dbparser

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

https://github.com/ropensci/dbparser

Last synced: 10 months ago · JSON representation

Repository

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

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/dbparser
Size: 3.39 MB

Statistics

Stars: 61
Watchers: 4
Forks: 19
Open Issues: 3
Releases: 10

Created over 7 years ago · Last pushed almost 2 years ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

README.Rmd

---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
library(dplyr)
library(ggplot2)
```
# dbparser 

[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/dbparser)](https://cran.r-project.org/package=dbparser)
[![codecov](https://codecov.io/gh/ropensci/dbparser/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/dbparser)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![metacran downloads](https://cranlogs.r-pkg.org/badges/grand-total/dbparser)](https://cran.r-project.org/package=dbparser)
[![](https://img.shields.io/badge/Doc-Rdoc-blue.svg)](https://www.rdocumentation.org/packages/dbparser)
[![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/3311/badge)](https://bestpractices.coreinfrastructure.org/projects/3311)
[![](https://badges.ropensci.org/347_status.svg)](https://github.com/ropensci/software-review/issues/347)

## Overview
Drugs databases vary too much in their formats and structures which making related 
data analysis not a very easy job and requires a lot of efforts to work on only
two databases together such as [DrugBank](https://go.drugbank.com/) and [KEGG](https://www.genome.jp/kegg/).

Hence, `dbparser` package aims to parse different public drugs databases as [DrugBank](https://go.drugbank.com/) or [KEGG](https://www.genome.jp/kegg/) into
single and unified format R object called `dvobject` (stands for drugverse object).

That should help in:

- working with single data object and not multiple databases in different formats,
- using R analysis capabilities easily on drugs data,
- ease of transferring data between researchers after performing required data
analysis or `dvobject` and storing results in the same object in a very easy manner

### dvobject Structure
`dvobject` introduces a unified and compressed format of drugs data.
It is an R list object that contains one or more of the following sub-lists:

- **drugs**: list of data.frames that contain drugs information (i.e. synonyms, classifications, ...) and it is the only mandatory list
- **salts**: data.frame contains drugs salts information
- **products**: data.frame of commercially available drugs products in the world
- **references**: data.frame of articles, links and textbooks about drugs or CETT data
- **cett**: list of data.frames contain targets, enzymes, carriers and transporters information

## Drug Databases
Parsers are available for the following databases (it is in progress list)

### DrugBank

[DrugBank](https://go.drugbank.com/) 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](https://go.drugbank.com/about).

In its raw form, the DrugBank database is a single
XML file. Users must create an [account](https://go.drugbank.com/public_users/sign_up)
with DrugBank and request permission to [download](https://go.drugbank.com/releases/latest)
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](https://docs.ropensci.org/dbparser/articles/dbparser.html) 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](https://interstellar-consultation-services.github.io/dbdataset/), which contains
the DrugBank database already parsed into `dvobject`. 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 *5.1.12*
successfully. If you find errors with these versions or any other
version please submit an issue
[here](https://github.com/ropensci/dbparser/issues).

## Installation

You can install the released version of dbparser from 
[CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("dbparser")
```
or you can install the latest updates directly from the repo

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

## Code of Conduct
Please note that the 'dbparser' project is released with a
  [Contributor Code of Conduct](https://docs.ropensci.org/dbparser/CODE_OF_CONDUCT.html).
  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](https://docs.ropensci.org/dbparser/CONTRIBUTING.html).

## Share the love ❤️

Think **dbparser** is useful? Let others discover it, by telling them in person, via Twitter or a blog post.

Using **dbparser** for a paper you are writing? Consider citing it
```{r}
citation("dbparser")
```

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

JOSS Publication

dbparser: An R Package for Parsing and Integrating Pharmacological Databases

Published

February 13, 2026

DOI

10.21105/joss.09950

Volume 11, Issue 118, Page 9950

Authors

Mohammed Ali

Independent Researcher

Ali Ezzat
Independent Researcher

Editor

Arfon Smith

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Name	Email	Commits
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Mohammed Ali	m**d@a**m	47
Mohammed Ali	m**s@y**m	15
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Emma Mendelsohn	m**n@e**g	2
Mohammed Ali	m**i@d**m	1
amrrs	a**s@o**m	1
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dbparser

Science Score: 26.0%

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Basic Info

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README.Rmd

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JOSS Publication

dbparser: An R Package for Parsing and Integrating Pharmacological Databases

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