genomic_data.yaml

# this is an example of the OncoBlocks API
# as a demonstration of an API spec in YAML
swagger: '2.0'
info:
  title: OncoBlocks API
  description: OncoBlocks Open Cancer Genomics API.
  version: "1.0.0"
# the domain of the service
host: api.oncoblocks.org
# array of all schemes that your API supports
schemes:
  - https
# will be prefixed to all paths
basePath: /v1
produces:
  - application/json
paths:
  /signal:
    get:
      summary: Get discrete or continuous signal data.
      description: Get discrete or continuous signal data, such as expression data, phosphoproteomic data or discretized copy number data.
      parameters:
        - name: sample_id
          in: query
          description: Samples ID(s).
          required: false
          type: array
          items:
            type: string
        - name: entrez_gene_id
          in: query
          description: Entrez Gene ID(s).
          required: false
          type: array
          items:
            type: integer
        - name:  genome_coordinate
          in:  query
          description:  Genome coordinate(s), of the form chr:start-end.
          required:  false
          type:  array
          items:
            type:  string
        - name: study_id
          in: query
          description: Study ID(s).
          required: false
          type: string
        - name:  data_set_id
          in:  query
          description:  Data set ID.
          required:  true
          type:  string
      responses:
        200:
          description: an array of signal objects.
          schema:
            title:  Signals
            type: array
            items:
              $ref: SignalData
  /copy_number_regions:
    get:
      summary: Get copy number regions of interest.
      description: Get copy number regions of interest, e.g. statistically significant regions of amplification or deletion identified by the GISTIC algorithm.
      parameters:
        - name: study_id
          in: query
          description: Study ID.
          required: true
          type: string
        - name:  data_set_id
          in:  query
          description:  Data Set ID.
          required:  true
          type:  string
      responses:
        200:
          description: an array of copy number region objects.
          schema:
            title:  RegionsOfInterest
            type: array
            items:
              $ref: RegionOfInterest
  /mutations:
    get:
      summary: Get mutation data.
      description: Retrieves mutation data by mutation properties, sample, or gene.
      parameters:
        - name: sample_id
          in: query
          description: Samples ID(s).
          required: false
          type: array
          items:
            type: string
        - name: entrez_gene_id
          in: query
          description: Entrez Gene ID(s).
          required: false
          type: array
          items:
            type: integer
        - name: study_id
          in: query
          description: Study ID(s).
          required: false
          type: array
          items:
            type: string
        - name:  data_set_id
          in:  query
          description:  Data set ID.
          required:  false
          type:  array
          items:
            type: integer
        - name: variant_classification
          in: query
          description: Mutation type(s).
          required: false
          type: array
          items:
            type: string
      responses:
        200:
          description: an array of mutation data objects.
          schema:
            title:  MutationData
            type: array
            items:
              $ref: MutationData
              
definitions:
  SignalData:
    properties:
      stable_sample_id:
        type: integer
        format: int32
        description: Sample ID.
      gene_id:
        type: integer
        format: int32
        description: Entrez gene ID.
      gene_symbol:
        type: string
        description:  Official gene symbol.
      genome_coordinates:
        type:  string
        description:  Genomic coordinates.
      signal_value:
        type:  number
        description:  Signal intensity.
      annotation_list:
        description:  Curated annotations regarding the signal or event.
        type: array
        items:
          type: string
  RegionOfInterest:
      properties:
        cytoband:
          type: string
          description: Cytoband.
        q_value:
          type:  number
          description:  Q-Value.
        residual_q_value:
          type:  number
          description:  Residual Q-Value.
        wide_peak_boundaries:
          type:  string
          description:  Wide peak boundaries.
        entrez_gene_list:
          type:  array
          items:
            type: integer
            format: int32
  MutationData:
    properties:
      stable_sample_id:
        type: integer
        format: int32
        description: Sample ID.
      gene_id:
        type: integer
        format: int32
        description: Entrez gene ID.
      gene_symbol:
        type: string
        description:  Official gene symbol.
      reference_genome:
        type: string
        description: Reference genome to which the DNA coordinates are aligned.
      chromosome:
        type: string
        description: Chromosome in which the mutation is located.
      dna_start_position:
        type: integer
        format: int32
        description: Start position of the mutation in genomic DNA.
      dna_end_position:
        type: integer
        format: int32
        description: End position of the mutation in genomic DNA.
      strand:
        type: string
        description: Chromosome strand in which the mutation is located.
      variant_classification:
        type: string
        description: Specific category of mutation.
      variant_type:
        type: string
        description: General category of mutation.
      reference_allele:
        type: string
        description: Nucleotides of the reference DNA sequence.
      variant_allele:
        type: string
        description: Nucelotides of the mutated DNA sequence.
      alternative_allele_reads:
        type: integer
        format: int32
        description: Number of reads supporting the mutant allele.
      reference_allele_reads:
        type: integer
        format: int32
        description: Number of reads supporting the wild type allele.
      dbsnp_rsid:
        type: string
        description: dbSNP RS ID of the record of the mutation.
      annotation_transcript:
        type: string
        description: Database ID of the cDNA transcript to which the cDNA coordinates are aligned. 
      transcript_strand:
        type: string
        description: Strand in the reference transcript to which the mutation coordinates are aligned.
      cdna_change:
        type: string
        description: Change in he cDNA sequence.
      codon_change:
        type: string
        description: Change in the cDNA sequence in the context of the codon.
      protein_change:
        type: string
        description: Change in the amino acid sequence.
      other_transcripts:
        type: string
        description: Delimited list of additional transcripts and amino acid changes associated with the genomic DNA mutation.
      refseq_mrna_id:
        type: string
        description: ID of the RefSeq mRNA transcript for the mutated gene.
      refseq_prot_id:
        type: string
        description: ID of the RefSeq amino acid transcript for the mutated protein.
      swissprot_accession:
        type: string
        description: ID of the Swissprot amino acid transcript for the mutated protein.
      swissprot_entry:
        type: string
        description: ID of the Swissprot gene record.
      uniprot_aa_position:
        type: integer
        format: int32
        description: Mutation position in the Uniprot amino acid transcript.
      uniprot_region:
        type: string
        description: Protein region in which the mutation occurs in the Uniprot transcript.
      uniprot_site:
        type: string
        description: Protein site in which the mutation occurs in the Uniprot transcript.