Add metpo-proposal skill#75
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Three files under proposals/metpo_communitymech_v1/ mirror the existing kg-microbe METPO proposal format and lift 9 CommunityMech enums plus 14 schema predicates into METPO classes and object properties: - metpo_proposal_classes_robot.tsv: 74 class rows (11 columns, two-row ROBOT header). Includes 3 new top-level domain classes (microbial community, microbial community ecological interaction, microbial community evidence item) plus 9 enum-parent grouping classes, 10 intermediate grouping classes (positive/negative/ partitioning interaction valence; primary/secondary trophic role; 5 thematic community-category groupings), and 52 enum-leaf classes. All 52 CommunityMech enum permissible values are covered; all parent references resolve within the file or to known METPO IRIs (METPO:1000000 root, METPO:1000525 microbe). - metpo_proposal_properties_robot.tsv: 14 owl:ObjectProperty rows (12 columns) with domain/range mapped to the new top-level classes or external IRIs (NCBITaxon, CHEBI, GO). Captures EcologicalInteraction.source_taxon/target_taxon/interaction_type/ scope/metabolites/biological_processes/evidence, TaxonomicComposition.functional_role/abundance_level, MicrobialCommunity.community_category/community_origin/ ecological_state, and EvidenceItem.supports/evidence_source. - proposal.md: narrative walking through scope, hierarchy decisions (InteractionType valence groupings, FunctionalRole trophic tiers, CommunityCategory thematic groupings, COMPETITION / STRAIN_COMPETITION parent/child relationship), predicate domain/range rationale, ID-space conventions, verification procedure (robot template + reason), and the upstream path to kg-microbe/mappings/. ID space: METPO:1007100-1007220 for classes and METPO:2007100-2007113 for properties, all marked as placeholder per the kg-microbe SKILL.md placeholder policy; real METPO IDs will be minted upstream after sign-off. Subset tag on every row: metpo_communitymech_2026_05. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Document the workflow used to produce proposals/metpo_communitymech_v1/ (PR #74) so future cohorts can follow the same conventions: ROBOT-template column structure (11 classes / 12 properties), ID-space conventions (METPO:1007NNN and METPO:2007NNN placeholder ranges), Aristotelian definitions with schema-anchored definition_source values, hierarchy-design rules for intermediate parents, predicate domain/range conventions, trailing-tab fix-up for the ROBOT header row, and the verification commands (awk column-count check, enum-coverage check, parent- integrity check, optional robot template + reason). Points at the upstream kg-microbe metpo-proposal SKILL.md for the shared conventions and at proposals/metpo_communitymech_v1/ as the reference cohort. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
Adds a project-level Claude Code skill (metpo-proposal) and a reference METPO ROBOT-template proposal cohort (proposals/metpo_communitymech_v1/) to document and preserve the conventions for lifting CommunityMech schema elements into METPO-compatible ROBOT templates.
Changes:
- Added
.claude/skills/metpo-proposal/skill.mddocumenting the end-to-end workflow and conventions for generating METPO proposal TSVs + narrative. - Added a reference proposal cohort under
proposals/metpo_communitymech_v1/including the class/property ROBOT templates and a narrativeproposal.md. - Encoded placeholder ID-space, subset tagging, hierarchy/grouping decisions, and verification steps for repeatable future cohorts.
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
proposals/metpo_communitymech_v1/proposal.md |
Narrative description of scope, hierarchy decisions, predicate proposals, verification, and upstream path for the reference cohort. |
proposals/metpo_communitymech_v1/metpo_proposal_classes_robot.tsv |
11-column ROBOT class template capturing proposed METPO classes for lifted enums and supporting parents. |
proposals/metpo_communitymech_v1/metpo_proposal_properties_robot.tsv |
12-column ROBOT property template capturing proposed METPO object properties for CommunityMech slots. |
.claude/skills/metpo-proposal/skill.md |
New Claude Code skill documenting the conventions/workflow used to produce the reference cohort. |
Comments suppressed due to low confidence (1)
.claude/skills/metpo-proposal/skill.md:69
- The “Required reading” section hard-codes absolute local paths under
/Users/marcin/.... These paths won’t exist for other contributors or in CI, which makes the workflow hard to follow. Replace these with GitHub links to the upstreamkg-microbefiles (or repo-relative paths if vendored here) and, if needed, add a short note about cloningkg-microbealongside this repo.
Before generating a proposal, read:
1. **`/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/.claude/skills/metpo-proposal/SKILL.md`** —
the upstream metpo-proposal skill. Defines:
- Aristotelian definition style
- `definition_source` citation forms (PMID, DOI, BacDive, `TODO:add_citation`)
- Numeric ID-range conventions
- Parent-class selection (audit for siblings before falling back to
`METPO:1000000`)
- The 12-point pre-submission checklist
2. **`/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/mappings/metpo_proposal_classes_robot.tsv`** —
the canonical 11-column class template. Copy the two-row header verbatim.
3. **`/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/mappings/metpo_proposal_properties_robot.tsv`** —
the canonical 12-column property template.
4. **`proposals/metpo_communitymech_v1/`** in this repo — the reference
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The initial skill assumed every invocation creates a new cohort. Add an "Updating an existing proposal" section covering the three real update paths and the decision rule for picking between them: - Path A: edit in place on an open PR before merge. IDs and subset tag unchanged; just modify rows in response to reviewer feedback. - Path B: extend in place after merge. Append-only rows in the same cohort directory, contiguous fresh ID block at least 10 above the highest existing ID, same subset tag, new entries in the Scope/ID-space/Change-log sections of proposal.md. - Path C: new cohort version. Fresh proposals/<name>_v<N>/ dir, fresh subset tag, non-overlapping ID block, mandatory "Relationship to vN-1" section in the new proposal.md, original cohort marked superseded but retained on disk. Each path lists what NOT to do: never edit merged IDs, never mix Path B + Path C in the same PR, never delete rows (mark LOW priority instead and retire via Path C). Decision rule lives at the top of the section as a table keyed on review/merge state and the type of change. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Per the same broken-link finding that triggered the Path A fix on PR #74, the skill.md had two more relative paths into the kg-microbe repo that 404 on GitHub: - "Do NOT use for..." section: relative link to upstream skill replaced with absolute GitHub URL - "Required reading" section: three local absolute paths under /Users/marcin/... replaced with GitHub URLs to the kg-microbe source files, keeping the local clone path as a hint for developers with a checkout. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…-skill # Conflicts: # proposals/metpo_communitymech_v1/metpo_proposal_classes_robot.tsv # proposals/metpo_communitymech_v1/metpo_proposal_properties_robot.tsv # proposals/metpo_communitymech_v1/proposal.md
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Summary
Add a project-level Claude Code skill that documents the workflow used to produce `proposals/metpo_communitymech_v1/` (PR #74), so future METPO cohorts from this repo follow the same conventions.
The skill captures:
Points reviewers to:
Surfaces as `metpo-proposal` in the Claude Code skill list when running from `CommunityMech/CommunityMech/`.
🤖 Generated with Claude Code