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

[realmarcin]

Summary

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. PR #72 partially resolved this (biomass → CHEMICAL); this PR adds the three missing enum values and finishes the cleanup.

Label	Before	After	Nodes
microbial biomass	BIOLOGICAL_PROCESS	CHEMICAL (PR #72)	16
proton motive force	BIOLOGICAL_PROCESS	STATE	16
membrane fluidity	BIOLOGICAL_PROCESS	QUALITY	6
reducing power	CHEMICAL	CAPACITY	4

Schema (src/traitmech/schema/traitmech.yaml)

CausalNodeTypeEnum gains three permissible values:

• STATE — a bioenergetic or molecular state of the cell (e.g. proton motive force, redox state of the quinone pool). Distinct from a process: the state is the gradient/steady-value, not its establishment.
• QUALITY — 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.
• CAPACITY — 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.

Migration (scripts/retype_causal_nodes.py)

RETYPES extended from 1 → 4 entries; DEFERRED list now empty. Re-run produces 26 retypes across 25 files.

v1 cohort: Path B extend-in-place

Three new leaf rows under METPO:1007410 (trait causal node type), keeping subset tag metpo_traitmech_2026_05:

• METPO:1007421 — causal-graph state node
• METPO:1007422 — causal-graph quality node (xref PATO:0000001)
• METPO:1007423 — causal-graph capacity node

verify-proposal reports all 13 CausalNodeTypeEnum values lifted.

v3 cohort

proposals/metpo_traitmech_v3/proposal.md "Node-typing notes" section rewritten to document the post-merge resolution.

Mapping TSV

Three rows in mappings/node_grounding.tsv updated to use the new node_type keys so future seeded nodes ground correctly. All three still ground to their cohort-v3 METPO CURIEs (METPO:1007500/1007503/1007505).

Verified locally

$ just validate-strict
  files with ERROR:   0

$ just verify-proposal metpo_traitmech_v1
  scope-C: all 13 CausalNodeTypeEnum values lifted
  failures: 0

$ just robot-validate-proposal metpo_traitmech_v1
  delta: +6
  status: PASS (no UNSAT, ELK exited 0)

$ just verify-proposal metpo_traitmech_v3
  failures: 0

$ uv run python scripts/retype_causal_nodes.py --apply
  nodes retyped: 26

$ uv run python scripts/retype_causal_nodes.py    # idempotency
  nodes retyped: 0

$ uv run pytest tests/
  56 passed

Test plan

• Schema validates the new enum values
• Migration is idempotent
• v1 + v3 cohorts verify + robot-validate clean
• All 56 existing tests pass against the extended schema
• CI runs pytest + validate-strict on the diff

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Extends the TraitMech schema’s CausalNodeTypeEnum to represent three previously-missing semantics (STATE, QUALITY, CAPACITY) and updates the corpus + grounding mappings so affected causal-graph nodes are correctly typed going forward.

Changes:

• Add STATE / QUALITY / CAPACITY to CausalNodeTypeEnum (schema extension).
• Extend scripts/retype_causal_nodes.py to migrate the remaining mis-typed labels and mark the deferred list resolved.
• Retype affected causal-graph nodes across the corpus and update mappings/node_grounding.tsv + proposal artifacts to match the new node_type keys.

Reviewed changes

Copilot reviewed 30 out of 30 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/traitmech/schema/traitmech.yaml	Adds STATE, QUALITY, CAPACITY permissible values to CausalNodeTypeEnum.
scripts/retype_causal_nodes.py	Extends RETYPES to include the three newly-supported node types and clears DEFERRED.
proposals/metpo_traitmech_v3/proposal.md	Updates the “Node-typing notes” section to reflect post-merge resolution.
proposals/metpo_traitmech_v1/metpo_proposal_classes_robot.tsv	Adds three new leaf rows for the v1 cohort’s enum lift (STATE/QUALITY/CAPACITY).
mappings/node_grounding.tsv	Updates the (label, node_type) keys for the three affected mappings to use the new enum values.
data/traits/environment/facultative_psychrophilic.yaml	Retypes membrane fluidity node to QUALITY and appends curation event.
data/traits/environment/mesophilic.yaml	Retypes membrane fluidity node to QUALITY and appends curation event.
data/traits/environment/neutrophilic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/environment/obligately_aerobic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/environment/ph_optimum.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/environment/psychrophilic.yaml	Retypes membrane fluidity node to QUALITY and appends curation event.
data/traits/environment/psychrotolerant.yaml	Retypes membrane fluidity node to QUALITY and appends curation event.
data/traits/environment/temperature_optimum.yaml	Retypes membrane fluidity node to QUALITY and appends curation event.
data/traits/environment/temperature_preference.yaml	Retypes membrane fluidity node to QUALITY and appends curation event.
data/traits/metabolism/aerobic_respiration.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/metabolism/oxidative_phosphorylation.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/metabolism/respiration.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/morphology/gliding.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/physiology/carboxydotrophic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/physiology/chemolithoautotrophic.yaml	Retypes proton motive force→STATE and reducing power→CAPACITY; appends curation event.
data/traits/physiology/chemolithoheterotrophic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/physiology/chemoorganotrophic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/physiology/chemotrophic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/physiology/hydrogenotrophic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/physiology/lithoautotrophic.yaml	Retypes reducing power node to CAPACITY and appends curation event.
data/traits/physiology/lithotrophic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/physiology/organotrophic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/physiology/photolithoautotrophic.yaml	Retypes reducing power node to CAPACITY and appends curation event.
data/traits/physiology/photoorganoheterotrophic.yaml	Retypes proton motive force node to STATE and appends curation event.
data/traits/physiology/phototrophic.yaml	Retypes reducing power node to CAPACITY and appends curation event.

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