id: https://w3id.org/cofactormech/schema
name: cofactormech
title: CofactorMech evidence-backed cofactors
license: CC0-1.0
prefixes:
  linkml: https://w3id.org/linkml/
  CofactorMech: https://w3id.org/cofactormech/record/
  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
default_prefix: CofactorMech
default_range: string
imports:
  - linkml:types
  - mech_shared
  - history
enums:
  CofactorCategory:
    permissible_values:
      COENZYME:
      PROSTHETIC_GROUP:
      METAL_ION:
  LinkCorpus:
    permissible_values:
      mediaingredientmech:
      pathwaymech:
      proteintraitsmech:
  LinkRelation:
    permissible_values:
      SUPPLIED_BY:
      PRECURSOR_SUPPLIED_BY:
      PRODUCED_BY:
      USED_BY:
      REQUIRED_BY:
      CONJUGATE_FORM_PRODUCED_BY:
      CONJUGATE_FORM_USED_BY:
      CONJUGATE_FORM_REQUIRED_BY:
  LinkStatus:
    permissible_values:
      PROVISIONAL:
      VERIFIED:
  CurationAction:
    permissible_values:
      CREATE:
      EDIT:
      REVIEW:
      AUDIT:
classes:
  CofactorRecord:
    tree_root: true
    description: A defined chemical species with evidence for its cofactor function.
    attributes:
      id:
        identifier: true
        required: true
        pattern: '^CofactorMech:[a-z0-9]+(?:-[a-z0-9]+)*$'
      name:
        required: true
      chemical_id:
        required: true
        pattern: '^CHEBI:[0-9]+$'
      categories:
        description: Categories can overlap; binding and organism context belong in the evidence.
        range: CofactorCategory
        required: true
        multivalued: true
        minimum_cardinality: 1
      description:
        required: true
      evidence:
        range: EvidenceItem
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
      related_records:
        range: CofactorCrossCorpusLink
        multivalued: true
        inlined_as_list: true
      research_gaps:
        range: ResearchGap
        multivalued: true
        inlined_as_list: true
      curation_history:
        range: CurationEvent
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
  EvidenceItem:
    description: Source supporting the accompanying claim, with a precise locator.
    attributes:
      reference:
        required: true
        pattern: '^https://[^ ]+$'
      title:
        required: true
      claim:
        required: true
      locator:
        required: true
      source_license:
        description: Licence verified for the cited source; omit if not established.
  CofactorCrossCorpusLink:
    is_a: CrossCorpusLink
    description: A curator-verified target at an immutable revision, plus evidence for the relation.
    slot_usage:
      corpus:
        range: LinkCorpus
      relation:
        range: LinkRelation
      source_version:
        required: true
        pattern: '^[0-9a-f]{40}$'
    attributes:
      status:
        range: LinkStatus
        required: true
      target_chemical_id:
        description: Chemical species in the target when explicitly linking a conjugate form.
        pattern: '^CHEBI:[0-9]+$'
      source_path:
        required: true
      source_url:
        required: true
        pattern: '^https://github.com/[^ ]+$'
      evidence:
        range: EvidenceItem
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
  ResearchGap:
    attributes:
      corpus:
        range: LinkCorpus
        required: true
      reason:
        required: true
  CurationEvent:
    attributes:
      timestamp:
        required: true
        pattern: '^20[0-9]{2}-'
      curator:
        required: true
      action:
        range: CurationAction
        required: true
      summary:
        required: true
      history_file:
        description: Canonical append-only HistoryRecord sidecar for this event.
        required: true