kangsli/dbparser

Source code for the R package, "dbparser" (i.e. DrugBank Parser)

dbparser

Introduction

DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. As both a bioinformatics and a cheminformatics resource, DrugBank combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. More information about DrugBank can be found here.

In its raw form, the DrugBank database is a single XML file. Users must create an account with DrugBank and request permission to download the database. Note that this may take a couple of days.

The dbparser package parses the DrugBank XML database into R tibbles that can be explored and analyzed by the user, check this tutorial for more details.

Also, the package offers the option to save these tibbles in databases including SQL Server DB and Maria DB just by enabling save_table option, check this tutorial for more details.

If you are waiting for access to the DrugBank database, or do not intend to do a deep dive with the data, you may wish to use the dbdataset package, which contains the DrugBank database already parsed into R tibbles. Note that this is a large package that exceeds the limit set by CRAN. It is only available on GitHub.

dbparser is tested against DrugBank versions 5.1.0 through 5.1.6 successfully. If you find errors with these versions or any other version please submit an issue here.

Installation

You can install the released version of dbparser from CRAN with:

install.packages("dbparser")

or you can install the latest updates directly from the repo

library(devtools)
devtools::install_github("ropensci/dbparser")

Code of Conduct

Please note that the ‘dbparser’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Contributing Guide

👍🎉 First off, thanks for taking the time to contribute! 🎉👍 Please review our Contributing Guide.

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Using dbparser for a paper you are writing? Consider citing it

citation("dbparser")
#> 
#> To cite dbparser in publications use:
#> 
#>   Mohammed Ali, Ali Ezzat (). dbparser: DrugBank Database XML Parser. R
#>   package version 1.2.0.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {DrugBank Database XML Parser},
#>     author = {Mohammed Ali and Ali Ezzat},
#>     organization = {Dainanahan},
#>     note = {R package version 1.2.0},
#>     url = {https://CRAN.R-project.org/package=dbparser},
#>   }