Extend METPO v1: AtmosphereEnum + MediaRelationshipEnum (Path B)#76
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…Enum Path B append-only extension of the v1 cohort per the metpo-proposal skill (.claude/skills/metpo-proposal/skill.md). Adds 14 class rows and 2 property rows in a fresh ID block, leaving existing v1 IDs unchanged and the same subset tag (metpo_communitymech_2026_05). Added classes (METPO:1007300-1007315): - 1 new top-level domain class "community-relevant growth medium" (METPO:1007300, parent METPO:1007100) lifting GrowthMedia and RelatedMedia - AtmosphereEnum: 1 enum-parent + 6 flat leaves (AEROBIC / ANAEROBIC / MICROAEROBIC / FACULTATIVE_ANAEROBIC / FACULTATIVE_AEROBIC / CAPNOPHILIC) - MediaRelationshipEnum: 1 enum-parent + 5 flat leaves (CULTIVATION_MEDIUM / ISOLATION_MEDIUM / ENVIRONMENT_ANALOG / REFERENCED_IN_STUDY / SELECTIVE_ENRICHMENT) Added predicates (METPO:2007200-2007201): - has atmosphere requirement: GrowthMedia.atmosphere -> METPO:1007300 -> METPO:1007301 - has growth media relationship: RelatedMedia.relationship_type -> METPO:1007300 -> METPO:1007310 proposal.md updates per the Path B convention: - Scope table extended with two new rows flagged "(v1.1)" - ID space section now shows separate v1 and v1.1 blocks - Files section row-count updated (90 / 18) - Change log entry "v1.1, 2026-05" describing the extension and ID block choice (1007300 / 2007200, both well above the v1 high water marks 1007220 / 2007113 per the skill's >=10-above rule) Coverage check: 11/11 new enum permissible values mapped to leaf class rows; 88/88 SC % parent references resolve in-file or to existing METPO IRIs (METPO:1000000, METPO:1000525). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
Append-only “Path B” extension to the existing metpo_communitymech_v1 proposal, adding METPO placeholder IDs for two additional CommunityMech enums related to growth media (atmosphere requirements and media relationship types), plus two corresponding object properties.
Changes:
- Extended
proposal.mdto document the v1.1 ID blocks, scope rows, file row counts, and a v1.1 changelog entry. - Added 14 new class rows (including a new growth-medium domain class and enum parents/leaves) to the classes ROBOT template.
- Added 2 new object property rows to the properties ROBOT template for
GrowthMedia.atmosphereandRelatedMedia.relationship_type.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| proposals/metpo_communitymech_v1/proposal.md | Updates proposal narrative to describe the v1.1 extension (scope, ID blocks, row counts, changelog). |
| proposals/metpo_communitymech_v1/metpo_proposal_classes_robot.tsv | Adds new growth-media-related class IDs (domain class + enum parents/leaves). |
| proposals/metpo_communitymech_v1/metpo_proposal_properties_robot.tsv | Adds two new object properties for atmosphere requirement and growth media relationship type. |
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- proposal.md: update the "three top-level domain classes" wording and the table beneath it to include the v1.1 addition, METPO:1007300 community-relevant growth medium (lifts GrowthMedia + RelatedMedia). Also corrected the "total class rows" tally to reflect the new accumulated count (88: 4 + 11 + 10 + 63). - classes TSV: change METPO:1007300 parent from METPO:1007100 (microbial community) to METPO:1000000 (METPO root). The intent always was a peer top-level domain class — growth media are not a kind of microbial community, they're a separate domain that communities relate to. The previous parent would have asserted GrowthMedia subclass-of MicrobialCommunity, which yields incorrect inferences. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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* Absorb metpo_communitymech_metals_v1 into v1 as v1.2 Path B Per discussion, the separate metals cohort was a judgment call rather than an enforced rule. The CHEBI-reuse policy difference (per-element leaves remain CHEBI IRIs) is real but can be documented as a section within v1's proposal rather than partitioned into its own subset tag. Consolidating into v1 reduces upstream-side bookkeeping (one subset tag, one proposal directory to maintain) at the cost of one extra proposal.md section explaining the CHEBI-reuse policy. Changes: - Append the 8 class rows and 3 property rows from the metals cohort to v1's TSVs. Subset tag updated from metpo_communitymech_metals_2026_05 -> metpo_communitymech_2026_05. METPO:1008000 parent changed from METPO:1007100 (microbial community) to METPO:1000000 (peer top-level domain class, same fix pattern as METPO:1007300 in PR #76 review). - v1's proposal.md updated: - Scope table: 3 new rows for MetalElementEnum (CHEBI-reuse), RareEarthElementEnum (CHEBI-reuse), MetalRelevanceEnum - Top-level domain classes table: 5 rows now (added METPO:1008000 community-relevant metal context for v1.2) - New "MetalElementEnum and RareEarthElementEnum - CHEBI-reuse" subsection under Hierarchy decisions - Predicate-proposals table: 19 rows now (added cohort column, v1.2 entries for has_metal_element_present / has_rare_earth_element_present / has_metal_relevance) - ID space section: v1.2 block documented (1008000-1008013 / 2008000-2008002, deliberately starting at 1008000 to visually separate CHEBI-reuse from all-leaves-minted classes) - Files row counts: 98 / 21 lines now - Change log: v1.2 entry covering the absorbed cohort and CHEBI- reuse policy - proposals/metpo_communitymech_metals_v1/ directory removed. Final state on main: - proposals/metpo_communitymech_v1/ only (single cohort) - 96 class rows + 19 property rows (was 88+16 in v1.1, plus 8+3 absorbed from the standalone metals cohort) - Same subset tag (metpo_communitymech_2026_05) on every row - Coverage: 67/67 enum permissible values across 12 enums covered by leaf or grouping-parent class rows - Parent integrity: 96/96 SC % references resolve Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Address Copilot review on PR #78 - proposal.md Context paragraph: update stale "9 community-shaped enums" / "14 object properties" tallies to the v1+v1.1+v1.2 accumulated scope. Explicit enumeration of the 12 in-scope enums plus the 2 CHEBI-anchor enums (MetalElementEnum, RareEarthElementEnum) plus the 4 out-of-scope machine-identifier enums (DatasetTypeEnum, DatasetRepositoryEnum, ExternalResourceRepositoryEnum, CultureCollectionEnum) so the total accounting matches the Scope table and Files row counts. - METPO:1008001 definition (community-relevant metal element): fix grammatical flip ("metals that community members are present in, oxidize, reduce, ...") which read as organisms being present IN metals. Reworded to: "metals (atoms or cations) ... that are present in the community and/or oxidized, reduced, sequestered, leached, or otherwise metabolized by community members" so the metals-are-the-passive-objects relation matches the schema slot MicrobialCommunity.metals_present. Re-ran the kg-microbe ROBOT pipeline locally (robot template -> merge -> reason --reasoner ELK with SubClass + EquivalentClass axiom generators) - all four steps exit 0; 0 owl:Nothing references in the reasoned output. 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
Path B append-only extension of the merged `metpo_communitymech_v1` cohort per the `metpo-proposal` skill. Adds 14 class rows and 2 property rows in a fresh ID block, leaving existing v1 IDs unchanged and reusing the same subset tag.
Added classes (METPO:1007300–METPO:1007315)
Added predicates (METPO:2007200–METPO:2007201)
proposal.md changes (per skill's Path B convention)
Verification
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