Django app to parse/load phenotype ontologies (OncoTree, HPO, MONDO, etc)
Project description
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)
Updated sync to sync_ontology to make it more descriptive
0.1.2 (2018-04-10)
Added better support for MONDO. A few oddities were causing errors w/ pronto.
0.1.3 (2018-04-18)
Updated 3rd party libs
0.1.4 (2018-05-16)
Updated setup.py to read from requirements.txt
0.2.0 (2018-06-01)
Removed support for GraphQL
0.2.1 (2018-07-27)
Updated NCIT to be OncoTree - since we are using the onco tree specific ontology
0.2.2 (2018-08-13)
Updated 3rd party requirements. Some requirements had changed so it was causing failures
0.2.3 (2018-10-29)
Updated 3rd party requirements.
0.2.4 (2018-11-27)
Updated 3rd party requirements.
0.2.5 (2019-02-08)
Updated 3rd party requirements.
Updated tests to use py.test fixtures
0.2.6 (2019-04-10)
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)
Updated package to use latest cookiecutter template
0.2.8 (2019-07-26)
Updated 3rd party requirements.
0.2.9 (2019-08-09)
Updated 3rd party requirements.
0.2.10 (2019-09-09)
Updated 3rd party requirements.
1.0.0 (2019-11-01)
First production release
1.0.1 (2019-11-01)
pronto > v1.0.0 is not compatible
1.1.0 (2019-11-26)
Updated dependencies
Release history Release notifications | RSS feed
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