Hi,
I am trying to get the l2g score and pval along with study, variant and gene information. I have downloaded the data from ftp website for the l2g pipeline (Index of /pub/databases/opentargets/genetics/latest/l2g) .
However, I don’t see pval and trait_category in the schema. How can I get those from the dowloaded data?
Thanks,
Kamalika
Hi Kamalika,
The l2g dataset contains purely l2g related information (eg. l2g prediction, locus info, gene id etc), depending on what details you are after, you need to fetch and join other datasets as well. The v2d dataset (https://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/latest/v2d/) contains GWAS association statistics for all loci + most of the relevant study level metadata eg. traits. (You need to join this dataset to l2g by study_id, lead_chrom, lead_pos, lead_ref, lead_alt) Gene information can be found under https://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/latest/lut/genes-index .
It worth exploring other datasets for fields you might need. Please let us know if you need anything else.
Best,
Daniel