biodbKegg

An R Bioconductor package for accessing KEGG online database, based on Bioconductor package/framework biodb.

Introduction

biodbKegg is an an extension package of the biodb package. It allows to connect to KEGG for retrieving entries, searching for entries by name or mass, and searching for pathways related to compounds. It implements biodb connectors for the following KEGG databases:

• KEGG Compound.
• KEGG Enzyme.
• KEGG Genes.
• KEGG Module.
• KEGG Orthology.
• KEGG Pathway.
• KEGG Reaction.

Examples

Getting a single entry:

bdb <- boidb::newInst()
kegg <- bdb$getFactory()$createConn('kegg.compound')
entries <- kegg$getEntry(c('C00133', 'C00751'))
bdb$entriesToDataframe(entries)

Search by mass:

ids <- kegg$searchForEntries(list(monoisotopic.mass=list(value=64, delta=2.0)),
    max.results=10)

Installation

Install the latest stable version using Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install('biodbKegg')

Documentation

See the introduction vignette:

vignette('biodbKegg', package='biodbKegg')

Citations

• Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000), https://doi.org/10.1093/nar/28.1.27.