grounding.tsv b/mappings/node_grounding.tsv
index 1e8bf14..4fb1794 100644
--- a/mappings/node_grounding.tsv
+++ b/mappings/node_grounding.tsv
@@ -39,13 +39,13 @@ low temperature	ENVIRONMENTAL_FACTOR	PATO:0000383	decreased temperature	PATO	hig
 anaerobic condition	ENVIRONMENTAL_FACTOR	ENVO:01001057	anaerobic environment	ENVO	high	exact ENVO term
 anoxic condition	ENVIRONMENTAL_FACTOR	ENVO:01001057	anaerobic environment	ENVO	high	ENVO collapses anoxic and anaerobic into one environment class
 carotenoid biosynthesis	BIOLOGICAL_PROCESS	GO:0016117	carotenoid biosynthetic process	GO	high	exact GO term; pigmentation contexts
-proton motive force	STATE	METPO:1007500	proton motive force	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 16 nodes — re-typed BIOLOGICAL_PROCESS → STATE in PR_D after CausalNodeTypeEnum gained the STATE permissible value (bioenergetic gradient, not a process)
+proton motive force	STATE	METPO:1007500	proton motive force	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 16 nodes — re-typed BIOLOGICAL_PROCESS → STATE after CausalNodeTypeEnum gained the STATE permissible value (bioenergetic gradient, not a process)
 biomass	CHEMICAL	METPO:1007501	microbial biomass	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 16 nodes — re-typed BIOLOGICAL_PROCESS → CHEMICAL via scripts/retype_causal_nodes.py (closest existing CausalNodeTypeEnum fit for aggregate biochemistry)
 inorganic electron donor	CHEMICAL	METPO:1007502	inorganic electron donor	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 7 nodes — class-of-chemicals abstraction for lithotrophy
-reducing power	CAPACITY	METPO:1007503	reducing power	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 4 nodes — re-typed CHEMICAL → CAPACITY in PR_D after CausalNodeTypeEnum gained the CAPACITY permissible value (electron-donating pool, not a single chemical)
+reducing power	CAPACITY	METPO:1007503	reducing power	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 4 nodes — re-typed CHEMICAL → CAPACITY after CausalNodeTypeEnum gained the CAPACITY permissible value (electron-donating pool, not a single chemical)
 terminal electron acceptor	CHEMICAL	METPO:1007504	terminal electron acceptor	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 3 nodes as CHEMICAL (also 2 as MOLECULAR_FUNCTION below)
 terminal electron acceptor	MOLECULAR_FUNCTION	METPO:1007504	terminal electron acceptor	METPO	high	same proposed METPO class covers both senses; MOLECULAR_FUNCTION typing surfaces the role-of interpretation
-membrane fluidity	QUALITY	METPO:1007505	membrane fluidity	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 6 nodes — re-typed BIOLOGICAL_PROCESS → QUALITY in PR_D after CausalNodeTypeEnum gained the QUALITY permissible value (PATO-style attribute, not a process)
+membrane fluidity	QUALITY	METPO:1007505	membrane fluidity	METPO	high	proposed upstream in proposals/metpo_traitmech_v3; 6 nodes — re-typed BIOLOGICAL_PROCESS → QUALITY after CausalNodeTypeEnum gained the QUALITY permissible value (PATO-style attribute, not a process)
 mreb	GENE_OR_PROTEIN	UniProtKB:A0A1B1UYY2	MreB	UniProt	high	representative UniProt entry selected via kg-microbe merged-kg_uniprot_nodes.tsv (name-ends-with-label + alphabetic-first CURIE)
 na+/h+ antiporter	GENE_OR_PROTEIN	UniProtKB:A0A068T423	Na+/H+ antiporter	UniProt	high	representative UniProt entry selected via kg-microbe merged-kg_uniprot_nodes.tsv (name-ends-with-label + alphabetic-first CURIE)
 ftsz	GENE_OR_PROTEIN	UniProtKB:C0LUM8	FtsZ	UniProt	high	representative UniProt entry selected via kg-microbe merged-kg_uniprot_nodes.tsv (name-ends-with-label + alphabetic-first CURIE)
diff --git a/proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv b/proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv
index e92d554..bfd2aa8 100644
--- a/proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv
+++ b/proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv
@@ -14,6 +14,6 @@ METPO:1007417	causal-graph organelle node	A trait causal node that denotes a mic
 METPO:1007418	causal-graph cellular localization node	A trait causal node that denotes a cellular component or subcellular localization (cytoplasm, membrane, periplasm, cell wall, etc.) at which a trait mechanism is realized.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.CELLULAR_LOCALIZATION	METPO:1007410	cellular component node|localization node	GO:0005575	metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.CELLULAR_LOCALIZATION
 METPO:1007419	causal-graph molecular function node	A trait causal node that denotes a molecular activity or function (catalysis, transport, binding) contributing to the trait mechanism.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.MOLECULAR_FUNCTION	METPO:1007410	molecular function node|molecular activity node	GO:0003674	metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.MOLECULAR_FUNCTION
 METPO:1007420	causal-graph biological process node	A trait causal node that denotes a biological process (e.g. respiration, nitrogen fixation, biofilm formation) that is part of, or causally upstream of, the trait mechanism.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.BIOLOGICAL_PROCESS	METPO:1007410	biological process node	GO:0008150	metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.BIOLOGICAL_PROCESS
-METPO:1007421	causal-graph state node	A trait causal node that denotes a bioenergetic or molecular state of the cell — a gradient or steady-value (e.g. proton motive force, redox state of the quinone pool) that mediates the trait mechanism. Distinct from a process: the state is the thing maintained, not its establishment.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.STATE	METPO:1007410	state node|bioenergetic state node		metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.STATE (extended in PR_D)
-METPO:1007422	causal-graph quality node	A trait causal node that denotes a quality or measurable attribute of a cellular component (PATO-style axis attached to a microbial entity) — e.g. membrane fluidity, GC content, motility speed — that modulates the trait mechanism.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.QUALITY	METPO:1007410	quality node|attribute node	PATO:0000001	metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.QUALITY (extended in PR_D)
-METPO:1007423	causal-graph capacity node	A trait causal node that denotes a metabolic or functional capacity — an electron-donating pool, ATP charge, or other reservoir-of-X notion that is neither a single chemical species nor a process (e.g. reducing power, energy charge).	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.CAPACITY	METPO:1007410	capacity node|reservoir node		metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.CAPACITY (extended in PR_D)
+METPO:1007421	causal-graph state node	A trait causal node that denotes a bioenergetic or molecular state of the cell — a gradient or steady-value (e.g. proton motive force, redox state of the quinone pool) that mediates the trait mechanism. Distinct from a process: the state is the thing maintained, not its establishment.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.STATE	METPO:1007410	state node|bioenergetic state node		metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.STATE (extended via the STATE/QUALITY/CAPACITY enum extension)
+METPO:1007422	causal-graph quality node	A trait causal node that denotes a quality or measurable attribute of a cellular component (PATO-style axis attached to a microbial entity) — e.g. membrane fluidity, GC content, motility speed — that modulates the trait mechanism.	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.QUALITY	METPO:1007410	quality node|attribute node	PATO:0000001	metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.QUALITY (extended via the STATE/QUALITY/CAPACITY enum extension)
+METPO:1007423	causal-graph capacity node	A trait causal node that denotes a metabolic or functional capacity — an electron-donating pool, ATP charge, or other reservoir-of-X notion that is neither a single chemical species nor a process (e.g. reducing power, energy charge).	TraitMech:src/traitmech/schema/traitmech.yaml#CausalNodeTypeEnum.CAPACITY	METPO:1007410	capacity node|reservoir node		metpo_traitmech_2026_05	HIGH		leaf — CausalNodeTypeEnum.CAPACITY (extended via the STATE/QUALITY/CAPACITY enum extension)
diff --git a/proposals/metpo_traitmech_v3/proposal.md b/proposals/metpo_traitmech_v3/proposal.md
index ad22ce0..7b01101 100644
--- a/proposals/metpo_traitmech_v3/proposal.md
+++ b/proposals/metpo_traitmech_v3/proposal.md
@@ -87,10 +87,10 @@ values:
 All four are now correctly typed:
 - `biomass` → `CHEMICAL` (PR #72, the closest existing fit at
   the time).
-- `proton motive force` → `STATE` (PR_D, after the enum was
+- `proton motive force` → `STATE` (after the enum was
   extended with `STATE`/`QUALITY`/`CAPACITY`).
-- `membrane fluidity` → `QUALITY` (PR_D).
-- `reducing power` → `CAPACITY` (PR_D).
+- `membrane fluidity` → `QUALITY` (same enum-extension batch).
+- `reducing power` → `CAPACITY` (same enum-extension batch).
 
