The downloads that are available are described here: Data Download - Open Targets Genetics Documentation
You can also find a step-by-step guide to the data downloads on our blog, in the third part of our Crash Course in Open Targets.
Please note, we don’t make our GWAS summary statistics files available for download, because these are generally available from either the GWAS Catalog or the relevant biobanks directly.
Individual data tables (e.g. Associated studies: locus-to-gene pipeline) can be downloaded from the user interface (genetics.opentargets.org).
You can download OT Genetics data files through:
- EMBL-EBI’s FTP: Open Targets Genetics,
- Google Big Query (paywalled): open-targets-genetics
- Google Cloud Storage (paywalled public bucket): open-targets-genetics-releases
For FTP download, most files are in parquet format or in jsonlines format. The tables available correspond to what is known in the OT Genetics user interface.
For example, to download the full table of associations by data type in JSON format, the documentation lists this command:
‘wget --recursive --no-parent --no-host-directories --cut-dirs 8’
ftp://ftp.ebi.ac.uk/pub/databases/opentargets/platform/21.06/output/etl/json/associationByDatatypeDirect
You could filter this for only lines with genetic associations, such as:
‘cat associationByDatatypeDirect/*.json | grep ‘genetic_association’ | gzip > genetic_associations.json.gz’
If there are specific tables and formats that would be highly desirable, we may be able to make these available on request.