opentargets-py

Python client for the Open Targets REST API at platform-api.opentargets.io

Why should you use this client instead of the REST API directly?

Include wrappers for all public methods, with query validation
Tools for the most common calls (E.g. get data for a target gene symbol even if you do not know its Ensembl Gene Id)
Supports automatic retrieval of paginated results with an iterator pattern
Easily save query results as JSON, CSV or Excel file
Handles Authentication
Handles fair usage limits transparently
Follows HTTP cache as set by the REST API
Experimental HTTP2 support for better performance (beware the client library is in alpha)
Support for advanced SSL and proxy configuration

This client is supported for Python 3.5 and upper. Works on pythoon 2.7 on a best effort basis.

Documentation is available on ReadTheDocs

QUICK START

from opentargets import OpenTargetsClient

ot = OpenTargetsClient()

search_result = ot.search('BRAF')
print(search_result[0])

a_for_target = ot.get_associations_for_target('BRAF')
for a in a_for_target:
    print(a['id'], a['association_score']['overall'])

a_for_disease = ot.get_associations_for_disease('cancer')

print(ot.get_association('ENSG00000157764-EFO_0005803')[0])

e_for_target = ot.get_evidence_for_target('BRAF')
print(e_for_target.to_json())

e_for_disease = ot.get_evidence_for_disease('medulloblastoma')

print(ot.get_evidence('5cf863da265c32d112ff4fc3bfc25ab3')[0])

print(ot.get_stats().info)

...

Contributing

To create a development environment:

git clone <this repo>
cd opentargets-py
virtualenv venv
source venv/bin/activate
pip install -r requirements.txt

How to contribute:

(if you are not part of the open targets team) fork the repo
branch from master, always start with git checkout -b yourname-featureyouareadding
code
push your branch and submit a PR
ask for reviews for your PR
Travis tests have to pass
Your PR is approved and merged