<!-- vimvars: b:markdown_embedded_syntax={'r':''} --> # biodbChebi [![Codecov test coverage](https://codecov.io/gh/pkrog/biodbChebi/branch/master/graph/badge.svg)](https://codecov.io/gh/pkrog/biodbChebi?branch=master) An R Bioconductor package for accessing [ChEBI](https://www.ebi.ac.uk/chebi/) online database, based on Bioconductor package/framework [biodb](https://github.com/pkrog/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: ```r bdb <- biodb::newInst() chebi <- bdb$getFactory()$createConn('chebi') entries <- chebi$getEntry(c('2528', '7799', '15440')) bdb$entriesToDataframe(entries) ``` Searching by name and mass: ```r 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: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install('biodbChebi') ``` ## Documentation See the introduction vignette: ```r 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>.