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realmarcin merged 2 commits into from
May 20, 2026
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Extend METPO v1: AtmosphereEnum + MediaRelationshipEnum (Path B) #76

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aca1658
Extend metpo_communitymech_v1 with AtmosphereEnum + MediaRelationship…
realmarcin May 20, 2026
9f60892
Address Copilot review on PR #76
realmarcin May 20, 2026
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14 changes: 14 additions & 0 deletions proposals/metpo_communitymech_v1/metpo_proposal_classes_robot.tsv
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Expand Up @@ -74,3 +74,17 @@ METPO:1007217 biotechnology community A microbial community category for communi
METPO:1007218 extreme environment community A microbial community category for communities from extreme conditions (acidophilic, alkaliphilic, thermophilic, halophilic, hyperbaric, irradiated, etc.). CommunityMech:communitymech.yaml#CommunityCategoryEnum.EXTREME_ENVIRONMENT METPO:1007205 extremophile community metpo_communitymech_2026_05 HIGH CommunityCategoryEnum.EXTREME_ENVIRONMENT
METPO:1007219 syntrophy-defined community A microbial community category for communities defined primarily by syntrophic metabolic cooperation between members (e.g., interspecies hydrogen transfer in anaerobic digestion). CommunityMech:communitymech.yaml#CommunityCategoryEnum.SYNTROPHY METPO:1007205 syntrophic community metpo_communitymech_2026_05 HIGH CommunityCategoryEnum.SYNTROPHY
METPO:1007220 other community category A microbial community category for communities that do not fit any of the predefined functional or environmental groupings. CommunityMech:communitymech.yaml#CommunityCategoryEnum.OTHER METPO:1007200 uncategorized community metpo_communitymech_2026_05 MEDIUM CommunityCategoryEnum.OTHER
METPO:1007300 community-relevant growth medium A growth medium or environmentally-related medium associated with a microbial community, either used for cultivation of community members or designated by curators as analogous to the community's environment. Top-level domain class lifting CommunityMech GrowthMedia and RelatedMedia. CommunityMech:communitymech.yaml#GrowthMedia METPO:1000000 growth medium|culture medium|community medium metpo_communitymech_2026_05 HIGH top-level domain class for v1.1 extension
METPO:1007301 atmosphere requirement The atmospheric or oxygen requirement of a growth medium, distinguishing aerobic, anaerobic, microaerobic, facultative, and specialized (e.g., CO2-requiring) cultivation conditions. CommunityMech:communitymech.yaml#AtmosphereEnum METPO:1007300 atmosphere category|oxygen requirement category metpo_communitymech_2026_05 HIGH enum-parent for AtmosphereEnum
METPO:1007302 aerobic atmosphere requirement An atmosphere-requirement value indicating that the medium requires oxygen for growth. CommunityMech:communitymech.yaml#AtmosphereEnum.AEROBIC METPO:1007301 obligate aerobic atmosphere|oxygen-required atmosphere metpo_communitymech_2026_05 HIGH AtmosphereEnum.AEROBIC
METPO:1007303 anaerobic atmosphere requirement An atmosphere-requirement value indicating that the medium supports growth only in the absence of oxygen (strict anaerobe). CommunityMech:communitymech.yaml#AtmosphereEnum.ANAEROBIC METPO:1007301 strict anaerobic atmosphere|obligate anaerobic atmosphere metpo_communitymech_2026_05 HIGH AtmosphereEnum.ANAEROBIC
METPO:1007304 microaerobic atmosphere requirement An atmosphere-requirement value indicating that the medium requires low oxygen levels (typically 2-10%). CommunityMech:communitymech.yaml#AtmosphereEnum.MICROAEROBIC METPO:1007301 microaerophilic atmosphere|low-oxygen atmosphere metpo_communitymech_2026_05 HIGH AtmosphereEnum.MICROAEROBIC
METPO:1007305 facultative anaerobic atmosphere requirement An atmosphere-requirement value indicating that the medium supports growth with or without oxygen, with no preference required. CommunityMech:communitymech.yaml#AtmosphereEnum.FACULTATIVE_ANAEROBIC METPO:1007301 facultatively anaerobic atmosphere metpo_communitymech_2026_05 HIGH AtmosphereEnum.FACULTATIVE_ANAEROBIC
METPO:1007306 facultative aerobic atmosphere requirement An atmosphere-requirement value indicating that the medium is preferentially aerobic but supports growth anaerobically as well. CommunityMech:communitymech.yaml#AtmosphereEnum.FACULTATIVE_AEROBIC METPO:1007301 facultatively aerobic atmosphere metpo_communitymech_2026_05 HIGH AtmosphereEnum.FACULTATIVE_AEROBIC
METPO:1007307 capnophilic atmosphere requirement An atmosphere-requirement value indicating that the medium requires elevated CO2 levels. CommunityMech:communitymech.yaml#AtmosphereEnum.CAPNOPHILIC METPO:1007301 CO2-requiring atmosphere|elevated-CO2 atmosphere metpo_communitymech_2026_05 HIGH AtmosphereEnum.CAPNOPHILIC
METPO:1007310 growth media relationship type The type of relationship between a microbial community and a growth medium, distinguishing actual cultivation media from environmentally analogous or study-referenced media. CommunityMech:communitymech.yaml#MediaRelationshipEnum METPO:1007300 medium relationship category metpo_communitymech_2026_05 HIGH enum-parent for MediaRelationshipEnum
