API Documentation

The DoCM API allows you to access variant data in a programatic fashion. The DoCM API can be used with simple HTTP requests from any tool or programming language of your choice.

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GET Variants List Endpoint

/api/v1/variants.{format}?{parameters}

This endpoint allows you to retrieve filtered lists of variants in tsv, json, or vcf format. Filter parameters can be added to the query string of the request to filter the returned list. You can combine as many filter paramters as you'd like to narrow your query down more effectively.

Parameter	Description	Example
amino_acids	This parameter should contain a comma separated list of amino acids you would like to see variants for	amino_acids=p.Q228P,p.Q61L
chromosomes	This parameter should contain a comma separated list of chromosomes you would like to see variants for	chromosomes=1,7
diseases	This parameter should contain a comma separated list of diseases you would like to see variants for	diseases=AML,BRC
genes	This parameter should contain a comma separated list of genes you would like to see variants for	genes=FLT3
mutation_types	This parameter should contain a comma separated list of mutation types you would like to see variants for	mutation_types=missense,silent
publications	This parameter should contain a comma separated list of pubmed ids you would like to see variants for	publications=21234,53124
tags	This parameter should contain a comma separated list of tags you would like to see variants for	tags=actionable
position_start	This parameter should contain a single value for a starting position you would like to see variants for. It can be combined with position_stop to create a range query	position_start=178936091
position_stop	This parameter should contain a single value for an ending position you would like to see variants for. It can be combined with position_start to create a range query	position_stop=178936093
detailed_view	This parameter should be specified if you would like additional information returned about each variant in the response (at the cost of a slower query)	detailed_view=true
version	By default, the API will return results for the current version of the DoCM database. If you would like results from a previous version, you can specify it by name with this parameter.	version=1

Example Request

Returns all variants on the gene KRAS between positions 25398284 and 25398285 in JSON.

/api/v1/variants.json?genes=KRAS&position_start=25398284&position_stop=25398285

By default, the latest version of the DoCM database will be used. If you wish to use a previous version, you can specify it via the version parameter.

/api/v1/variants.json?genes=KRAS&version=2

Example Response

[
  {
    "hgvs":"ENST00000256078:c.35G>A",
    "chr":"12",
    "start":25398284,
    "stop":25398284,
    "read":"G",
    "variant":"A",
    "reference_version":"GRCh37",
    "gene":"KRAS",
    "mutation_type":"missense",
    "amino_acid":"p.G12V",
    "diseases":[
      "NSCLC",
      "CC"
    ],
    "pubmed_sources":[
      18316791,
      12460918
    ]
  },
  {
    "hgvs":"ENST00000256078:c.35G>C",
    "chr":"12",
    "start":25398284,
    "stop":25398284,
    "read":"G",
    "variant":"C",
    "reference_version":"GRCh37",
    "gene":"KRAS",
    "mutation_type":"silent",
    "amino_acid":"p.G12",
    "dieases":[
      "NSCLC",
      "CC"
    ],
    "pubmed_sources":[
      18316791,
      12460918
    ],
    "tags":[
      "actionable"
    ]
  },
  ...]

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GET Variant Detail Endpont

/api/v1/variants/{hgvs}.json

This endpoint allows you to retrieve detailed information about a single variant in DoCM. it is queried using HGVS identifiers which are provided in the list API output. The variant detail endpoint only supports JSON output.

Example Request

Returns all all the information DoCM has about the variant ENST00000078429:c.626A>C

/api/v1/variants/ENST00000078429:c.626A>C.json

Example Response

{

  "hgvs": "ENST00000078429:c.626A>C",
  "chromosome": "19",
  "start": 3118942,
  "stop": 3118942,
  "strand": "1",
  "transcript": {
    "name": "ENST00000078429",
    "source": "ensembl",
    "version": "74_37"
  },
  "reference_version": "GRCh37",
  "gene": "GNA11",
  "reference": "A",
  "variant": "C",
  "amino_acid": "p.Q209P",
  "variant_type": "SNV",
  "mutation_type": "missense",
  "cdna_change": "c.626",
  "diseases": [
    {

      "disease": "uveal melanoma",
      "doid": "6039",
      "source_pubmed_id": 25157968
    },
    {

      "disease": "melanoma",
      "doid": "1909",
      "source_pubmed_id": 1328859
    },
    {
      "disease": "uveal melanoma",
      "doid": "6039",
      "source_pubmed_id": 22733540
    },
    {
      "disease": "melanoma",
      "doid": "1909",
      "source_pubmed_id": 22733540
    },
    {
      "disease": "melanoma",
      "doid": "1909",
      "source_pubmed_id": 2549426
    },
    {
      "disease": "melanoma",
      "doid": "1909",
      "source_pubmed_id": 21083380
    },
    {
      "disease": "melanoma",
      "doid": "1909",
      "source_pubmed_id": 22808163
    }
  ],
  "drug_interactions": [
    {
      "drug": "PI3K pathway inhibitors + MEK inhibitors",
      "pathway": "activation",
      "effect": "gain-of-function",
      "association": "response",
      "status": "preclinical",
      "evidence_type": "emerging",
      "source_pubmed_id": ​22733540,
      "aggregated_by": "Dienstman Knowledge Database - https://www.synapse.org/#!Synapse:syn2370773"
    }
  ]
}