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
main
branch) - Latest documentation (bleeding edge, latest commit on
development
branch)
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
hpo_toolkit-0.5.3.tar.gz
(103.9 kB
view hashes)
Built Distribution
hpo_toolkit-0.5.3-py3-none-any.whl
(108.4 kB
view hashes)
Close
Hashes for hpo_toolkit-0.5.3-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 331a7479be71c74d3ab687a1822bde6168744681fc3bafe35824f1ed130d9eeb |
|
MD5 | cd6d595e5e91ccab9c51fea9a9ed6764 |
|
BLAKE2b-256 | 431815ebf37edc7bad06d6742730f191eccdea53bb662367c7f10ef53bab0719 |