PheWAS Download

Data Access GraphQL API
1

Hi,

How do I download the exact results of this API in bulk. I want to download the result for 3000 variants.
query search($variantId: String!) {
pheWAS(variantId: $variantId) {
totalGWASStudies
associations {
pval
beta
oddsRatio
study {
studyId
source
pmid
pubDate
traitReported
traitCategory
}
nTotal
}
}
}
Does the v2d data on the FTP site contain pheWAS results?

Thanks

2

Hello,

For 3k variants you should be able to use the “otargen” package in R which contains the “phewas” function that can return the Open targets genetics results.

Best,
Elena

3

Hi Elena,

It’s 3k for just 1 gene, I have 15000 genes.
Is there a way I can download it in bulk? Where can I find this data on the FTP website?

Thanks.

4

Hi @kamalika_ray,

Next week’s release of the Open Targets Platform will include updated variant information, including data downloads.

Thanks,

Helena

5

Hi @hcornu

Thanks for your message. Where can I find the data about diseases associated with genetic variants in the new ftp download site. I am a bit confused due to the change in the terminologies.

Thanks,
Kamalika

6

Hi @kamalika_ray,

that would be our credible set dataset. You’d want to filter for variation that has been linked to GWAS studies (studyType == gwas).

You can learn more about it in our documentation.

Best,
Irene

7

Hi Irene,

Thanks for your message. I don’t see the reported traits (disease name/study.trait_reported) in that table. Do I have to extract it from some other table?

Thanks,
Kamalika

8

The reported trait would be in traitFromSource in the GWAS studies table.

Best,
Irene

9

Thanks a lot! That was very helpful