biodbChebi

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

Introduction

biodbChebi is an extension package of the biodb package. It allows to connect to ChEBI for retrieving entries, searching for entries by name or mass, and convert CAS IDs or InChI to ChEBI IDs.

Examples

Getting a single entry:

bdb <- biodb::newInst()
chebi <- bdb$getFactory()$createConn('chebi')
entries <- chebi$getEntry(c('2528', '7799', '15440'))
bdb$entriesToDataframe(entries)

Searching by name and mass:

bdb <- biodb::newInst()
chebi <- bdb$getFactory()$createConn('chebi')
ids <- chebi$searchCompound(name='aspartic', mass=133,
    mass.field='molecular.mass', mass.tol=0.3, max.results=3)

See the vignette for more examples.

Installation

Install the latest stable version using Bioconductor:

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

Documentation

See the introduction vignette:

vignette('biodbChebi', package='biodbChebi')

Citations

• Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M., and Steinbeck, C. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res, http://dx.doi.org/10.1093/nar/gks1146.