This project contains LinkML representation of Reactome schema and functionality to generate the following from it:
- graph-core Java classes
- GraphQL representation
- JSON schema representation (e.g. in order to validate the syntax of schema.yaml)
- MySQL DDL and data update statements for Reactome MySQL gk_central instance
The virtual environment needed to run the above functionality is as follows:
conda create -n linkml python=3.9
conda activate linkml
pip install linkml
pip install pytz
pip install pyyaml
# The following command displays the available options
./help.py
Please see the presentations under https://github.com/reactome/reactome-schemas/tree/main/doc for more information about the project.