bio2bel / phewascatalog

Bio2BEL PheWAS Catalog

Disease associations to variants and genes

Installation

bio2bel_phewascatalog can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_phewascatalog

or from the latest code on GitHub with:

$ python3 -m pip install git+https://github.com/bio2bel/phewascatalog.git

Setup

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

Python REPL

>>> import bio2bel_phewascatalog
>>> phewascatalog_manager = bio2bel_phewascatalog.Manager()
>>> phewascatalog_manager.populate()

Command Line Utility

bio2bel_phewascatalog populate

phewascatalog's Issues

Normalize gene symbols and MeSH terms

It's nice to have these names, but we need to normalize them and get their relevant identifiers from HGNC and MeSH. Is that available somewhere else in the database?