Downloading and extracting DrugBank data using R
2
5
Entering edit mode
9.5 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 • 10k views
ADD COMMENT
2
Entering edit mode
9.5 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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
5.7 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

ADD COMMENT

Login before adding your answer.

Traffic: 1302 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6