In pkrog/biodbExpasy: biodbExpasy, a library for connecting to Expasy ENZYME database.

Introduction

biodbExpasy is a biodb extension package that implements a connector to the Expasy ENZYME database [@bairoch2000_expasy].

Installation

Install using Bioconductor:

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

Initialization

The first step in using biodbExpasy, is to create an instance of the biodb class Biodb 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 Expasy ENZYME database.

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

conn <- mybiodb$getFactory()$createConn('expasy.enzyme')

Accessing entries

To get the number of entries stored inside the database, run:

conn$getNbEntries()

To get some of the first entry IDs (accession numbers) from the database, run:

ids <- conn$getEntryIds(2)
ids

To retrieve entries, use:

entries <- conn$getEntry(ids)
entries

To convert a list of entries into a dataframe, run:

x <- mybiodb$entriesToDataframe(entries)
x

Running the "wsEnzymeByName" web service

You can access the web service "find" directly with the wsEnzymeByName method:

conn$wsEnzymeByName(name="Alcohol", retfmt="ids")

Running the "wsEnzymeByComment" web service

You can access the web service "find" directly with the wsEnzymeByComment method:

conn$wsEnzymeByComment(comment="best", retfmt="ids")

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/biodbExpasy documentation built on March 29, 2022, 9:52 a.m.