METPO:1007311 cultivation medium relationship A growth-media-relationship value indicating that the medium was actually used for cultivation of community members. CommunityMech:communitymech.yaml#MediaRelationshipEnum.CULTIVATION_MEDIUM METPO:1007310 cultivation medium|primary cultivation medium metpo_communitymech_2026_05 HIGH MediaRelationshipEnum.CULTIVATION_MEDIUM
METPO:1007312 isolation medium relationship A growth-media-relationship value indicating that the medium was used for initial isolation of community members from the environment. CommunityMech:communitymech.yaml#MediaRelationshipEnum.ISOLATION_MEDIUM METPO:1007310 isolation medium metpo_communitymech_2026_05 HIGH MediaRelationshipEnum.ISOLATION_MEDIUM
METPO:1007313 environment analog medium relationship A growth-media-relationship value indicating that the medium was designed to mimic the community's natural environment. CommunityMech:communitymech.yaml#MediaRelationshipEnum.ENVIRONMENT_ANALOG METPO:1007310 environment-mimicking medium|environmental analog medium metpo_communitymech_2026_05 HIGH MediaRelationshipEnum.ENVIRONMENT_ANALOG
METPO:1007314 referenced-in-study medium relationship A growth-media-relationship value indicating that the medium is referenced in a study of this community but not necessarily used for cultivation. CommunityMech:communitymech.yaml#MediaRelationshipEnum.REFERENCED_IN_STUDY METPO:1007310 study-referenced medium metpo_communitymech_2026_05 MEDIUM MediaRelationshipEnum.REFERENCED_IN_STUDY
METPO:1007315 selective enrichment medium relationship A growth-media-relationship value indicating that the medium was used for selective enrichment of specific functional groups within the community. CommunityMech:communitymech.yaml#MediaRelationshipEnum.SELECTIVE_ENRICHMENT METPO:1007310 selective enrichment medium|enrichment medium metpo_communitymech_2026_05 HIGH MediaRelationshipEnum.SELECTIVE_ENRICHMENT
2 changes: 2 additions & 0 deletions proposals/metpo_communitymech_v1/metpo_proposal_properties_robot.tsv
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Expand Up @@ -14,3 +14,5 @@ METPO:2007110 has community origin A relation between a microbial community and
METPO:2007111 has ecological state A relation between a microbial community and an ecological-state class describing whether the community is stable, perturbed, engineered, or transient/developing. CommunityMech:communitymech.yaml#MicrobialCommunity.ecological_state owl:ObjectProperty METPO:1007100 METPO:1007180 metpo_communitymech_2026_05 HIGH community ecological state 0..1 cardinality
METPO:2007112 has evidence support level A relation between a microbial community evidence item and an evidence-support-level class indicating how the cited reference relates to the claim (direct support, partial support, no evidence, misattribution, or active refutation). CommunityMech:communitymech.yaml#EvidenceItem.supports owl:ObjectProperty METPO:1007102 METPO:1007150 metpo_communitymech_2026_05 HIGH support level of cited reference required, 1..1 cardinality
METPO:2007113 has evidence source type A relation between a microbial community evidence item and an evidence-source class indicating the provenance category of the evidence (in vitro, in vivo, computational, review, other). CommunityMech:communitymech.yaml#EvidenceItem.evidence_source owl:ObjectProperty METPO:1007102 METPO:1007160 metpo_communitymech_2026_05 HIGH provenance of evidence required, 1..1 cardinality
METPO:2007200 has atmosphere requirement A relation between a community-relevant growth medium and the atmosphere-requirement class describing its O2 / CO2 needs. CommunityMech:communitymech.yaml#GrowthMedia.atmosphere owl:ObjectProperty METPO:1007300 METPO:1007301 metpo_communitymech_2026_05 HIGH atmosphere assignment to growth medium 0..1 cardinality
METPO:2007201 has growth media relationship A relation between a community-relevant growth medium and a growth-media-relationship-type class describing how the medium relates to the community (actual cultivation, isolation, environmental analog, etc.). CommunityMech:communitymech.yaml#RelatedMedia.relationship_type owl:ObjectProperty METPO:1007300 METPO:1007310 metpo_communitymech_2026_05 HIGH media-to-community relationship category 0..1 cardinality
63 changes: 45 additions & 18 deletions proposals/metpo_communitymech_v1/proposal.md
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Expand Up @@ -33,21 +33,26 @@ level assertions the same way.
| `CommunityCategoryEnum` | `community functional category` (`METPO:1007200`) | 15 | 5 (thematic groupings) | 123–155 |
| `CommunityOriginEnum` | `community origin type` (`METPO:1007190`) | 3 | 0 (flat) | 97–105 |
| `EcologicalStateEnum` | `community ecological state` (`METPO:1007180`) | 4 | 0 (flat) | 85–95 |
| `AtmosphereEnum` (v1.1) | `atmosphere requirement` (`METPO:1007301`) | 6 | 0 (flat) | 228–243 |
| `MediaRelationshipEnum` (v1.1) | `growth media relationship type` (`METPO:1007310`) | 5 | 0 (flat) | 107–121 |

