alphaCKG (Clemini Edition)

Modernized Clinical Knowledge Graph Updated for Python 3.10+, Neo4j 5.x, and "Batteries Included" ease of use.

🚀 Quick Start (Internal Deployment)

This version is pre-packaged with all required databases and binaries for the Mann Labs HPC cluster.

1. Setup Environment

./install.sh

What this does:

• Creates/Updates the Python virtual environment (venv)
• Verifies local Neo4j and Redis installations (pre-packaged)
• Ensures configuration is correct

2. Start Services

./start.sh start

Services started:

• Web App: http://localhost:5000 (or http://<HOSTNAME>:5000)
• Neo4j Browser: http://localhost:7474 (or http://<HOSTNAME>:7474)
  • User: neo4j
  • Password: ckg_password

📂 Project Structure

• ckg/: Core Source Code - Main Python package.
• data/: Data Storage - Pre-loaded databases, experiments, and ontologies.
• neo4j/: Graph Database - Pre-configured Neo4j 5.x installation.
• redis/: Cache - Pre-compiled Redis server.
• scripts/: Utilities
  • slurm/: HPC job submission scripts.
  • utils/: Maintenance scripts (e.g., database builders).
• docker/: Containerization - Dockerfiles (Legacy/Development).
• legacy_files/: Archive - Old scripts and deprecated tools.
• demo_queries.cypher: Examples - Copy-pasteable Cypher queries for Neo4j.

🔧 Configuration

The system is pre-configured. If you need to change ports or passwords:

• ckg/graphdb_connector/connector_config.yml
• neo4j/neo4j-community-5.26.0/conf/neo4j.conf

📝 Credits

Based on the original MannLabs/CKG. Modernized by Peter, Claude & Gemini.