https://github.com/chopdgd/django-phenotype-ontologies

Django app for parsing/loading Phenotype ontologies (HPO, MONDO, OncoTree, etc)
https://github.com/chopdgd/django-phenotype-ontologies

bioinformatics django ontologies phenotypes

Last synced: 4 months ago
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Django app for parsing/loading Phenotype ontologies (HPO, MONDO, OncoTree, etc)

• Host: GitHub
• URL: https://github.com/chopdgd/django-phenotype-ontologies
• Owner: chopdgd
• License: mit
• Created: 2018-04-09T19:39:09.000Z (about 8 years ago)
• Default Branch: develop
• Last Pushed: 2026-02-04T14:12:22.000Z (5 months ago)
• Last Synced: 2026-02-05T01:34:20.159Z (5 months ago)
• Topics: bioinformatics, django, ontologies, phenotypes
• Language: Python
• Homepage:
• Size: 280 KB
• Stars: 7
• Watchers: 3
• Forks: 1
• Open Issues: 66
• Metadata Files:
  • Readme: README.rst
  • Changelog: HISTORY.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE
  • Authors: AUTHORS.rst

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README

          
=============================

Django Phenotype Ontologies

=============================

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.. image:: https://codecov.io/gh/chopdgd/django-phenotype-ontologies/branch/develop/graph/badge.svg

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     :alt: Updates

.. image:: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/python-3-shield.svg

      :target: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/

      :alt: Python 3

Django app to parse/load phenotype ontologies (OncoTree, HPO, MONDO, etc)

Documentation

-------------

The full documentation is at https://django-phenotype-ontologies.readthedocs.io.

Quickstart

----------

Install Django Phenotype Ontologies::

    pip install django-phenotype-ontologies

Add it to your `INSTALLED_APPS`:

.. code-block:: python

    INSTALLED_APPS = (

        ...

        'phenotype_ontologies',

        ...

    )

Add Django Phenotype Ontologies's URL patterns:

.. code-block:: python

    from phenotype_ontologies import urls as phenotype_ontologies_urls

    urlpatterns = [

        ...

        url(r'^', include(phenotype_ontologies_urls, namespace='phenotype_ontologies')),

        ...

    ]

Features

--------

* syncs OBO from MONDO, HPO, and NCIT (OncoTree)

* REST API to interact with models

* GraphQL Nodes to be incorporated to existing GraphQL setups with graphene_django

Running Tests

-------------

Does the code actually work?

::

    source /bin/activate

    (myenv) $ pip install tox

    (myenv) $ tox

Credits

-------

Tools used in rendering this package:

*  Cookiecutter_

*  `cookiecutter-djangopackage`_

.. _Cookiecutter: https://github.com/audreyr/cookiecutter

.. _`cookiecutter-djangopackage`: https://github.com/pydanny/cookiecutter-djangopackage