DOI: 10.18129/B9.bioc.biodb    

This is the development version of biodb; for the stable release version, see biodb.

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

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel


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 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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  

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Source Package biodb_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone
Source Repository (Developer Access) git clone
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