id: https://w3id.org/assaymech/schema
name: assaymech
title: AssayMech evidence-backed microbial and critical-materials assays
license: CC0-1.0
prefixes:
  linkml: https://w3id.org/linkml/
  AssayMech: https://w3id.org/assaymech/record/
  METPO: https://w3id.org/metpo/
default_prefix: AssayMech
default_range: string
imports:
  - linkml:types
  - mech_shared
  - history
enums:
  AssayCategory:
    permissible_values:
      MICROBIAL_CHARACTERIZATION:
      BIOPROCESSING:
      BIOTRANSFORMATION:
      BIOACCUMULATION:
  RecordKind:
    permissible_values:
      ONTOLOGY_ASSAY_CONCEPT:
      OPERATIONAL_ASSAY:
  OntologyEntityType:
    permissible_values:
      CLASS:
      OBJECT_PROPERTY:
  GroundingRelation:
    permissible_values:
      ASSAY_IDENTITY:
      MEASURES_PHENOTYPE:
      TESTS_PREDICATE:
  LinkCorpus:
    permissible_values:
      cmmmech:
  LinkRelation:
    permissible_values:
      MEASURES_PROCESS:
      MEASURES_CAPABILITY:
  GapScope:
    permissible_values:
      metpo:
      cmmmech:
      method:
      measurement:
      controls:
      protocol_parameters:
  CurationAction:
    permissible_values:
      CREATE:
      EDIT:
      REVIEW:
      AUDIT:
classes:
  AssayRecord:
    tree_root: true
    description: An assay concept or sourced operational assay, never an organism-level result.
    attributes:
      id:
        identifier: true
        required: true
        pattern: '^AssayMech:[a-z0-9]+(?:-[a-z0-9]+)*$'
      name:
        required: true
      record_kind:
        range: RecordKind
        required: true
      categories:
        range: AssayCategory
        required: true
        multivalued: true
        minimum_cardinality: 1
      description:
        required: true
      limitations:
        description: Explicit scope limits; curator-identified missing protocol detail is not an experimental finding.
        required: true
        multivalued: true
        minimum_cardinality: 1
      evidence:
        range: EvidenceItem
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
      ontology_groundings:
        range: OntologyGrounding
        multivalued: true
        inlined_as_list: true
      method:
        range: AssayMethod
        inlined: true
      measurement:
        range: AssayMeasurement
        inlined: true
      controls:
        range: AssayControl
        multivalued: true
        inlined_as_list: true
      related_records:
        range: AssayCrossCorpusLink
        multivalued: true
        inlined_as_list: true
      research_gaps:
        range: ResearchGap
        multivalued: true
        inlined_as_list: true
      curation_history:
        range: CurationEvent
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
  EvidenceItem:
    description: Source supporting the accompanying claim, with a precise locator.
    attributes:
      reference:
        required: true
        pattern: '^https://[^ ]+$'
      title:
        required: true
      claim:
        required: true
      locator:
        required: true
      source_license:
        description: Licence verified for the cited source; omit if not established.
  OntologyGrounding:
    description: A versioned METPO entity with an explicit relationship to the assay.
    attributes:
      term_id:
        required: true
        pattern: '^METPO:[0-9]{7}$'
      term_name:
        required: true
      entity_type:
        range: OntologyEntityType
        required: true
      relation:
        range: GroundingRelation
        required: true
      source_version:
        required: true
        pattern: '^[0-9a-f]{40}$'
      source_path:
        required: true
      source_url:
        required: true
        pattern: '^https://github.com/[^ ]+$'
      evidence:
        range: EvidenceItem
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
  AssayMethod:
    attributes:
      summary:
        required: true
      evidence:
        range: EvidenceItem
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
  AssayMeasurement:
    attributes:
      target:
        required: true
      readout:
        required: true
      interpretation:
      unit:
        description: Omit for categorical outcomes or when the source does not establish a unit.
      evidence:
        range: EvidenceItem
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
  AssayControl:
    attributes:
      description:
        required: true
      evidence:
        range: EvidenceItem
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
  AssayCrossCorpusLink:
    is_a: CrossCorpusLink
    description: A CMM target mechanism or capability measured within the stated assay scope.
    slot_usage:
      corpus:
        range: LinkCorpus
      relation:
        range: LinkRelation
      source_version:
        required: true
        pattern: '^[0-9a-f]{40}$'
    attributes:
      source_path:
        required: true
      source_url:
        required: true
        pattern: '^https://github.com/[^ ]+$'
      target_locator:
        description: A JSON Pointer locating the actual target mechanism or capability in the source record.
        required: true
        pattern: '^/[^ ]+$'
      scope:
        description: The biological system and measured endpoint supported by the source, without generalization to an entire material.
        required: true
      evidence:
        range: EvidenceItem
        required: true
        multivalued: true
        minimum_cardinality: 1
        inlined_as_list: true
  ResearchGap:
    attributes:
      scope:
        range: GapScope
        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