 The v1 cohort's `CausalNodeTypeEnum` lift was extended in-place
 (Path B per the metpo-proposal skill) to mint three new leaf
diff --git a/scripts/retype_causal_nodes.py b/scripts/retype_causal_nodes.py
index f78261a..66aff68 100644
--- a/scripts/retype_causal_nodes.py
+++ b/scripts/retype_causal_nodes.py
@@ -46,7 +46,7 @@
 #
 # Scope rule: only re-type when an existing CausalNodeTypeEnum value
 # is a clean semantic fit. The first entry (biomass) landed in
-# PR #72; the next three landed in PR_D after the enum was extended
+# PR #72; the next three landed after the enum was extended
 # with STATE / QUALITY / CAPACITY values.
 RETYPES: dict[tuple[str, str], str] = {
     # Microbial biomass is aggregate biochemistry — best existing fit
@@ -54,22 +54,22 @@
     ("biomass", "BIOLOGICAL_PROCESS"): "CHEMICAL",
 
     # Proton motive force is a bioenergetic state (electrochemical
-    # gradient), not a process. STATE was added to the enum in PR_D.
+    # gradient), not a process. STATE was added to the enum in the same batch.
     ("proton motive force", "BIOLOGICAL_PROCESS"): "STATE",
 
     # Membrane fluidity is a PATO-style quality of the membrane, not
-    # a process. QUALITY was added to the enum in PR_D.
+    # a process. QUALITY was added to the enum in the same batch.
     ("membrane fluidity", "BIOLOGICAL_PROCESS"): "QUALITY",
 
     # Reducing power is a metabolic capacity (electron-donating
     # pool), not a single chemical species. CAPACITY was added to
-    # the enum in PR_D.
+    # the enum in the same batch.
     ("reducing power", "CHEMICAL"): "CAPACITY",
 }
 
 # All mis-typed labels surfaced in the v3 proposal are now resolved
-# (PR #72 for biomass; PR_D for the other three). New mis-typings
-# discovered post-PR_D should be appended above with a comment
+# (PR #72 for biomass; the STATE/QUALITY/CAPACITY batch for the other three). New mis-typings
+# discovered after this batch should be appended above with a comment
 # pointing at where the new enum value (if needed) was added.
 DEFERRED: list[tuple[str, str, str]] = []