ieu gwas database api

Status

  • 3.3.1 Version
  • public Access level

111,907,810,420 genetic associations
31,282 GWAS summary datasets.

  • Available Neo4j status
  • Available ElasticSearch status
  • Available LD reference panel
  • Available PLINK executable
  • Available Cromwell

Overview

This is a RESTful API for programmatic access to the IEU GWAS database. The API is designed to support the following operations:

  • Make available study information about all the GWAS datasets in the database
  • Obtain the top hits from a GWAS, with optional automatic clumping.
  • Find any set of variant-trait associations based on rsid or chromosome:position.
  • Automatically find LD proxies if a variant is missing from a GWAS database.
  • Calculate LD matrices across a set of variants.
  • Phenome-wide association study (PheWAS) - Perform fast lookups of a particular variant across all datasets.
  • Get dbSNP information and annotations on a set of variants.

The API can be used directly in applications, or accessed through convenient packages in R and python. More information on those below. The TwoSampleMR R package, and MR-Base web apps both use this API in order to automatically perform Mendelian randomization for causal inference. The gwasglue R package aims to extend the use of these data to further types of statistical methods. The LD Hub platform also uses the data underlying this database.


Authentication

The documentation provides a list of endpoints, the parameters they require, descriptions of the data that is returned, and an interactive way to try out each of the endpoints.

The database of GWAS summary data mostly contains public data, however there are some 'private' datasets, which can only be accessed by authorised users. Authentication is managed using Google OAuth 2.0. In order to authenticate, you will need to generate a 'token' for each session in which private access is required.

The simplest way to obtain an authentication token is to use a browser to authenticate with your gmail account at this link.

The access token can also be obtained using the ieugwasr::get_access_token() function, more information about that here.


Related tools

For ease of use we have developed two packages which are solely designed to create easy interfaces to the API endpoints:

  • The ieugwasr R package [link]
  • The ieugwaspy python package [link]

The following packages also connect to these data:

  • The TwoSampleMR R package automatically performs Mendelian randomization on the data accessed through the API [link]
  • The gwasglue R packages connects the data to several other analytical tools related to e.g. colocalisation, fine mapping, etc [link]
  • The https://gwas.mrcieu.ac.uk page provides an interactive way to browse through the available datasets.
  • The MR-Base web app uses the underlying data for basic interactive [link]