enzymeml-db

Example: Building and working with an EnzymeML database

The following example demonstrates a practical example of how to build and work with an EnzymeML database. The example is based on the EnzymeML schema and datasets are provided in datasets. The example is based on the following steps:

1. Create tables based on the EnzymeML schema
2. Populate the database with datasets
3. Filter the database based on a query for reactants
4. Extract the corresponding EnzymeMLDocuments

Files to look into

• populate_db.py - Sets up the database and adds datasets found in this example
• Extract.ipynb - Demonstrates how to filter a database and recover documentes

Database setup

This example includes a docker-composerecipe to spawn a new instance of a MySQL database. For this, run the following command:

sudo docker-compose up --build  # Start MySQL database
python populate_db.py           # Populate database