Get DrugBank data with Python

Question

[Jack]

I'm trying to get a list of all FDA-approved drugs from DrugBank. Is there a Python or R script that can do that for me?

[natasha.sernova]

Let's consider this Drugbank.

https://www.drugbank.ca/

There is a comprehensive guide below how to do a lot of things manually:

https://www.drugbank.ca/help

Below there is some python scripts as an artenative:

https://github.com/macarthur-lab/gene_lists

Look through the page, you will find some python script-links, for example:

https://github.com/macarthur-lab/gene_lists/blob/master/src/drug_targets.py

There are a lot of databases that provide similar information:

http://www.cureffi.org/2013/10/04/list-of-fda-approved-drugs-and-cns-drugs-with-smiles/

See this link as well: Downloading and extracting DrugBank data using R

WIKI is not a bad source of some information:

https://en.wikipedia.org/wiki/DrugBank

Answer 1

[mohfcis]

Hi, you can use dbparser package https://github.com/Dainanahan/dbparser, it is designed to parse DrugBank database and return R dataframes. The generated dataframes are avaiable in https://dainanahan.github.io/dbdataset/.