Bio2BEL Entrez

This package downloads, parses, and stores the Entrez Gene and HomoloGene databases then provides utilities for converting to BEL.

Installation

bio2bel_entrez can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_entrez

or from the latest code on GitHub with:

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

Setup

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

Python REPL

>>> import bio2bel_entrez
>>> entrez_manager = bio2bel_entrez.Manager()
>>> entrez_manager.populate()

Command Line Utility

bio2bel_entrez populate

Citations

• Maglott, D., et al. (2011). Entrez Gene: gene-centered information at NCBI. Nucleic Acids Research, 39(Database issue), D52–D57.