METPO metals cohort: MetalElement + RareEarthElement + MetalRelevance

[realmarcin]

Summary

New METPO cohort under `proposals/metpo_communitymech_metals_v1/` lifting three metal-related CommunityMech enums (`MetalElementEnum`, `RareEarthElementEnum`, `MetalRelevanceEnum`). Independent of the `metpo_communitymech_v1` cohort — separate ID block (`METPO:1008NNN` / `METPO:2008NNN`), separate subset tag (`metpo_communitymech_metals_2026_05`), separate proposal directory.

Scoping choice: CHEBI reuse for per-element values

The 17 `MetalElementEnum` and 16 `RareEarthElementEnum` permissible values all carry `meaning: CHEBI:xxxx` annotations in the schema. Per the upstream kg-microbe SKILL.md rule "if the lifted concept already exists in METPO under a different label, use the existing IRI; record the alias upstream", this proposal does not mint per-element METPO classes. Only the grouping-parent classes are minted; per-element CHEBI IRIs flow into `kg-microbe/mappings/metpo_existing_aliases.tsv` when the cohort is copied upstream.

Classes minted (8 rows)

ID	Label	Notes
`METPO:1008000`	community-relevant metal context	top-level domain class under `METPO:1007100`
`METPO:1008001`	community-relevant metal element	enum-parent for `MetalElementEnum`; no leaves (CHEBI IRIs serve as leaves)
`METPO:1008002`	community-relevant rare earth element	enum-parent for `RareEarthElementEnum`; no leaves (CHEBI IRIs)
`METPO:1008003`	community metal relevance level	enum-parent for `MetalRelevanceEnum`
`METPO:1008010`	primary metal relevance	`MetalRelevanceEnum.PRIMARY`
`METPO:1008011`	significant metal relevance	`MetalRelevanceEnum.SIGNIFICANT`
`METPO:1008012`	incidental metal relevance	`MetalRelevanceEnum.INCIDENTAL`
`METPO:1008013`	not-applicable metal relevance	`MetalRelevanceEnum.NOT_APPLICABLE`

The 4 MetalRelevance leaves are minted as fresh METPO classes — they're qualitative severity categories with no CHEBI equivalent.

Predicates minted (3 rows)

ID	Label	Domain	Range
`METPO:2008000`	has metal element present	`METPO:1007100`	`CHEBI:33521` metal cation
`METPO:2008001`	has rare earth element present	`METPO:1007100`	`CHEBI:33530` rare earth atom
`METPO:2008002`	has metal relevance	`METPO:1007100`	`METPO:1008003`

The first two predicates deliberately point `RANGE` at a CHEBI parent so per-element edges (e.g., `community has metal element present CHEBI:29033`) validate via CHEBI's existing `CHEBI:29033 ⊑ CHEBI:33521` axiom — no METPO per-element leaf needed.

Verification

• All 4 `MetalRelevanceEnum` leaves mapped to class rows
• 0 per-element `MetalElementEnum` / `RareEarthElementEnum` leaf rows leaked (correct — CHEBI reuse)
• All 8 `SC %` parents resolve in-file or to known METPO IRIs
• Both TSVs column-count clean (11 / 12)

Test plan

• `awk -F'\t' 'NF != 11' classes_robot.tsv` returns nothing
• `awk -F'\t' 'NF != 12' properties_robot.tsv` returns nothing
• (follow-up) `robot template` parses both TSVs cleanly
• (follow-up) Round-trip check on `Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml` and `Bayan_Obo_REE_Tailings_Consortium.yaml`

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Adds a new METPO “metals” cohort proposal under proposals/metpo_communitymech_metals_v1/, lifting CommunityMech’s metal/REE-related enums and slots into METPO ROBOT templates while reusing CHEBI IRIs for per-element values.

Changes:

• Introduces a narrative proposal describing scope, ID block, hierarchy decisions, and upstream workflow.
• Adds a ROBOT classes template minting 8 METPO classes (domain + enum parents + MetalRelevance leaves).
• Adds a ROBOT properties template minting 3 object properties linking METPO:1007100 (microbial community) to metal/REE presence and relevance.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.

File	Description
proposals/metpo_communitymech_metals_v1/proposal.md	Documents scoping choice (CHEBI reuse), hierarchy, and property/range rationale for the metals cohort.
proposals/metpo_communitymech_metals_v1/metpo_proposal_classes_robot.tsv	Defines the cohort’s new METPO classes (metal context + enum parents + relevance leaves).
proposals/metpo_communitymech_metals_v1/metpo_proposal_properties_robot.tsv	Defines object properties for metals/REE presence and metal relevance on microbial communities.

Comments suppressed due to low confidence (1)

proposals/metpo_communitymech_metals_v1/metpo_proposal_properties_robot.tsv:4

• As with METPO:2008000, the definition includes template-design rationale about why a particular CHEBI parent was chosen for the range. Since this field is emitted as the ontology definition (IAO:0000115), move the range-choice explanation to observations/proposal.md and keep the definition focused on the intended meaning of the relation.

METPO:2008001	has rare earth element present	A relation between a microbial community and a CHEBI rare-earth-element atom or cation that is present in or processed by the community (lanthanides plus Y, Sc). Range points at the CHEBI rare-earth-atom parent so per-REE leaves remain CHEBI IRIs.	CommunityMech:communitymech.yaml#MicrobialCommunity.rare_earth_elements_present	owl:ObjectProperty	METPO:1007100	CHEBI:33530		metpo_communitymech_metals_2026_05	HIGH	rare-earth-element membership of community	0..* cardinality

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