default_variant_in_sample_schema.yaml

openapi: 3.0.2
servers: []
info:
  version: "draft.3"
  title: GA4GH Beacon Variant in Sample Default Schema
  description: >-
    Schema for variant in sample to be used as default by the Beacon.
  contact:
    email: beacon@ga4gh.org
  license:
    name: Apache 2.0
    url: 'http://www.apache.org/licenses/LICENSE-2.0.html'
externalDocs:
  description: |
    Beacon Project
  url: 'http://beacon-project.io/'
paths: {}
components:
  schemas:
    ClinicalRelevance: 
      description: |
        Descriptor of clinical relevance as described to the variant, including 
        the variant classification, the disease identifier and references of 
        studies supporting the association.
      type: object
      properties:
        clinicalEffect: ##todo copy from variant annotation schema?
          description: |
            Value from Sequence types and features ontology (SO) variant 
            phenotype (SO:0001769), e.g. "disease causing variant" (SO:0001772).
          type: string
          enum:
            - benign
            - likely benign
            - pathogenic
            - likely pathogenic
            - unknown
          example: pathogenic
        diseaseId:
          description: |
            Reference to DiseaseId from Disease object from Individual schema, 
            e.g. MONDO:0003582 (Hereditary breast ovarian cancer syndrome).
          type: string
          example: 'MONDO:0003582'
        evidenceType:
          description: |
            Ontology value for type of evidence supporting variant-disease 
            association from the Evidence & Conclusion Ontology (ECO)
          type: string
          example: 'experimental evidence'
    PhenotypicEffect:
      description: |
        List of annotated effect on disease.
      type: object
      properties:
        phenotypeId:
          description: |
            Descriptor of phenotype found associated in this study
          type: string
          example: "" ##todo provide example
        phenotypeEffect:
          description: |
            Ontology value for phenotypic effect classification determined in this study
          type: string
          example: '' ##todo example?
        evidenceType:
          description: |
            Ontology value for type of evidence supporting variant-disease 
            association from the Evidence & Conclusion Ontology (ECO)
          type: string
          example: 'experimental evidence'
    VariantInSample:
      description: |
        Todo
      type: object
      properties:
        variantId:
          description: |
            ID referencing the variant in beacon (internal ID) ##todo check?
          type: string
        analysisId:
          description: |
            Reference to run (Run.runId)
          type: string
          example: 'SRR10903401'
        biosampleId:
          description: |
            Reference to biosample ID.
          type: string
        variantFrequency:
          description: |
            Variant frequency in sample, as in AF field in VCF for case-level datasets.
            Frequency in dataset for aggregated variant-level datasets.
          type: number
          minimum: 0
          example: 1
        zigosity:
          description: |
            Ontology value for zigosity in which variant is present in the sample 
            from the Zigosity Ontology (GENO:0000133) , e.g "heterozygous" (GENO:0000135)
          type: string
          example: 'GENO:0000135'
        alleleOrigin:
          description: |
            Ontology value for allele origin of variant in sample from the Variant Origin (SO:0001762). 
            Categories are "somatic variant", "germline variant", "maternal variant", 
            "paternal variant", "de novo variant", "pedigree specific variant", 
            "population specific variant". 
            Corresponds to Variant Inheritance in FHIR.
          type: string
          enum:
            - 'somatic variant'
            - 'germline variant'
            - 'maternal variant'
            - 'paternal variant'
            - 'de novo variant'
            - 'pedigree specific variant'
            - 'population specific variant'
          example: 'somatic variant'
        clinicalRelevance:
          type: array
          items:
            $ref: '#/components/schemas/ClinicalRelevance'
        phenotypicEffect:
          type: array
          items:
            $ref: '#/components/schemas/PhenotypicEffect'
        info:
          description: |
            Additional unspecified metadata about the dataset response or its 
            content.
          type: object
          example:
            additionalInfoKey1: 
              - additionalInfoValue1
              - additionalInfoValue2
            additionalInfoKey2: additionalInfoValue