hpo-toolkit 0.3.1

A toolkit for working with Human Phenotype Ontology in Python

hpo-toolkit

A toolkit for working with Human Phenotype Ontology in Python.

Loading HPO is as simple as:

import hpotk

hpo = hpotk.load_ontology('http://purl.obolibrary.org/obo/hp.json')

Loading HPO annotations is accomplished 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)

# Phenotype annotations for 12,468 rare diseases is at your fingertips.
assert len(diseases) == 12_468

Check out the User guide and the API reference for more info:

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