GraphQL API

The Open Targets Genetics 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:

https://api.genetics.opentargets.org/graphql

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.

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 prioritised genes from study locus sample query:

Python

#!/usr/bin/env python3

# Import relevant libraries for HTTP request and JSON formatting
import requests
import json

# Set study_id and variant_id variables
study_id = "GCST009240_9"
variant_id = "1_55052794_A_G"

# Build query string
query_string = """
  query genePrioritisationUsingL2G($myVariantId: String!, $myStudyId: String! ){
    studyLocus2GeneTable(studyId: $myStudyId, variantId: $myVariantId){
      rows {
        gene {
          symbol
          id
        }
        yProbaModel
        yProbaDistance
        yProbaInteraction
        yProbaMolecularQTL
        yProbaPathogenicity
        hasColoc
        distanceToLocus
      }
    }
  }
"""

# Set variables object of arguments to be passed to endpoint
variables = {"myVariantId": variant_id, "myStudyId": study_id}

# Set base URL of Genetics Portal GraphQL API endpoint
base_url = "https://api.genetics.opentargets.org/graphql"

# Perform POST request and check status code of response
r = requests.post(base_url, json={"query": query_string, "variables": variables})
print(r.status_code)

# Transform API response into JSON 
api_response_as_json = json.loads(r.text)

# Print first element of JSON response data
print(api_response_as_json["data"]["studyLocus2GeneTable"]["rows"][0])

R

# Install relevant library for HTTP requests
library(httr)

# Set study_id and variant_id variables
study_id <- "GCST009240_9"
variant_id <- "1_55052794_A_G"

# Build query string
query_string = "
  query genePrioritisationUsingL2G($myVariantId: String!, $myStudyId: String! ){
    studyLocus2GeneTable(studyId: $myStudyId, variantId: $myVariantId){
      rows {
        gene {
          symbol
          id
        }
        yProbaModel
        yProbaDistance
        yProbaInteraction
        yProbaMolecularQTL
        yProbaPathogenicity
        hasColoc
        distanceToLocus
      }
    }
  }
"

# Set base URL of Genetics Portal GraphQL API endpoint
base_url <- "https://api.genetics.opentargets.org/graphql"

# Set variables object of arguments to be passed to endpoint
variables <- list("myStudyId" = study_id, "myVariantId" = variant_id)

# Construct POST request body object with query string and variables
post_body <- list(query = query_string, variables = variables)

# Perform POST request
r <- POST(url=base_url, body=post_body, encode='json')

# Print first entry of L2G data to RStudio console
head(content(r)$data$studyLocus2GeneTable$rows, 1)

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.