id: https://www.cdisc.org/cosmos/biomedical_concept_v1.0
name: COSMoS-Biomedical-Concepts-Schema

imports:
  - linkml:types

prefixes:
  linkml: https://w3id.org/linkml/
  cosmos_bc: https://www.cdisc.org/cosmos/biomedical_concept_v1.0
  NCIT: http://purl.obolibrary.org/obo/NCIT_

default_prefix: cosmos_bc
default_range: string

classes:

  BiomedicalConcept:
    tree_root: true
    slots:
      - packageDate
      - packageType
      - conceptId
      - ncitCode
      - href
      - parentConceptId
      - categories
      - shortName
      - synonyms
      - resultScales
      - definition
      - coding
      - dataElementConcepts
    slot_usage:
      conceptId:
        description: A unique identifier for a Biomedical Concept which will be assigned as the NCIt code if it exists or a placeholder identifier if the concept is not yet available in NCIt
      ncitCode:
        description: NCIt C-code for the Biomedical Concept
      href:
        description: URI link to NCIt for the Biomedical Concept; blank if  concept is not available in NCIt

  Coding:
    slots:
      - code
      - system
      - systemName

  DataElementConcept:
    slots:
      - conceptId
      - ncitCode
      - href
      - shortName
      - dataType
      - exampleSet
    slot_usage:
      conceptId:
        description: An identifier for a Data Element Concept (DEC) which will be assigned as the NCIt code if it exists or a placeholder identifier if the concept is not yet available in NCIt
      ncitCode:
        description: NCI C-code for the BC Data Element Concept
      href:
        description: Link to NCIt for the Data Element Concept

slots:
  conceptId:
    description: An identifier that uniquely represents an entity
    identifier: true
    range: string
    pattern: "^(C[0-9]+|NEW_[A-Z_]*[0-9]*)$"
    required: true
  ncitCode:
    description: NCIt code
    range: string
    pattern: "^(C[0-9]+)$"
  href:
    description: Link to NCIt for the Biomedical Concept
    range: uri
  packageDate:
    description: Biomedical Concept package release date indicating when the BC package was published to production
    range: date
    required: true
  packageType:
    description: Package type (bc for Biomedical Concepts)
    range: PackageTypeEnum
    required: true
  categories:
    description: Biomedical Concept category for the faciliation of API search and extract
    range: string
    required: true
    multivalued: true
    inlined_as_list: true
  parentConceptId:
    description: C-code for the parent concept in the NCIt hiearchy; blank if concept is not available in NCIt
    range: string
  shortName:
    description: NCI Preferred Name for the concept; provisional name will be used if concept is not available in NCIt
    range: string
    required: true
  synonyms:
    description: Biomedical Concept synonym equivalent to BC short name for the facilitation of API search and extraction
    range: string
    multivalued: true
    inlined_as_list: true
  resultScales:
    description: Scale of measurement for the Biomedical Concept result
    range: BiomedicalConceptResultScaleEnum
    multivalued: true
  definition:
    description: NCIt definition for the Biomedical Concept; provisional defintion if concept is not available in NCIt
    range: string
    required: true
  coding:
    description: Coding for the Biomedical Concept
    range: Coding
    multivalued: true
    inlined_as_list: true
  system:
    description: Identifies the code system for the synonym concept. The URL of the code system should be used if it exists
    range: string
    required: true
  systemName:
    description: Human-readable name for the code system
    range: string
  code:
    description: Synonym concept for the Biomedical Concept as defined in a code system
    range: string
    required: true
  dataElementConcepts:
    description: Data Element Concept
    range: DataElementConcept
    multivalued: true
    inlined_as_list: true
  dataType:
    description: Data Type for the Data Element Concept
    range: DataElementConceptDataTypeEnum
    required: true
  exampleSet:
    description: Example values for the Data Element Concept
    range: string
    multivalued: true
    inlined_as_list: true

enums:

  PackageTypeEnum:
    permissible_values:
      bc:

  BiomedicalConceptResultScaleEnum:
    permissible_values:
      Ordinal:
      Narrative:
      Nominal:
      Quantitative:
      Temporal:

  DataElementConceptDataTypeEnum:
    permissible_values:
      boolean:
      date:
      datetime:
      decimal:
      duration:
      float:
      integer:
      string:
      uri: