Research project

Developed at the MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, this resource is a manually curated collection of complete GWAS summary datasets made available as open source files for download, or by querying a database of the complete data. This project began as the underlying database for the MR-Base and LD Hub projects. These data now serve as an input source to a wider number of analytical tools that implement methods such as Mendelian randomization, fine mapping, colocalisation, GWAS visualisation etc. Please see the API page for a list of R and python packages that will connect to the data. The database comprises mainly publicly available datasets, but also includes a number of private datesets whose access is controlled through OAuth2.0 authentication. Please contact us if you have datasets that you would like to add, whether public or private.

Maintainer(s): Ben Elsworth, Matt Lyon, Tom Gaunt, Gibran Hemani

contact: https://github.com/MRCIEU/opengwas-requests/issues

Collaborator(s): Chris Zheng, Jon Hallett, Peter Matthews, Philip Haycock, Tessa Alexander, Valeriia Haberland, Yi Liu

Publication: 10.1101/2020.08.10.244293

Software components

OpenGWAS Elasticsearch Indexer

Python code to add data to OpenGWAS Elasticsearch

Maintainer(s): Ben Elsworth

contact: ben.elsworth[at]bristol.ac.uk

Collaborator(s): OpenGWAS team

Tags:

  • Active maintenance
  • Elasticsearch
  • OpenGWAS
  • Python

Point of development: Active maintenance

OpenGWAS Elasticsearch Cluster

Terraform code to create OpenGWAS Elasticsearch cluster on Oracle Cloud

Maintainer(s): Ben Elsworth

contact: ben.elsworth[at]bristol.ac.uk

Collaborator(s): OpenGWAS team

Source code: https://github.com/MRCIEU/oci-elastic

Tags:

  • Active maintenance
  • Elasticsearch
  • OpenGWAS
  • Terraform

Point of development: Active maintenance

ieugwaspy

Python package to access the IEU OpenGWAS API (modeled on ieugwasr)

Maintainer(s): Tom Gaunt

contact: tom.gaunt[at]bristol.ac.uk

Collaborator(s): Tom Gaunt

Software URL: https://pypi.org/project/ieugwaspy/

Source code: https://github.com/MRCIEU/ieugwaspy

Tags:

  • Active maintenance
  • MR-Base
  • OpenGWAS
  • Python

Point of development: Active maintenance