Plus three new **top-level domain classes** (children of `METPO:1000000`):
Plus four new **top-level domain classes** (children of `METPO:1000000`):

| ID | Label | Lifts CommunityMech class |
| --- | --- | --- |
| `METPO:1007100` | microbial community | `MicrobialCommunity` |
| `METPO:1007101` | microbial community ecological interaction | `EcologicalInteraction` |
| `METPO:1007102` | microbial community evidence item | `EvidenceItem` |
| ID | Label | Lifts CommunityMech class | Added in |
| --- | --- | --- | --- |
| `METPO:1007100` | microbial community | `MicrobialCommunity` | v1 |
| `METPO:1007101` | microbial community ecological interaction | `EcologicalInteraction` | v1 |
| `METPO:1007102` | microbial community evidence item | `EvidenceItem` | v1 |
| `METPO:1007300` | community-relevant growth medium | `GrowthMedia` and `RelatedMedia` | v1.1 |

Each `enum-parent` class is a child of one of those three domain classes (e.g.,
Each `enum-parent` class is a child of one of those four domain classes (e.g.,
`community functional category` sits under `microbial community`;
`evidence item support level` sits under `microbial community evidence item`).
`evidence item support level` sits under `microbial community evidence item`;
`atmosphere requirement` sits under `community-relevant growth medium`).

Total class rows: **74** (3 top-level domain + 9 enum-parents + 10 intermediate
groupings + 52 leaves from enums).
Total class rows: **88** (4 top-level domain + 11 enum-parents + 10 intermediate
groupings + 63 leaves from enums; the v1.1 extension added 1 top-level + 2
enum-parents + 11 leaves on top of v1's 3 + 9 + 10 + 52 = 74).

## Hierarchy decisions

Expand Down Expand Up @@ -127,22 +132,25 @@ semantically meaningful.

