In pkrog/biodbNci: biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database

Purpose

biodbNci is a biodb extension package that implements a connector to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS API [@nci2022_CACTUS].

Installation

Install using Bioconductor:

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

Initialization

The first step in using biodbNci, 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 CACTUS

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

conn <- mybiodb$getFactory()$createConn('nci.cactus')

For this vignette, we will avoid the downloading of the full NCI CACTUS database, and use instead an extract containing a few entries:

dbExtract <- system.file("extdata", 'generated', "cactus_extract.txt.gz",
    package="biodbNci")
conn$setPropValSlot('urls', 'db.gz.url', dbExtract)

Accessing entries

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

Chemical Identifier Resolver web service

Here is an example of calling the Chemical Identifier Resolver for converting a SMILES into an InChI:

conn$wsChemicalIdentifierResolver(structid='C=O', repr='InChI')

Convert CAS IDs

There are currently two methods in NCI CACTUS for converting from CAS IDs to InChI or InChI keys:

conn$convCasToInchi('87605-72-9')
conn$convCasToInchikey('87605-72-9')

The conversion is made thanks to the Chemical Identifier Resolver web service.

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/biodbNci documentation built on March 27, 2022, 4:30 p.m.