Downloading and extracting DrugBank data using R
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Entering edit mode
8.9 years ago
niveditaj20 ▴ 50

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.

R • 9.7k views
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2
Entering edit mode
8.9 years ago

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

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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

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5.0 years ago
mohfcis ▴ 20

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

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