Unfiltered data integrated from OT Genetics portal

Dear Community,

The OT Platform integrates and filters data (l2g >= 0.05) from the Genetics Portal, serving as the genetic association evidence. Although that helps ensure data quality, some well-known associations between diseases and targets (e.g., Alzheimer’s disease and gene TREM2) are absent from the downloadable data. Could anyone please talk about where or how to download the integrated, unfiltered OT Genetics data?

Best regards,
Tzu-Hao Kuo

Dear Tzu-Hao,

The full l2g output can be downloaded via the EBI ftp link here.

Hope this helps,

Thank you @Xiangyu ! I have a few more questions:
(1) Where can I find columns contained in those files?
(2) Is the json version also available?

Dear Tzu-Hao,

  1. I found a schema for the locus2gene table in bigquery here, it should be similar/the same as the one from the EBI ftp link.

  2. For the bulk download of all l2g scores, there is no json version. But if this file format is preferable for you, you can experiment with the GraphQL API to obtain a subset of l2g scores you are interested in. These would be returned in a nested json format.

    The table you will need to query is the " studyLocus2GeneTable", and there’s an useful example query on the left tab under “Prioritised genes from study locus”.

Best wishes,

Thank you for your kind recommendation, @Xiangyu . The l2g data seem to be part of what I need. My purpose is to build a local database having the same columns as those of the downloadable database. Besides the score, the database also includes VEP (the effect of the variant) and diseases. I need to build another database because the currently available database has been filtered with the score cutoff of 0.05.