drugbankR: R package for querying drugbank database

In yduan004/drugbankR: R package for querying DrugBank database in batch locally

Description

The drugbankR package is used for querying drugbank database in R.

Details

Transform drugbank database (xml file) into dataframe and store in SQLite database.

Query drugbank SQLite database to get

1. the entire dataframe.

2. all the drugbank ids.

3. given drugbank ids, determine whether the drugs are FDA approved.

4. given drugbank ids, get their targets ids (DrugBank_id, UniProt_id, symbol...).

Author(s)

Yuzhu Duan ([e-mail])

References

http://www.drugbank.ca/releases/latest

Examples

# devtools::install_github("yduan004/drugbankR")

# library(drugbankR)

## download the original drugbank database (http://www.drugbank.ca/releases/latest) (xml file) 

## into your current directory and rename as drugbank.xml

## convert drugbank dabase (xml file) into dataframe: 
## Not run: 
drugbank_dataframe <- dbxml2df(xmlfile="drugbank.xml")

## End(Not run) 

## store the converted drugbank dataframe into SQLite database. 

## The generated SQLite database (drugbank.db) is under your current directory

## Not run: 
df2SQLite(dbdf=drugbank_dataframe) 

## End(Not run)
df <- queryDB(type = "getAll")

ids <- queryDB(type = "getIDs")

queryDB(ids = c("DB00001","DB00002"),type = "whichFDA")

queryDB(ids = c("DB00001","DB00002"),type = "getTargets")

yduan004/drugbankR documentation built on Aug. 10, 2021, 5:21 p.m.