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
hpo = hpotk.load_ontology('http://purl.obolibrary.org/obo/hp.json')
Now you have HPO concepts and the ontology hierarchy 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-0.4.1.tar.gz
(95.7 kB
view hashes)
Built Distribution
hpo_toolkit-0.4.1-py3-none-any.whl
(100.6 kB
view hashes)
Close
Hashes for hpo_toolkit-0.4.1-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 5556c4b9fff4a2c2138edea547a0d9e18d5864c4d4ce989e673ccc3c3db94096 |
|
MD5 | 0bcf9c28aa1a70d369c53d0a5092f29e |
|
BLAKE2b-256 | 2c0425eedae16433a42f54989ac2447af2d3a26fb3e498ef33bc2606d00ee73a |