## ID space and subset

- **Classes**: `METPO:1007100`–`METPO:1007220` (placeholder, within the
KG-Microbe-reserved 1007xxx range per the SKILL.md placeholder policy)
- **Properties**: `METPO:2007100`–`METPO:2007113` (placeholder)
- **Classes**:
- v1: `METPO:1007100`–`METPO:1007220` (placeholder, within the KG-Microbe-reserved 1007xxx range per the SKILL.md placeholder policy)
- v1.1 extension: `METPO:1007300`–`METPO:1007315` (AtmosphereEnum + MediaRelationshipEnum + shared top-level domain class `community-relevant growth medium` at `METPO:1007300`)
- **Properties**:
- v1: `METPO:2007100`–`METPO:2007113`
- v1.1 extension: `METPO:2007200`–`METPO:2007201`
- **Subset tag** on every row: `metpo_communitymech_2026_05`
- **Definition source** on every leaf row: `CommunityMech:communitymech.yaml#<enum-name>.<value>`
for direct enum lifts; `TODO:add_citation` for the 10 intermediate grouping
parents (which are introduced in this proposal, not lifted from the schema).
for direct enum lifts; `CommunityMech:proposals/metpo_communitymech_v1/proposal.md#hierarchy-decisions`
for the 10 intermediate grouping parents introduced in this proposal.
- **Priority**: `HIGH` on all rows that come directly from CommunityMech enums;
`MEDIUM` on `OTHER` catch-all leaves.
`MEDIUM` on `OTHER` catch-all leaves and `REFERENCED_IN_STUDY` medium-relationship value.

## Files

| File | Rows | Notes |
| --- | --- | --- |
| `metpo_proposal_classes_robot.tsv` | 1 column header + 1 ROBOT header + 74 class rows = 76 lines | mirror of `kg-microbe/mappings/metpo_proposal_classes_robot.tsv` schema |
| `metpo_proposal_properties_robot.tsv` | 1 column header + 1 ROBOT header + 14 property rows = 16 lines | mirror of `kg-microbe/mappings/metpo_proposal_properties_robot.tsv` schema |
| `metpo_proposal_classes_robot.tsv` | 1 column header + 1 ROBOT header + 88 class rows = 90 lines (74 in v1 + 14 in v1.1 extension) | mirror of `kg-microbe/mappings/metpo_proposal_classes_robot.tsv` schema |
| `metpo_proposal_properties_robot.tsv` | 1 column header + 1 ROBOT header + 16 property rows = 18 lines (14 in v1 + 2 in v1.1 extension) | mirror of `kg-microbe/mappings/metpo_proposal_properties_robot.tsv` schema |
| `proposal.md` | (this file) | narrative for reviewer |

## Verification
Expand Down Expand Up @@ -203,3 +211,22 @@ When this proposal is approved here in CommunityMech:

- **v1, 2026-05**: Initial proposal. 74 class rows (9 enums, 3 top-level
domain classes, 10 intermediate grouping parents) + 14 property rows.
- **v1.0.1, 2026-05 (revised)**: Addressed Copilot review on PR #74.
Replaced kg-microbe relative link with absolute GitHub URL; added
`kb/communities/` prefixes to verification example YAMLs; narrowed
`has supporting evidence` (METPO:2007106) definition to match its
domain METPO:1007101; replaced 10 `TODO:add_citation` placeholders
with the proposal-narrative anchor URL; replaced overbroad
`ecological interaction` synonym on METPO:1007101 with two precise
variants.
- **v1.1, 2026-05**: Path B extension. Added `AtmosphereEnum`
(`METPO:1007301`–`METPO:1007307`, 1 enum-parent + 6 leaves) and
`MediaRelationshipEnum` (`METPO:1007310`–`METPO:1007315`, 1
enum-parent + 5 leaves), under a shared new top-level domain class
`community-relevant growth medium` (`METPO:1007300`). Added 2 new
predicates: `has atmosphere requirement` (`METPO:2007200`) and
`has growth media relationship` (`METPO:2007201`). New ID block
starts at `1007300` / `2007200` per the skill's Path B rule
(at least 10 above the v1 high-water marks of `1007220` /
`2007113`). Total now: 88 class rows + 16 property rows. Same
subset tag.