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Schemas of the OpenTargets Platform data models

This repository contains schema definitions of some of the data models the Open Targets Platform deals with. Either as an input or generated as an output.

Folders:

  • /schemas/ - List of schemas in JSON format.
  • /pydantic_models/ - Definitions of the data models using Python's Pydantic tool. jsontopydantic is helpful for the purpose of defining a JSON schema as a Pydantic model. While it may require some customization, it streamlines the majority of the Pydantic boilerplate.

Available schemas

  • TEP.json: description of Target Enabling Packages.
  • chemical_probes.json: description of the chemical probes data model.
  • disease_target_evidence.json: description of disease-target evidence input. Separate schemas are defined for each data sources.
  • target_safety.json: Description of target safety.
  • molecular_interactions.json: definition of the molecular interactions input.
  • molecular_interactions-output.json: Definition for the molecular interactions dataset generated by the Platform ETL.
  • gene-essentiality.json: definition of gene essentiality target annotation. Developed based on DepMap CRISPR/CAS9 screens.

Dev environment set up

# Clone the project
git clone https://github.com/opentargets/json_schema
cd json_schema

# Install Poetry
curl -sSL https://install.python-poetry.org | python -

# Install the project dependencies
poetry install
poetry shell