Masterdata
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.obohttp://purl.obolibrary.org/obo/hp/hpoa/phenotype_to_genes.txthttp://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
Updating to the most recent version
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()
Manually updating the masterdata
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/")