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