gene_phenotype_associations

Python scripts to load gene-to-phenotype db to supply gene to HPO terms (phenotypes) and gene to disease assocations.

Generating the database

Get the code:

git clone https://github.com/iobio/gene_phenotype_associations
cd gene_phenotype_associations

Create a python environment and install pandas:

python3 -m venv g2p
source g2p/bin/activate
pip install pandas

Generate the db:

./scripts/download.sh
./scripts/populate.sh

Sources of data

gene to phenotypes HPO https://hpo.jax.org/app/data/annotations gene to disease Orphanet http://www.orphadata.org/cgi-bin/index.php