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?
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?
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.