PyHPO ships with a full version of the HP ontology, including gene and disease associations. I try to keep this data up to date, but will frequently fall behind on the release schedule.
To build the ontology, the following 3 files are needed from the HPO masterdata:
http://purl.obolibrary.org/obo/hp.obo
http://purl.obolibrary.org/obo/hp/hpoa/phenotype_to_genes.txt
http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
To update to the most recent version of the masterdata, you can use the following Python script:
from pyhpo.update_data import download_data
download_data()
By default, the HPO masterdata is stored along the installed library. You could manually update the files in there, but that is not recommended. Instead, you can download the HPO masterdata into a local folder and specify that folder during instantiation of the Ontology:
from pyhpo import Ontology
_ = Ontology("/path/to/folder/with/masterdata/")