A toolkit for working with Human Phenotype Ontology in Python
Project description
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
mainbranch) - Latest documentation (bleeding edge, latest commit on
developmentbranch)
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