Target-Disease evidence are represented in JSON format in Open Targets. While it's possible to 'validate' json data using modules such as jsonschema and generate evidence strings with dictionaries and lists, we decided at the beginning of the project to have a python module to generate and validate evidence based on an object-oriented representation of the evidence.

Hence opentargets.datamodel is a simple module to generate, validate, and compare Open Targets evidence. The python code is auto-generated from the json schema itself meaning that any change can be reflected immediately in the data model.

The following instructions will get you a version of the module

Using python's pip installer:

pip install git+https://github.com/opentargets/data_model.git

To install a specific version of the code in a specific folder, here 1.2.8:

pip install -t data_model-1.2.8 git+https://github.com/opentargets/[email protected]

There is currently a file called test_data_model.py with examples on how to build evidence strings. This will be updated to the latest schema to reflect the recent changes.

Gautier Koscielny

Copyright 2014-2018 Biogen, Celgene Corporation, EMBL - European Bioinformatics Institute, GlaxoSmithKline, Takeda Pharmaceutical Company and Wellcome Sanger Institute

This software was developed as part of the Open Targets project. For more information please see: http://www.opentargets.org

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.