gfe-db

Graph database representing IPD-IMGT/HLA sequence data as GFE.

The gfe-db represents IPD-IMGT/HLA sequence data as GFE nodes and relationships in a Neo4j graph database. This application deploys and configures AWS resources for the GFE database and an automated data pipeline for updates.

Check out the source on GitHub.

Table of Contents

• Introduction
  • Gene Feature Enumeration
    • Approach
    • References
  • Architecture
    • Base Infrastructure
    • Database
    • Data Pipeline
• Usage
  • Deployment to AWS
    • Quick Start
    • Prerequisites
    • Environment
    • Makefile Usage
    • Deploying Configuration Files
    • Clean Up
  • Loading Releases
    • Input Parameters
    • Pipeline Execution
    • Retrieving logs, data and parameters
  • Developing Locally
    • Creating a Python Virtual Environment
• Reference
  • GFE Graph
    • GFE nodes
    • Feature nodes
    • Sequence nodes
    • IPD_Allele nodes
    • IPD_ACC nodes
    • Submitter nodes
    • HAS_FEATURE edges
    • HAS_SEQUENCE edges
    • HAS_IPD_Allele edges
    • HAS_IPD_Allele edges
    • SUBMITTED edges
    • Breaking down a GFE
  • Service Configurations
    • Graph Database
    • Data Pipeline
    • Logging
  • Makefile Command Reference
    • Deploy to AWS
    • Load releases
    • Retrieve logs, data and configuration values
    • Tear down infrastructure