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

[realmarcin]

Summary

Follow-on to PR #67 (predicate residual v3). Normalizes the next-tier of curator-paraphrased predicate labels to canonical synonyms already grounded in mappings/predicate_grounding.tsv, then re-runs ground-predicates to fill predicate_id on the 56 affected edges. No new METPO terms minted.

Renames

old label	new label	CURIE	edges	corpus pattern
influences	regulates	RO:0002211	7	env-axis → trait-pref
determines	causes	biolink:causes	6	X-utilization → trophic-type
sets	defines	METPO:2007500	6	tolerance → bounded-window (the new defines predicate from #73)
constrains	regulates	RO:0002211	6	X → Y where X bounds Y
input to	participates in	biolink:participates_in	6	substrate → pathway
powers	enables	RO:0002327	6	ATP/PMF → process
organizes	enables	RO:0002327	6	cytoskeleton → biosynthesis
occurs under	occurs in	biolink:occurs_in	5	metabolic process → env condition
requires	depends on	RO:0002502	4	process → cofactor/substrate
triggers	causes	biolink:causes	4	signal → response

Skipped (semantically vague or wrong-direction)

• engages (7 edges) — vague; no clean fit
• incorporated into (5 edges) — biolink:part_of is static structural; "incorporated into" is dynamic
• drives production of (5 edges) — too specific; would lose information mapping to bare causes

Corpus impact

	Before	After
Edges grounded	702	758 (+56, 68% → 74%)
Edges residual	317	261 (−56)
Distinct residual labels	173	166 (−7)

Verified locally

$ uv run python scripts/rename_predicate_labels.py --apply
  edges renamed: 56

$ uv run python scripts/ground_causal_predicates.py --apply
  edges grounded: 56
  by target CURIE:
    RO:0002211 ×13   RO:0002327 ×12   biolink:causes ×10
    METPO:2007500 ×6  biolink:participates_in ×6  biolink:occurs_in ×5
    RO:0002502 ×4

$ uv run python scripts/rename_predicate_labels.py   # idempotency
  edges renamed: 0

$ just validate-strict
  files with ERROR:   0

Test plan

• Idempotency on both rename + ground passes
• validate-strict clean
• All 56 renames pick up groundings on the next pass
• CI re-runs validate-strict + pytest

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Normalizes additional residual free-text causal-edge predicate labels to existing canonical predicate labels already mapped in mappings/predicate_grounding.tsv, then re-runs grounding to populate predicate_id for the affected edges (reducing residual edges by 56).

Changes:

• Expanded scripts/rename_predicate_labels.py with 10 additional label renames for the v5 residual cohort.
• Re-grounded affected trait YAML causal edges by updating predicate: and filling predicate_id for the 56 impacted edges.
• Updated the residual report to reflect the reduced set of ungrounded predicate labels.

