Getting Started

Installation

Set up OptimusKG with Python, uv, and Docker.

OptimusKG requires Python 3.12 or higher and uses uv as the project manager.

Prerequisites

Python 3.12+
uv - Package and project manager
Docker (optional) - Only required for Neo4j-JSONL export format

Install Dependencies

uv sync --all-groups

This installs all runtime and development dependencies.

Pre-commit Hooks

Install pre-commit hooks for code quality checks:

uv tool run pre-commit install

Verify Installation

uv run kedro info
uv run cli --help

Docker is not required if you don't need to export the graph in Neo4j-JSONL format.

Run make help for a list of available Make commands.

Quickstart

Generate a full biomedical knowledge graph in one command.

On this page

Prerequisites Install Dependencies Pre-commit Hooks Verify Installation