hpo-toolkit

A toolkit for working with Human Phenotype Ontology (HPO) and HPO disease annotations in Python.

Example

Loading HPO is as simple as:

import hpotk

store = hpotk.configure_ontology_store()
hpo = store.load_hpo()

Now you have the concepts and the hierarchy of the latest HPO release at your fingertips.

Next, load the HPO disease annotations by running:

from hpotk.annotations.load.hpoa import SimpleHpoaDiseaseLoader

hpoa_path = 'https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-10-09/phenotype.hpoa'

loader = SimpleHpoaDiseaseLoader(hpo)
diseases = loader.load(hpoa_path)

assert len(diseases) == 12_468

You got yourself phenotype annotations of 12,468 rare diseases.

Learn more

Find more info in our detailed documentation:

• Stable documentation (last release on main branch)
• Latest documentation (bleeding edge, latest commit on development branch)