Downloading and extracting DrugBank data using R

Question

[niveditaj20]

Hi all,

I need your help for Downloading and extracting DrugBank data using R. Like clinical trials is there any specific package to download data from DrugBank database?

Also I need to extract specific columns from DrugBank like-

DrugName
IUPAC
Accession number
Database ID

Kindly need your suggestions on this.

Answer 1

[learnBioinformatics]

Hi,

In fact, you can download their files (csv format is what your need)and deal with these files using R.

http://www.drugbank.ca/downloads#external-links

Kevin

[vasilislenis]

Hi Kevin,

I'm terribly sorry for bothering you with this old post, but I have the same problem and by following the link that you gave I can see that you can download the csv files with the drug name and the protein that correspond but I was wondering if you can have an information about the action (inhibitor, antagonist, etc.) This information exists only in the full xml file (as far as I understand) but not in the csv.

Thank you very much,
Vasilis

Answer 2

[mohfcis]

You can use dbparser package https://github.com/Dainanahan/dbparser, it is designed to parse DrugBank database and return R dataframes