# biodbHmdb
[](https://codecov.io/gh/pkrog/biodbHmdb?branch=master)
An R package for accessing [HMDB](http://www.hmdb.ca) online database, based on
R package/framework [biodb](https://github.com/pkrog/biodb/).
## Introduction
This extension package to [biodb](https://github.com/pkrog/biodb/) implements a
connector to the [HMDB](http://www.hmdb.ca) database.
## Installation
Install the latest stable version using Bioconductor:
```r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install('biodbHmdb')
```
## Examples
Searching for entries with multiple words inside the field "description":
```r
mybiodb <- biodb::newInst()
conn <- mybiodb$getFactory()$createConn('hmdb.metabolites')
ids <- conn$searchForEntries(fields=list(description=c('milk', 'Oligosaccharide')))
```
## Documentation
See the introduction vignette:
```r
vignette('biodbHmdb', package='biodbHmdb')
```
To get documentation on the implemented connector once inside R, run:
```r
?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>.
