## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install('biodbUniprot') ## ----results='hide'----------------------------------------------------------- mybiodb <- biodb::newInst() ## ----------------------------------------------------------------------------- conn <- mybiodb$getFactory()$createConn('uniprot') ## ----------------------------------------------------------------------------- entries <- conn$getEntry(c('P01011', 'P09237')) ## ----------------------------------------------------------------------------- mybiodb$entriesToDataframe(entries) ## ----------------------------------------------------------------------------- conn$wsSearch('reviewed:true AND organism_id:9606', fields=c('accession', 'id'), size=2, retfmt='plain') ## ----------------------------------------------------------------------------- conn$wsSearch('reviewed:true AND organism_id:9606', fields=c('accession', 'id'), size=2, retfmt='parsed') ## ----------------------------------------------------------------------------- conn$wsSearch('reviewed:true AND organism_id:9606', fields=c('accession', 'id'), size=2, retfmt='ids') ## ----------------------------------------------------------------------------- conn$wsSearch('reviewed:true AND organism_id:9606', fields=c('accession', 'id'), size=2, retfmt='request') ## ----------------------------------------------------------------------------- ids <- conn$geneSymbolToUniprotIds('G-CSF') mybiodb$entryIdsToDataframe(ids[['G-CSF']], 'uniprot', fields=c('accession', 'gene.symbol')) ## ----------------------------------------------------------------------------- ids <- conn$geneSymbolToUniprotIds('G-CSF', ignore.nonalphanum=TRUE) mybiodb$entryIdsToDataframe(ids[['G-CSF']], 'uniprot', fields=c('accession', 'gene.symbol')) ## ----------------------------------------------------------------------------- ids <- conn$geneSymbolToUniprotIds('G-CSF', partial.match=TRUE) mybiodb$entryIdsToDataframe(ids[['G-CSF']], 'uniprot', fields=c('accession', 'gene.symbol')) ## ----------------------------------------------------------------------------- mybiodb$terminate() ## ----------------------------------------------------------------------------- sessionInfo()