In pkrog/biodbUniprot: biodbUniprot, a library for connecting to the Uniprot Database

Introduction

biodbUniprot is a biodb extension package that implements a connector to Uniprot database.

The UniProt Knowledge Base [@uniprotConsortium2016UniProtKB] can be searched using its search web service.

We present here the way to contact this web service with this package.

Installation

Install using Bioconductor:

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

Initialization

The first step in using biodbUniprot, is to create an instance of the biodb class BiodbMain from the main biodb package. This is done by calling the constructor of the class:

mybiodb <- biodb::newInst()

During this step the configuration is set up, the cache system is initialized and extension packages are loaded.

We will see at the end of this vignette that the biodb instance needs to be terminated with a call to the terminate() method.

Creating a connector to Uniprot database

In biodb the connection to a database is handled by a connector instance that you can get from the factory. biodbUniprot implements a connector to a remote database. Here is the code to instantiate a connector:

conn <- mybiodb$getFactory()$createConn('uniprot')

Getting entries

To download entries, run the getEntry(), which returns a list of BiodbEntry objects:

entries <- conn$getEntry(c('P01011', 'P09237'))

To print the information contained in the entry objects as a data frame, run the entriesToDataframe() method attached to the BiodbMain instance:

mybiodb$entriesToDataframe(entries)

Using the search web service

The method wsSearch() (wsQuery() is now deprecated) implements the request to the search web service, and the parsing of its output.

To get the raw results returned by the UniProt server, run the following code:

conn$wsSearch('reviewed:true AND organism_id:9606', fields=c('accession', 'id'),
    size=2, retfmt='plain')

The first parameter is the query, as required by the web service. To learn how to write a query for UniProt, see a description of the query web service at http://www.uniprot.org/help/api_queries.

The fields parameter is the fields you want back for each entry returned by the database.

The size parameter is the maximum number of entries the server must return.

The retfmt parameter controls the type of output desired. Here "plain" states that we want the raw output from the server.

To get the output parsed by biodb and get a data frame, run:

conn$wsSearch('reviewed:true AND organism_id:9606', fields=c('accession', 'id'),
    size=2, retfmt='parsed')

To get only the list of UniProt identifiers, run:

conn$wsSearch('reviewed:true AND organism_id:9606', fields=c('accession', 'id'),
    size=2, retfmt='ids')

And if you are curious to see the URL request that is sent to the server, run:

conn$wsSearch('reviewed:true AND organism_id:9606', fields=c('accession', 'id'),
    size=2, retfmt='request')

Conversion of gene symbols to UniProt IDs

The method geneSymbolToUniprotIds() uses wsSearch() to search for UniProt entries that reference particular gene symbols.

For instance, if you want to get the UniProt entries that have the gene symbol G-CSF, just run:

ids <- conn$geneSymbolToUniprotIds('G-CSF')
mybiodb$entryIdsToDataframe(ids[['G-CSF']], 'uniprot', fields=c('accession',
    'gene.symbol'))

If you want to match also GCSF (no minus sign character), then run:

ids <- conn$geneSymbolToUniprotIds('G-CSF', ignore.nonalphanum=TRUE)
mybiodb$entryIdsToDataframe(ids[['G-CSF']], 'uniprot', fields=c('accession',
    'gene.symbol'))

If you want to match G-CSFa2 too, run:

ids <- conn$geneSymbolToUniprotIds('G-CSF', partial.match=TRUE)
mybiodb$entryIdsToDataframe(ids[['G-CSF']], 'uniprot', fields=c('accession',
    'gene.symbol'))

The way this method works is by running wsSearch() to get a first set of entry identifiers, and then download each entry and apply a filtering on them. The downloading of the entries may quite long, wsSearch() returning potentially thousands of entries, each entry being downloaded with a single separate request and the frequency limit being 3 request per second. Entries already in cache or memory will not be downloaded again, so running the same request a second time will be faster, as it is usually the case with biodb.

Closing biodb instance

When done with your biodb instance you have to terminate it, in order to ensure release of resources (file handles, database connection, etc):

mybiodb$terminate()

Session information

sessionInfo()

References

pkrog/biodbUniprot documentation built on Sept. 26, 2022, 3:50 p.m.