Cafe Variome Components

CV_Components.txt

components:  
  schemas:
  	sex:
  	  type: object
  	  properties:
      operator:
        type: string
        enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        term:
          type: string
        source:
          type: string

  	gender:
  	  type: object
  	  properties:
      operator:
        type: string
        enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        term:
          type: string
        source:
          type: string

  	age:
  	  type: object
  	  properties:
      operator:
        type: string
        enum: ["=", ">", "<", "<=", "=>", "!="]
        number:
          type: integer
        units:
          type: string

    disease:      
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
       	ontologyCode:
          type: string
        term:
          type: string
        source:   #ontology source
          type: string
        elements:
          type: array
          items:
            oneOf:
              - $ref: '#/components/schemas/ageOfOnset'
              - $ref: '#/components/schemas/evaluator'
              - $ref: '#/components/schemas/inheritanceMode'

    phenotype:      
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        ontologyCode:
          type: string
        term:
          type: string
        source:
          type: string
        elements:
          type: array
          items:
            oneOf:
              - $ref: '#/components/schemas/ageOfOnset'
              - $ref: '#/components/schemas/evaluator' 
              - $ref: '#/components/schemas/inheritanceMode'
    

    subjectVariant:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        variantID: 
          type: string
        reference:
          type: string
        source: #dbSNP, Nirvana, HGVS etc
          type: string
        elements:
          type: array
          items:
            oneOf:
              - $ref: '#/components/schemas/allele'
              - $ref: '#/components/schemas/genotype'
              - $ref: '#/components/schemas/variationType'
              - $ref: '#/components/schemas/gene'
              - $ref: '#/components/schemas/protein'
              - $ref: '#/components/schemas/zygosity'
              - $ref: '#/components/schemas/pathogenicity'
              - $ref: '#/components/schemas/geneConsequence' 
              - $ref: '#/components/schemas/proteinConsequence'  
              - $ref: '#/components/schemas/alleleFrequency'  
              - $ref: '#/components/schemas/genotypeFrequency'
              - $ref: '#/components/schemas/geneDomain'  
              - $ref: '#/components/schemas/phenotype'  
              - $ref: '#/components/schemas/disease'  
 

    subjectNucRegion:
      type: object
      properties:
        operator:
          type: string
          enum: ["EXACT", "EXCEED", "BEGIN_BETWEEN", "END_BETWEEN", "BEGIN_AND_END_BETWEEN", "ONLY_BEGIN_BETWEEN", "ONLY_END_BETWEEN", "BEGIN_AT_START", "END_AT_STOP"]
        regionType:
          type: string
        reference:
          type: string
        chrAcc:
       	  type: string
        start:
          type: integer
        stop:
          type: integer
        elements:
          type: array
          items:
            oneOf:
              - $ref: '#/components/schemas/allele'
              - $ref: '#/components/schemas/genotype'
              - $ref: '#/components/schemas/variationType'
              - $ref: '#/components/schemas/gene'
              - $ref: '#/components/schemas/protein'
              - $ref: '#/components/schemas/zygosity'
              - $ref: '#/components/schemas/pathogenicity'
              - $ref: '#/components/schemas/geneConsequence' 
              - $ref: '#/components/schemas/proteinConsequence'  
              - $ref: '#/components/schemas/alleleFrequency'  
              - $ref: '#/components/schemas/genotypeFrequency'
              - $ref: '#/components/schemas/geneDomain'  
              - $ref: '#/components/schemas/phenotype'  
              - $ref: '#/components/schemas/disease'  

    genericVariant:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        variantID: 
          type: string
        reference:
          type: string
        source: #dbSNP, Nirvana, HGVS etc
          type: string
        elements:
          type: array
          items:
            oneOf:
              - $ref: '#/components/schemas/allele'
              - $ref: '#/components/schemas/genotype'
              - $ref: '#/components/schemas/variationType'
              - $ref: '#/components/schemas/gene'
              - $ref: '#/components/schemas/protein'
              - $ref: '#/components/schemas/zygosity'
              - $ref: '#/components/schemas/pathogenicity'
              - $ref: '#/components/schemas/geneConsequence' 
              - $ref: '#/components/schemas/proteinConsequence'  
              - $ref: '#/components/schemas/alleleFrequency'  
              - $ref: '#/components/schemas/genotypeFrequency'
              - $ref: '#/components/schemas/geneDomain'  
              - $ref: '#/components/schemas/phenotype'  
              - $ref: '#/components/schemas/disease'  
 

