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README.md
# biodbUniprot [![Codecov test coverage](https://codecov.io/gh/pkrog/biodbUniprot/branch/master/graph/badge.svg)](https://codecov.io/gh/pkrog/biodbUniprot?branch=master) An R package for accessing [Uniprot](https://www.uniprot.org/) online database, based on R package/framework [biodb](https://github.com/pkrog/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: ```r bdb <- boidb::newInst() uniprot <- bdb$getFactory()$createConn('uniprot') entries <- uniprot$getEntry(c('P01011', 'P09237')) bdb$entriesToDataframe(entries) ``` Run a web service query: ```r 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: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install('biodbUniprot') ``` ## Documentation See the introduction vignette: ```r 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>.