ceabiodb / biodbUniprot

biodb connector to Uniprot (https://www.uniprot.org/) database.

biodbUniprot

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

Introduction

biodbUniprot is an extension package of the biodb package. It allows to connect to UniProt for retrieving entries, searching for entries by name or organism, and convert gene symbols to UniProt IDs.

Examples

Getting entries:

bdb <- boidb::newInst()
uniprot <- bdb$getFactory()$createConn('uniprot')
entries <- uniprot$getEntry(c('P01011', 'P09237'))
bdb$entriesToDataframe(entries)

Run a web service query:

bdb <- boidb::newInst()
uniprot <- bdb$getFactory()$createConn('uniprot')
uniprot$wsQuery('reviewed:yes AND organism:9606', columns=c('id', 'entry name'),
    limit=2, retfmt='parsed')

Installation

Install the latest stable version using Bioconductor:

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

Documentation

See the introduction vignette:

vignette('biodbUniprot', package='biodbUniprot')

Citations

• The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45: D158-D169 (2017), https://doi.org/10.1093/nar/gkw1099.
• Pundir S., Martin M.J., O’Donovan C. (2017) UniProt Protein Knowledgebase. In: Wu C., Arighi C., Ross K. (eds) Protein Bioinformatics. Methods in Molecular Biology, vol 1558. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6783-4_2.