depmap.yml

swagger: '2.0'
info:
  version: '2019Q2'
  title: Cancer Dependency Map API
  description: >-
    This site provides an API access to [Cancer Dependency Map (DepMap) data](https://depmap.org/portal/download/).
    The goal of the Cancer Dependency Map is to create a comprehensive preclinical reference map connecting 
    tumor features with tumor dependencies to accelerate the development of precision treatments. 
    By integrating data beyond those collected at the Broad, DepMap hopes to develop a complete 
    understanding of the vulnerabilities of cancer, identify targets for therapeutic development, 
    and design strategies to optimize patient responses to those therapies.
    By using this site, you agree to DepMap's [Terms and Conditions](https://depmap.org/portal/terms/).
  termsOfService: By using this site, you agree to DepMap's Terms and Conditions (https://depmap.org/portal/terms/)
  contact:
    name: Broad NCATS translator
    email: translator@broadinstitute.org
    
host: indigo.ncats.io
basePath: /depmap
paths:
  /genes:
    get:
      tags: 
      - types
      summary: Retrieve list of genes
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/gene'

  /cell_lines:
    get:
      tags: 
      - types
      summary: Retrieve list of cell lines
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/cell_line'

  /proteins:
    get:
      tags: 
      - types
      summary: Retrieve list of protein antibodies
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/protein'

  /gene_expression/by_gene/{ensembl_gene}:
    get:
      tags: 
      - values
      summary: Retrieve gene expression by gene
      parameters:
      - name: ensembl_gene
        in: path
        type: string
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/expression_value'

  /gene_expression/by_cell_line/{depmap_id}:
    get:
      tags: 
      - values
      summary: Retrieve gene expression by cell line
      parameters:
      - name: depmap_id
        in: path
        type: string
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/expression_value'
              
  /gene_dependency/by_gene/{entrez_gene_id}:
    get:
      tags: 
      - values
      summary: Retrieve gene dependency by gene
      parameters:
      - name: entrez_gene_id
        in: path
        type: integer
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/dependency_value'

  /gene_dependency/by_cell_line/{depmap_id}:
    get:
      tags: 
      - values
      summary: Retrieve gene dependency by cell line
      parameters:
      - name: depmap_id
        in: path
        type: string
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/dependency_value'
              
  /copy_number/by_gene/{entrez_gene_id}:
    get:
      tags: 
      - values
      summary: Retrieve copy-number values by gene
      parameters:
      - name: entrez_gene_id
        in: path
        type: integer
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/copy_number_value'

  /copy_number/by_cell_line/{depmap_id}:
    get:
      tags: 
      - values
      summary: Retrieve copy-number values by cell line
      parameters:
      - name: depmap_id
        in: path
        type: string
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/copy_number_value'
              
  /rnai/by_gene/{entrez_gene_id}:
    get:
      tags: 
      - values
      summary: Retrieve rnai values by gene
      parameters:
      - name: entrez_gene_id
        in: path
        type: integer
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/rnai_value'

  /rnai/by_cell_line/{depmap_id}:
    get:
      tags: 
      - values
      summary: Retrieve rnai values by cell line
      parameters:
      - name: depmap_id
        in: path
        type: string
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/rnai_value'
              
  /mutations/by_gene/{entrez_gene_id}:
    get:
      tags: 
      - values
      summary: Retrieve mutations by gene
      parameters:
      - name: entrez_gene_id
        in: path
        type: integer
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/mutation'

  /mutations/by_cell_line/{depmap_id}:
    get:
      tags: 
      - values
      summary: Retrieve mutations by cell line
      parameters:
      - name: depmap_id
        in: path
        type: string
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/mutation'
              
  /protein_array/by_protein/{antibody_name}:
    get:
      tags: 
      - values
      summary: Retrieve protein array values by gene
      parameters:
      - name: antibody_name
        in: path
        type: string
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/protein_array_value'

  /protein_array/by_cell_line/{depmap_id}:
    get:
      tags: 
      - values
      summary: Retrieve protein array values by cell line
      parameters:
      - name: depmap_id
        in: path
        type: string
        required: true
      responses:
        200:
          description: successful operation
          schema:
            type: array
            items:
              $ref: '#/definitions/protein_array_value'
              
definitions:

  gene:
    type: object
    properties:
      hgnc_id:
        type: string
      gene_symbol:
        type: string
      ensembl_gene:
        type: string
      entrez_gene_id:
        type: integer
      omim:
        type: array
        items:
          type: string

  cell_line:
    type: object
    properties:
      depmap_id:
        type: string
      stripped_cell_line_name:
        type: string
      ccle_name:
        type: string
      aliases:
        type: array
        items:
          type: string
      cosmic_id:
        type: string
      sanger_id:
        type: string
      disease:
        type: string
      disease_subtype:
        type: string
      disease_sub_subtype:
        type: string
      gender:
        type: string
      source:
        type: string
  
  protein:
    type: object
    properties:
      antibody_name:
        type: string
      target_genes:
        type: array
        items:
          type: string
      validation_status:
        type: string
      company:
        type: string
      catalog_number:
        type: string

  expression_value:
    type: object
    properties:
      ensembl_gene:
        type: string
      depmap_id:
        type: string
      value:
        type: number
    
  dependency_value:
    type: object
    properties:
      entrez_gene_id:
        type: integer
      depmap_id:
        type: string
      value:
        type: number
    
  copy_number_value:
    type: object
    properties:
      entrez_gene_id:
        type: integer
      depmap_id:
        type: string
      value:
        type: number
      
  rnai_value:
    type: object
    properties:
      entrez_gene_ids:
        type: array
        items:
          type: integer
      depmap_id:
        type: string
      value:
        type: number

  protein_array_value:
    type: object
    properties:
      protein:
        type: object
        properties:
          antibody_name:
            type: string
          target_genes:
            type: array
            items:
              type: string
      depmap_id:
        type: string
      value:
        type: number

  mutation:
    type: object
    properties:
      entrez_gene_id:
        type: integer
      gene_symbol:
        type: string
      depmap_id:
        type: string
      ncbi_build:
        type: integer
      chromosome:
        type: string
      start_position:
        type: integer
      end_position:
        type: integer
      strand:
        type: string
      variant_classification:
        type: string
      variant_type:
        type: string
      reference_allele:
        type: string
      tumor_seq_allele:
        type: string
      dbsnp_rs:
        type: array
        items:
          type: string
      dbsnp_val_status:
        type: string
      genome_change:
        type: string
      annotation_transcript:
        type: string
      cdna_change:
        type: string
      codon_change:
        type: string
      protein_change:
        type: string
      is_deleterious:
        type: string
      tcga_hotspot_count:
        type: string
      cosmic_hotspot_count:
        type: string
      exac_af:
        type: string
      cga_wes_ac:
        type: string
      sanger_wes_ac:
        type: string
      sanger_recalibwes_ac:
        type: string
      rnaseq_ac:
        type: string
      hc_ac:
        type: string
      rd_ac:
        type: string
      wgs_ac:
        type: string
      variant_annotation:
        type: string