Using DisGeNET SQLite to access more data

[colleenXu]

@DylanWelzel and I discussed today (2/22) how MyDisease's DisGeNET info lacks some of the useful info that we see on DisGeNET's website (example: https://www.disgenet.org/browser/0/1/1/C0001080/_a/_b./)

We looked at the gene-disease associations (GDA), but the info below probably applies to the variant-disease associations (VDA) as well.

• the "Evidence for GDAs" tab has "association type" (type of gene-disease relationship) and supporting sentence info for PMIDs ➡️ this looks particularly interesting!
• the "Summary of GDAs" tab has the EL (evidence level), and EI (evidence index) for each gene-disease relationship, and a pLI measure.

MyDisease is using the tsv downloads, which lack this info (look at the README). However, we realized that the SQLite file has this info! So it may be a good idea to rewrite the parser to use the SQLite data and provide more info. This may involve changing the structure of the documents/objects.

(Side note: we do have DSI/DPI in MyDisease right now, but these are actually gene-level properties...not directly related to the gene-disease relationship)