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
mainbranch) - Latest documentation (bleeding edge, latest commit on
developmentbranch)
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-0.4.3.tar.gz
(96.8 kB
view details)
Built Distribution
hpo_toolkit-0.4.3-py3-none-any.whl
(101.8 kB
view details)
File details
Details for the file hpo-toolkit-0.4.3.tar.gz.
File metadata
- Download URL: hpo-toolkit-0.4.3.tar.gz
- Upload date:
- Size: 96.8 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.10.12
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 2270d349ad072da17454281b41cca42506dfffd712d7306a0061d5cccae6062c |
|
| MD5 | d8374b61f77e8c571f62f6e407de8b2b |
|
| BLAKE2b-256 | 8b7a50e9d93aef25d7467d30a9df6e4154c5bc0b712577486a7d613b554ab0d6 |
File details
Details for the file hpo_toolkit-0.4.3-py3-none-any.whl.
File metadata
- Download URL: hpo_toolkit-0.4.3-py3-none-any.whl
- Upload date:
- Size: 101.8 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.10.12
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 0cc9bc289c259601ef60532f7e58ff63456c8c05d414b568e0d3f7dcedc42ad8 |
|
| MD5 | 11facb6df32773f79948036145e0f1a6 |
|
| BLAKE2b-256 | c20fc558cf50e4598a5aeefcced9bfff1abf8a75554cb8facf22563d728de88a |
