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

Project description

https://badge.fury.io/py/django-phenotype-ontologies.svg https://travis-ci.org/chopdgd/django-phenotype-ontologies.svg?branch=develop https://codecov.io/gh/chopdgd/django-phenotype-ontologies/branch/develop/graph/badge.svg Updates 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:

INSTALLED_APPS = (
    ...
    'phenotype_ontologies',
    ...
)

Add Django Phenotype Ontologies’s URL patterns:

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 <YOURVIRTUALENV>/bin/activate
(myenv) $ pip install tox
(myenv) $ tox

Credits

Tools used in rendering this package:

History

0.1.0 (2018-04-10)

  • Models for Phenotype Ontologies
  • REST API
  • GraphQL Nodes
  • Sync methods for PURL of MONDO, HPO, NCIT

0.1.1 (2018-04-10)

0.1.1 Changelog

  • Updated sync to sync_ontology to make it more descriptive

0.1.2 (2018-04-10)

0.1.2 Changelog

  • Added better support for MONDO. A few oddities were causing errors w/ pronto.

0.1.3 (2018-04-18)

0.1.3 Changelog

  • Updated 3rd party libs

0.1.4 (2018-05-16)

0.1.4 Changelog

  • Updated setup.py to read from requirements.txt

0.2.0 (2018-06-01)

0.2.0 Changelog

  • Removed support for GraphQL

0.2.1 (2018-07-27)

0.2.1 Changelog

  • Updated NCIT to be OncoTree - since we are using the onco tree specific ontology

0.2.2 (2018-08-13)

0.2.2 Changelog

  • Updated 3rd party requirements. Some requirements had changed so it was causing failures

0.2.3 (2018-10-29)

0.2.3 Changelog

  • Updated 3rd party requirements.

0.2.4 (2018-11-27)

0.2.4 Changelog

  • Updated 3rd party requirements.

0.2.5 (2019-02-08)

0.2.5 Changelog

  • Updated 3rd party requirements.
  • Updated tests to use py.test fixtures

0.2.6 (2019-04-10)

0.2.6 Changelog

  • Updated 3rd party requirements.
  • Updated travis to use xenial distribution. Django 2.1 dropped support for SQLite < 3.8.3

0.2.7 (2019-05-31)

0.2.7 Changelog

  • Updated package to use latest cookiecutter template

0.2.8 (2019-07-26)

0.2.8 Changelog

  • Updated 3rd party requirements.

0.2.9 (2019-08-09)

0.2.9 Changelog

  • Updated 3rd party requirements.

Project details


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