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2 changes: 1 addition & 1 deletion scripts/.vendored_canon_ref
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f27502fe02b73460af7b9c86d9fa97f72ac67933
7c516fd6d694915a1c2c5829c201251c4d04ac69
46 changes: 44 additions & 2 deletions src/cellstructuremech/schema/mech_shared.yaml
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id: https://w3id.org/kg-microbe/mech-shared
name: mech_shared
title: Mech shared module — Discussions (knowledge gaps) + Datasets
title: Mech shared module — Discussions, Datasets and cross-corpus links
description: >-
Canonical, byte-identical LinkML module shared across the Mech knowledge
bases (CultureMech / MIM / CommunityMech / TraitMech). It carries two
bases (CultureMech / MIM / CommunityMech / TraitMech). It carries three
domain-general record sections ported from monarch-initiative/dismech:

* Discussion — the discourse / "knowledge gap" layer. A broad supertype
Expand All @@ -18,6 +18,11 @@ description: >-
of the existing CultureMech and CommunityMech enums (plus microbial
additions) so the Phase-2 migration of those two repos is loss-preserving.

* CrossCorpusLink — a provenance-bearing link to a record in another Mech.
The importing schema owns the relation vocabulary and which slots admit
links. Sharing a protein or a reaction supplies a curation lead, not an
assertion of record equivalence or biological mechanism.

The module is SELF-CONTAINED: it defines its own `SupportingReference`
evidence class (and `SupportLevelEnum`) rather than referencing each repo's
`EvidenceItem`, so it validates standalone, imposes no per-repo dependency
Expand Down Expand Up @@ -192,6 +197,43 @@ enums:

classes:

CrossCorpusLink:
description: >-
A directed link from the containing record or sub-object to a record in
another Mech corpus. The five field names preserve NaturalProductMech's
existing link shape. Consumers define allowed relations and evidence
requirements; this class alone does not verify a target, its version,
organism scope, or the scientific basis of the relation.
attributes:
corpus:
description: Canonical target corpus name, for example PathwayMech or AntibioticMech.
range: string
required: true
identifier:
description: Target record identifier, verbatim, in the named corpus.
range: string
required: true
relation:
description: >-
Directed relation from the containing record or sub-object to the
target. Consumers may constrain this string with a local enum through
slot_usage on a subclass, without changing the shared module.
range: string
required: true
basis:
description: >-
How the relation was established, for example SAME_INCHIKEY for an
exact chemical-structure join. A match on a protein or reaction must
not be presented as sufficient evidence for a stronger relation.
range: string
required: true
source_version:
description: >-
Pinned commit or release of the target corpus that was checked.
Optional for compatibility with existing NaturalProductMech links;
consumers should require a full immutable version for newly added links.
range: string

SupportingReference:
description: >-
A lightweight literature/database citation supporting a Discussion or
Expand Down
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