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A toolkit for working with Human Phenotype Ontology in Python

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


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 = ''

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:

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