    genericNucRegion:
      type: object
      properties:
        operator:
          type: string
          enum: ["EXACT", "EXCEED", "BEGIN_BETWEEN", "END_BETWEEN", "BEGIN_AND_END_BETWEEN", "ONLY_BEGIN_BETWEEN", "ONLY_END_BETWEEN", "BEGIN_AT_START", "END_AT_STOP"]
        regionType:
          type: string
        reference:
          type: string
        chrAcc:
       	  type: string
        start:
          type: integer
        stop:
          type: integer
        elements:
          type: array
          items:
            oneOf:
              - $ref: '#/components/schemas/allele'
              - $ref: '#/components/schemas/genotype'
              - $ref: '#/components/schemas/variationType'
              - $ref: '#/components/schemas/gene'
              - $ref: '#/components/schemas/protein'
              - $ref: '#/components/schemas/zygosity'
              - $ref: '#/components/schemas/pathogenicity'
              - $ref: '#/components/schemas/geneConsequence' 
              - $ref: '#/components/schemas/proteinConsequence'  
              - $ref: '#/components/schemas/alleleFrequency'  
              - $ref: '#/components/schemas/genotypeFrequency'
              - $ref: '#/components/schemas/geneDomain'  
              - $ref: '#/components/schemas/phenotype'  
              - $ref: '#/components/schemas/disease'  


    allele:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        sequence:
          type: string
        molecule:
       	  type: string

    genotype:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        sequence:
          type: string
        molecule:
       	  type: string

    variationType:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        type:
          type: string
        ontologyID:
          type: string
        source:
       	  type: string         

    zygosity:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        term:
          type: string
        id:
          type: string
        source:
       	  type: string

    gene:  
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        geneID:
          type: string
        source: #gene symbol, geneID, name
          type: string

    protein:  
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        geneID:
          type: string
        source: 
          type: string

    pathogenicity:
      type: object
      properties:
        class:
          type: string
        source:
          type: string
        elements:
          type: array
          items:
            oneOf:
              - $ref: '#/components/schemas/phenotype'
              - $ref: '#/components/schemas/disease'
              - $ref: '#/components/schemas/inheritanceMode' 

    inheritanceMode:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        id:
          type: string
        term:
          type: string
        source:
          type: string

    geneConsequence:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        ontologyID:
          type: string
        term: 
          type: string
        source:
          type: string
        elements:
          type: array
          items:
            oneOf:
              - $ref: '#/components/schemas/gene'

    protienConsequence:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        ontologyID:
          type: string
        term: 
          type: string
        source:
          type: string
        elements:
          type: array
          items:
            oneOf:
              - $ref: '#/components/schemas/protein'
              - $ref: '#/components/schemas/gene'

    evaluator:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE", "=", ">", "<", "<=", "=>", "!="]
        evaluatorValue:
          type: string
        units:
          type: string

    ageOfOnset:
      type: object
      properties:
        operator:
          type: string
          enum: ["=", ">", "<", "<=", "=>", "!="]
        id:
          type: string
        term:
          type: string
        source:
          type: string

    alleleFrequency:
      type: object
      properties:
        operator:
          type: string
          enum: ["=", ">", "<", "<=", "=>", "!="]
        value:
        units:
        collection:        

    genotypeFrequency:
      type: object
      properties:
        operator:
          type: string
          enum: ["=", ">", "<", "<=", "=>", "!="]
        value:
        units:
        collection:   

    geneDomain:
      type: object
      properties:
        operator:
          type: string
          enum: ["IS", "IS lIKE", "IS NOT", "IS NOT LIKE"]
        term:
        ontologyID:
        source: