biodbHmdb

An R package for accessing HMDB online database, based on R package/framework biodb.

Introduction

This extension package to biodb implements a connector to the HMDB database.

Installation

Install the latest stable version using Bioconductor:

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

Examples

Searching for entries with multiple words inside the field “description”:

mybiodb <- biodb::newInst()
conn <- mybiodb$getFactory()$createConn('hmdb.metabolites')
ids <- conn$searchForEntries(fields=list(description=c('milk', 'Oligosaccharide')))

Documentation

See the introduction vignette:

vignette('biodbHmdb', package='biodbHmdb')

To get documentation on the implemented connector once inside R, run:

?biodbHmdb::HmdbMetabolitesConn

Citations

HMDB website: http://www.hmdb.ca.

• Wishart DS, Tzur D, Knox C, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6, https://doi.org/10.1093/nar/gkl923.
• Wishart DS, Knox C, Guo AC, et al., HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 37(Database issue):D603-610, https://doi.org/10.1093/nar/gkn810.
• Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013. Jan 1;41(D1):D801-7, https://doi.org/10.1093/nar/gks1065.