Reviewed changes

Copilot reviewed 43 out of 43 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
scripts/rename_predicate_labels.py	Adds the next cohort of predicate-label renames (old → canonical label) used prior to grounding.
reports/predicate_grounding_residual.tsv	Updates residual predicate report after renames + grounding remove several labels from the residual set.
data/traits/physiology/trophic_type.yaml	Renames determines→causes and adds predicate_id: biolink:causes on affected edges.
data/traits/physiology/photolithotrophic.yaml	Renames powers→enables and adds predicate_id: RO:0002327.
data/traits/physiology/nutrient_adaptation.yaml	Renames triggers→causes and adds predicate_id: biolink:causes.
data/traits/physiology/methanotrophic.yaml	Renames input to→participates in and adds predicate_id: biolink:participates_in.
data/traits/physiology/carboxydotrophic.yaml	Renames requires→depends on and adds predicate_id: RO:0002502.
data/traits/morphology/spiral_shaped.yaml	Renames influences→regulates and adds predicate_id: RO:0002211.
data/traits/morphology/sphere_shaped.yaml	Renames organizes→enables and adds predicate_id: RO:0002327.
data/traits/morphology/rod_shaped.yaml	Renames organizes→enables and adds predicate_id: RO:0002327.
data/traits/morphology/motility.yaml	Renames powers→enables and adds predicate_id: RO:0002327.
data/traits/morphology/motile.yaml	Renames powers→enables and adds predicate_id: RO:0002327.
data/traits/morphology/gram_stain.yaml	Renames influences→regulates and determines→causes, adds corresponding predicate_ids.
data/traits/morphology/gliding.yaml	Renames powers→enables and adds predicate_id: RO:0002327.
data/traits/morphology/flagellated.yaml	Renames powers→enables and adds predicate_id: RO:0002327.
data/traits/morphology/filament_shaped.yaml	Renames organizes→enables and adds predicate_id: RO:0002327.
data/traits/morphology/crescent_shaped.yaml	Renames constrains→regulates and adds predicate_id: RO:0002211.
data/traits/morphology/cell_width.yaml	Renames organizes→enables and constrains→regulates, adds corresponding predicate_ids.
data/traits/morphology/cell_width_small.yaml	Renames organizes→enables and adds predicate_id: RO:0002327.
data/traits/morphology/cell_shape.yaml	Renames determines→causes and adds predicate_id: biolink:causes.
data/traits/morphology/cell_length.yaml	Renames triggers→causes and adds predicate_id: biolink:causes.
data/traits/morphology/bacillus_shaped.yaml	Renames organizes→enables and adds predicate_id: RO:0002327.
data/traits/metabolism/syntrophy.yaml	Renames input to→participates in and adds predicate_id: biolink:participates_in.
data/traits/metabolism/methanogenesis.yaml	Renames occurs under→occurs in and adds predicate_id: biolink:occurs_in.
data/traits/metabolism/metabolism.yaml	Renames powers→enables and adds predicate_id: RO:0002327.
data/traits/metabolism/homoacetogenesis.yaml	Renames occurs under→occurs in and input to→participates in, adds corresponding predicate_ids.
data/traits/metabolism/disproportionation.yaml	Renames occurs under→occurs in and adds predicate_id: biolink:occurs_in.
data/traits/metabolism/anaerobic_respiration.yaml	Renames occurs under→occurs in and adds predicate_id: biolink:occurs_in.
data/traits/metabolism/acetogenesis.yaml	Renames occurs under→occurs in and input to→participates in, adds corresponding predicate_ids.
data/traits/environment/thermotolerant.yaml	Renames triggers→causes and adds predicate_id: biolink:causes.
data/traits/environment/temperature_range.yaml	Renames sets→defines and adds predicate_id: METPO:2007500 on affected edges.
data/traits/environment/temperature_preference.yaml	Renames influences→regulates and constrains→regulates, adds predicate_id: RO:0002211.
data/traits/environment/temperature_optimum.yaml	Renames influences→regulates and adds predicate_id: RO:0002211.
data/traits/environment/stenohaline.yaml	Renames constrains→regulates and adds predicate_id: RO:0002211.
data/traits/environment/ph_range.yaml	Renames sets→defines and adds predicate_id: METPO:2007500 on affected edges.
data/traits/environment/ph_growth_preference.yaml	Renames influences→regulates and adds predicate_id: RO:0002211.
data/traits/environment/obligately_alkaphilic.yaml	Renames constrains→regulates and adds predicate_id: RO:0002211.
data/traits/environment/obligately_aerobic.yaml	Renames requires→depends on and adds predicate_id: RO:0002502.
data/traits/environment/nacl_range.yaml	Renames sets→defines and adds predicate_id: METPO:2007500 on affected edges.
data/traits/environment/nacl_optimum.yaml	Renames triggers→causes and adds predicate_id: biolink:causes.
data/traits/environment/halophily_preference.yaml	Renames influences→regulates and adds predicate_id: RO:0002211.
data/traits/environment/aerobic.yaml	Renames requires→depends on and adds predicate_id: RO:0002502 on affected edges.
data/traits/ecology/biosafety_level.yaml	Renames determines→causes and adds predicate_id: biolink:causes.

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