mappingVersion: 2

source:
  profile: cbioportal

target:
  model: beacon
  schemaVersion: '2.0.0'

project:
  id: acyc_mgh_2016
  version: test-1
  description: Optional semantic augmentation for the cBioPortal fixture

defaults:
  ontology: ncit

records: {}

beacon:
  individuals:
    id:
      sourceFields: [PATIENT_ID]
      primaryKey: PATIENT_ID
    sex:
      sourceField: STUDY
      term: { id: 'NCIT:C46109', label: Unknown }
    info:
      sourceFields: [STUDY]

  biosamples:
    defaults:
      id: { from: sourceValue }
      individualId: { sourceField: PATIENT_ID }
      biosampleStatus:
        term: { id: 'NCIT:C126101', label: Not Available }
      sampleOriginType:
        term: { id: 'NCIT:C126101', label: Not Available }
      info:
        sourceFields: [PLATFORM, TMB_NONSYNONYMOUS]
    rules:
      - sourceField: SAMPLE_ID