cthoyt / cthoyt.github.io

My personal website, served at https://cthoyt.com

https://cthoyt.com/

Creative Commons Attribution 4.0 International

3 stars 4 forks source link

Making DrugBank Reproducible | Biopragmatics #44

Open utterances-bot opened 2 years ago

utterances-bot commented 2 years ago

Making DrugBank Reproducible | Biopragmatics

If you’re reading my blog, there’s a pretty high chance you’ve used DrugBank, a database of drug-target interations, drug-drug interactions, and other high-granularity information about clinically-studied chemicals. DrugBank has two major problems, though: its data are password-protected, and its license does not allow redistribution. Time to solve these problems once and for all.

https://cthoyt.com/2020/12/14/taming-drugbank.html

Gayathri609 commented 2 years ago

Hi Charles, I am trying to download Drugbank XML data and found your code very useful. Really appreciate your work. Just wanted to understand if our account with Drugbank should have been approved to download the file using your script. I am waiting for their approval and when I use your script I end up getting the error 'zipfile.BadZipFile: File is not a zip file'. So wondering if it's an issue with my account or something else.

cthoyt commented 2 years ago

Yes, there’s a manual account approval process. Before that happens, you will get bad data (I think it redirects to an HTML page which clearly isn’t a zip file). Maybe I can add code that raises an exception and cleans up the bad zip file in this case