METPO ROBOT-template proposal: CommunityMech roles/interactions/evidence#74
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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>
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Pull request overview
Adds a METPO ROBOT-template proposal package to lift CommunityMech community-role / interaction / evidence enums and key predicates into METPO-ready TSV templates, enabling upstream ID minting and integration into the KG-Microbe METPO proposal pipeline.
Changes:
- Added a narrative proposal (
proposal.md) describing scope, hierarchy decisions, predicates, ID ranges, and verification steps. - Added a ROBOT class template TSV defining new domain classes plus lifted enum classes and groupings.
- Added a ROBOT property template TSV defining 14 object properties that connect interactions/communities/evidence items to taxa and ontology terms.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 6 comments.
| File | Description |
|---|---|
| proposals/metpo_communitymech_v1/proposal.md | Narrative spec for the METPO lift (scope, hierarchy, predicates, verification, upstream steps). |
| proposals/metpo_communitymech_v1/metpo_proposal_classes_robot.tsv | ROBOT class template with new domain classes and lifted enum class hierarchy. |
| proposals/metpo_communitymech_v1/metpo_proposal_properties_robot.tsv | ROBOT property template mapping CommunityMech slots to METPO object properties with domain/range. |
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realmarcin
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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>
Merged
Five fixes for the five actionable Copilot comments: - proposal.md: rewrite the broken relative link to the kg-microbe metpo-proposal SKILL.md as an absolute GitHub URL (the SKILL.md is not in this repo, so the prior relative link 404'd on GitHub). - proposal.md: add `kb/communities/` prefixes to the three example YAML filenames in the verification round-trip section so reviewers can copy-paste the paths. - properties TSV: narrow the `has supporting evidence` (METPO:2007106) definition by dropping the "(or community claim)" parenthetical that disagreed with the declared domain METPO:1007101 (community interaction only). The definition now matches the domain exactly. - classes TSV: replace the 10 `TODO:add_citation` placeholder definition_source values on the intermediate grouping parents with a project-internal anchor URL `CommunityMech:proposals/metpo_communitymech_v1/proposal.md#hierarchy-decisions`. These 10 classes are organizational scaffolding introduced in this proposal (not lifted from an external textbook), so citing the proposal narrative is the honest provenance; the per-enum-value leaves continue to cite the CommunityMech schema directly. - classes TSV: replace the overbroad `ecological interaction` exact synonym on METPO:1007101 with two precise variants (`microbial community interaction|microbial ecological interaction`). The previous `ecological interaction` synonym dropped the community qualifier and would have asserted a misleading exact equivalence with the broader ecological-interaction concept. One Copilot comment (markdown table leading `||`) could not be reproduced - the proposal.md tables use standard single-pipe GFM syntax with no `||` anywhere in the file; replied to the thread asking for clarification. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
realmarcin
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May 20, 2026
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>
realmarcin
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* Add METPO ROBOT-template proposal lifting CommunityMech enums 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> * Add metpo-proposal skill 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> * Extend metpo-proposal skill with update-path guidance 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> * Address Copilot review on PR #75: replace kg-microbe relative links 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> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Lift 9 CommunityMech enums plus 14 schema predicates into a METPO ROBOT-template proposal under `proposals/metpo_communitymech_v1/`, mirroring the existing kg-microbe `metpo_proposal_*.tsv` format. After sign-off here, the two TSVs copy upstream to `kg-microbe/mappings/` for ID minting.
The METPO proposal pipeline currently covers phenotypic traits, tolerance ranges, and enzyme assays — but has zero coverage of community-level roles, interaction types, and evidence framing. This proposal closes that gap.
Deliverables
Class hierarchy at a glance
Plus 3 new top-level domain classes under `METPO:1000000`:
Predicates
14 object properties mapping CommunityMech slots to domain/range pairs over the new classes plus NCBITaxon / CHEBI / GO. Highlights:
No paired "does not X" predicates — the SKILL.md positive/negative pairing convention applies to chemical-tolerance relations, not domain-modeling relations.
ID space and subset
Verification
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