Hello Open Targets team,
I’m currently working at the EFO-to-gene level to assess gene causality. In the new release, I couldn’t find a file on the downloads page that maps study IDs to EFO IDs. Previously, I relied on this mapping to understand how studies correspond to traits.
Could you please let me know if this file is still available or if there is an alternative way to link study IDs to EFO terms? This is essential for my causality-focused analysis.
Thank you very much
Hi, Yes, we provide dataset with study metadata that contains a list of EFO disease identifiers assigned for each GWAS studies: http://ftp.ebi.ac.uk/pub/databases/opentargets/platform/25.03/output/study
As the study index also contains molecular QTL studies, which don’t have assigned EFOs, not all rows in this dataset have EFOs. The EFOs are in the diseaseIds column. Just for hyping up the upcoming new release, we are soon provide schemas and column descriptions (and more!) for all datasets available in the downloads section!