Bio2BEL HMDB

Converts the Human Metabolite Database (HMDB) to BEL

Installation

bio2bel_hmdb can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_hmdb

or from the latest code on GitHub with:

$ python3 -m pip install git+https://github.com/bio2bel/hmdb.git@master

Setup

HMDB can be downloaded and populated from either the Python REPL or the automatically installed command line utility.

Python REPL

>>> import bio2bel_hmdb
>>> hmdb_manager = bio2bel_hmdb.Manager()
>>> hmdb_manager.populate()

Command Line Utility

bio2bel_hmdb populate

Citations

• Wishart DS, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6