Record METPO GC-bin label corrections (berkeleybop/metpo#432)

[realmarcin]

Summary

Adds a new proposal artifact mappings/metpo_label_corrections.tsv that captures upstream label-fix requests for existing METPO terms whose rdfs:label disagrees with their numeric-threshold synonyms. Each row cites a berkeleybop/metpo issue. This is distinct from metpo_existing_aliases.tsv (which routes a kg-microbe-side label to an existing METPO ID as-is) — corrections request that the upstream record itself be amended.

First cohort: berkeleybop/metpo#432

The four GC-content bin records have labels that don't line up with their numeric-threshold synonyms. Sorted by ascending GC%, the synonyms are the source of truth; three of the four labels are wrong:

METPO ID	Current label	Corrected label	Threshold synonym
METPO:1000432	GC high	GC low	GC_<=42.65 (lowest range)
METPO:1000429	GC low	GC mid1	GC_42.65_57.0 (second-lowest)
METPO:1000431	GC mid2	GC mid2 (no change)	GC_57.0_66.3 (already correct)
METPO:1000430	GC mid1	GC high	GC_>66.3 (highest range)

Why this works as a separate artifact

KG-Microbe transforms don't directly reference any of METPO:1000429-1000432. The GC-content bins in custom_curies.yaml use independent gc:low/mid1/mid2/high placeholders that are already correctly labeled by numeric range:

gc:low   = "GC content <= 42.65%"     ← matches METPO:1000432 numeric range
gc:mid1  = "GC content 42.65% - 57.0%"
gc:mid2  = "GC content 57.0% - 66.3%"
gc:high  = "GC content > 66.3%"        ← matches METPO:1000430 numeric range

The merged graph is therefore unaffected by the upstream bug. The label-corrections TSV is purely a curator-facing artifact for the upstream PR — once berkeleybop/metpo#432 is fixed, the entries become stale and the freshness check will fail loudly.

Implementation

• scripts/extract_metpo_proposals.py:
  • new LabelCorrection dataclass + LABEL_CORRECTION_HEADER
  • new METPO_LABEL_CORRECTIONS list with 4 GC-bin entries (3 changes + 1 unchanged-for-completeness)
  • new validate_label_corrections(): reads data/transformed/ontologies/metpo_nodes.tsv and confirms each entry's current_label still matches what METPO actually has — fails if upstream has already fixed a row (stale entry) or the METPO ID is missing entirely
  • new write_label_correction_tsv() writer
  • main() invokes both, after the existing-aliases write
• tests/test_extract_metpo_proposals.py: adds metpo_label_corrections.tsv to PROPOSAL_FILES so the regenerate-and-diff CI gate catches drift between the script and the committed TSV
• .claude/skills/metpo-proposal/SKILL.md: documents the new artifact in the artifacts table + adds a skill-checklist item for the freshness check

Verification

$ poetry run python scripts/extract_metpo_proposals.py
…
[ok] label-correction freshness check passed for 4 upstream label-fix request(s)
[ok] metpo_label_corrections.tsv          (4 upstream label-fix request(s); 3 actual label change(s) — see GitHub refs in TSV)
…
[ok] ROBOT template + ELK reason passed (no UNSAT classes)

$ poetry run pytest tests/test_extract_metpo_proposals.py -v
PASSED

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Adds a new curator-facing artifact mappings/metpo_label_corrections.tsv that tracks upstream label-fix requests for existing METPO terms whose rdfs:label disagrees with their numeric-threshold synonyms. The first cohort addresses berkeleybop/metpo#432 (four GC-content bin records with mis-ordered labels). A freshness validator reads the local METPO snapshot to ensure each correction's current_label still matches upstream, failing loudly if entries are stale or IDs missing.

Changes:

• Introduce LabelCorrection dataclass, METPO_LABEL_CORRECTIONS cohort, validate_label_corrections(), and write_label_correction_tsv() in scripts/extract_metpo_proposals.py; wire into main().
• Commit generated mappings/metpo_label_corrections.tsv and add it to PROPOSAL_FILES so the regenerate-and-diff CI gate catches drift.
• Document the new artifact and freshness check in .claude/skills/metpo-proposal/SKILL.md.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
scripts/extract_metpo_proposals.py	Adds dataclass, header, cohort list, validator, writer, and main() wiring for label corrections
mappings/metpo_label_corrections.tsv	New generated TSV with the four GC-bin label-correction rows
tests/test_extract_metpo_proposals.py	Adds new TSV to PROPOSAL_FILES for CI regenerate-and-diff check
.claude/skills/metpo-proposal/SKILL.md	Documents the new artifact and adds a checklist item

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