DOI: 10.18129/B9.bioc.biodb    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see biodb.

biodb, a library and a development framework for connecting to chemical and biological databases

Bioconductor version: 3.14

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Author: Pierrick Roger [aut, cre] , Alexis Delabrière [ctb]

Maintainer: Pierrick Roger <pierrick.roger at>

Citation (from within R, enter citation("biodb")):


To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Creating a new connector class for accessing a database.
HTML R Script Creating a new field for entries.
HTML R Script Details on general *biodb* usage and principles
HTML R Script Introduction to the biodb package.
HTML R Script Manipulating entry objects
PDF   Reference Manual
Text   NEWS


biocViews DataImport, Infrastructure, KEGG, Software
Version 1.2.2
In Bioconductor since BioC 3.13 (R-4.1) (1 year)
License AGPL-3
Depends R (>= 4.1.0)
Imports BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, jsonlite, lgr, lifecycle, methods, openssl, plyr, progress, rappdirs, stats, stringr, tools, withr, yaml
LinkingTo Rcpp, testthat
Suggests BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2, git2r
Depends On Me
Imports Me biodbChebi, biodbHmdb, biodbKegg, biodbLipidmaps, biodbUniprot
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package biodb_1.2.2.tar.gz
Windows Binary (32- & 64-bit)
macOS 10.13 (High Sierra) biodb_1.2.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: