GraphQL API

The Open Targets Genetics Portal API is a GraphQL API that powers the user interface and that supports language-agnostic access to our data.
Compared to a REST API, our GraphQL API offers five key benefits:
1.You can construct a query that returns only the fields that you need
2.You can build graphical queries that traverse a data graph through resolvable entities and this reduces the need for multiple queries
3.You can access the GraphQL API playground with built-in documentation to build your query and run it in real-time 
4.You can view the schema that shows the available fields for each object along with a description and data type attribute 
5.You only have to use POST requests with a query string and variables object
Available endpoints
The base URL endpoint for the Genetics Portal GraphQL API is:
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https://api.genetics.opentargets.org/graphql
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Our GraphQL API supports queries for a single variant, gene, study, or study-variant pair. For more systematic queries (e.g. for multiple variants), please use our data downloads or our Google BigQuery instance - open-targets-prod.
Sample GraphQL query
Below is a sample GraphQL API query for the Locus2Gene data for FINNGEN_R5_E4_DM2 (Type 2 diabetes) and 11_72752390_G_A that you can run in the GraphQL API browser.
The query will recreate the data table available in the "Gene prioritisation using locus-to-gene pipeline" section on the FINNGEN_R5_E4_DM2 and 11_72752390_G_A study-locus page.
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query genePrioritisationUsingL2G {
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  studyLocus2GeneTable(studyId: "FINNGEN_R5_E4_DM2", variantId: "11_72752390_G_A") {
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    rows {
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      gene {
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        symbol
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        id
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      }
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      yProbaModel
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      yProbaDistance
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      yProbaInteraction
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      yProbaMolecularQTL
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      yProbaPathogenicity
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      hasColoc
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      distanceToLocus
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    }
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  }
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}
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Using GraphQL's query strings and variables object constructs, you can also access the data using any programming language that supports HTTP POST requests. While this is a valid approach, we discourage users from repeatedly querying the GraphQL API one entity at a time. Instead, our comprehensive datasets available for download provide a simpler and more performant strategy to achieve the same result.
Sample scripts
Below is a sample script in Python for the same sample query above -  FINNGEN_R5_E4_DM2 (Type 2 diabetes) and 11_72752390_G_A.
Python
R
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#!/usr/bin/env python3
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​
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# Import relevant libraries for HTTP request and JSON formatting
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import requests
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import json
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​
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# Set study_id and variant_id variables
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study_id = "FINNGEN_R5_E4_DM2"
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variant_id = "11_72752390_G_A"
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​
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# Build query string
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query_string = """
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  query genePrioritisationUsingL2G($myVariantId: String!, $myStudyId: String! ){
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    studyLocus2GeneTable(studyId: $myStudyId, variantId: $myVariantId){
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      rows {
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        gene {
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          symbol
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          id
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        }
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        yProbaModel
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        yProbaDistance
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        yProbaInteraction
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        yProbaMolecularQTL
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        yProbaPathogenicity
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        hasColoc
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        distanceToLocus
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      }
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    }
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  }
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"""
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​
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# Set variables object of arguments to be passed to endpoint
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variables = {"myVariantId": variant_id, "myStudyId": study_id}
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​
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# Set base URL of Genetics Portal GraphQL API endpoint
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base_url = "https://api.genetics.opentargets.org/graphql"
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​
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# Perform POST request and check status code of response
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r = requests.post(base_url, json={"query": query_string, "variables": variables})
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print(r.status_code)
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​
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# Transform API response into JSON 
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api_response_as_json = json.loads(r.text)
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​
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# Print first element of JSON response data
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print(api_response_as_json["data"]["studyLocus2GeneTable"]["rows"][0])
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# Install relevant library for HTTP requests
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library(httr)
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​
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# Set study_id and variant_id variables
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study_id <- "FINNGEN_R5_E4_DM2"
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variant_id <- "11_72752390_G_A"
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​
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# Build query string
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query_string = "
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  query genePrioritisationUsingL2G($myVariantId: String!, $myStudyId: String! ){
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    studyLocus2GeneTable(studyId: $myStudyId, variantId: $myVariantId){
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      rows {
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        gene {
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          symbol
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          id
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        }
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        yProbaModel
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        yProbaDistance
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        yProbaInteraction
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        yProbaMolecularQTL
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        yProbaPathogenicity
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        hasColoc
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        distanceToLocus
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      }
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    }
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  }
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"
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​
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# Set base URL of Genetics Portal GraphQL API endpoint
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base_url <- "https://api.genetics.opentargets.org/graphql"
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​
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# Set variables object of arguments to be passed to endpoint
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variables <- list("myStudyId" = study_id, "myVariantId" = variant_id)
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​
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# Construct POST request body object with query string and variables
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post_body <- list(query = query_string, variables = variables)
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​
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# Perform POST request
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r <- POST(url=base_url, body=post_body, encode='json')
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​
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# Print first entry of L2G data to RStudio console
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head(content(r)$data$studyLocus2GeneTable$rows, 1)
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Tutorials and how-to guides
For more information on how to use the GraphQL API and example queries based on actual use cases and research questions, check out the Open Targets Community.

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Contents

Available endpoints

Sample GraphQL query

Sample scripts

Tutorials and how-to guides