In pkrog/biodbLipidmaps: biodbLipidmaps, a library for connecting to the Lipidmaps Structure database

Introduction

biodbLipidmaps is a biodb extension package that implements a connector to Lipidmaps Structure [@sud2007_LipidMaps_LMSD].

Installation

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

Initialization

The first step in using biodbLipidmaps, 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 Lipidmaps Structure

In biodb connections to databases are handled by connector instances that you can get from the factory. Here is the code to instantiate a connector to Lipidmaps Structure database:

conn <- mybiodb$getFactory()$createConn('lipidmaps.structure')

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 data frame, run:

x <- mybiodb$entriesToDataframe(entries)
x

Running the "LMSDSearch" web service

You can access the web service "LMSDSearch" directly with the wsLmsdSearch method:

ids <- conn$wsLmsdSearch(mode='ProcessStrSearch', name="fatty", retfmt="ids")
ids

From this list of identifiers, we can obtain the full entry objects:

entries <- conn$getEntry(ids)

And then a data frame:

entriesDf <- mybiodb$entriesToDataframe(entries)

That you can see in table \@ref(tab:entriesTable).

knitr::kable(entriesDf, "pipe", caption="The entries listed in the result of the search.")

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/biodbLipidmaps documentation built on Dec. 1, 2022, 3:52 p.m.