Gene Curator

A flexible, methodology-agnostic platform for genetic evidence curation and gene-disease validity assessment.

Purpose

Gene Curator enables clinical genetics teams to curate gene-disease associations using any methodology—whether ClinGen SOP, GenCC standards, or institution-specific approaches. The platform ensures scientific rigor through structured evidence capture, automated scoring, peer review workflows, and complete provenance tracking.

Core Capabilities

• Methodology Flexibility: Support for ClinGen, GenCC, or custom curation frameworks through configurable schemas
• Clinical Organization: Scope-based structure for specialty domains (kidney genetics, cardiology, neurology, etc.)
• Quality Assurance: Multi-stage workflow with mandatory peer review (4-eyes principle)
• Evidence Management: Structured capture with real-time validation and automated scoring
• Team Collaboration: Role-based access control with curator workload management
• Scientific Integrity: Complete audit trails with cryptographic record verification

Quick Start

Prerequisites

• Docker and Docker Compose
• Make (optional, for convenience commands)
• Git

Development Setup

1. Clone and start the development environment:

   git clone https://github.com/halbritter-lab/gene-curator.git
   cd gene-curator
   make dev

2. Access the applications:

   • Frontend Application: http://localhost:3051
   • API Documentation: http://localhost:8051/docs
   • Database: localhost:5454 (credentials in docker-compose.dev.yml)

3. Check service health:

   make health

Common Commands

# Environment management
make dev          # Start development environment
make dev-build    # Rebuild and start
make dev-down     # Stop environment
make status       # Show service status

# Database operations
make db-init      # Initialize database with schema and seed data
make db-reset     # Reset database completely

# Code quality
make test         # Run all tests
make lint         # Run linting (backend + frontend)
make format       # Format code (backend + frontend)

How It Works

Multi-Stage Curation Workflow

1. Entry: Genes are assigned to clinical scopes and curators
2. Precuration: Initial disease association assessment with lumping/splitting analysis
3. Curation: Detailed evidence collection following the selected methodology
4. Review: Independent peer review by a different curator (4-eyes principle)
5. Active: Approved curations become the authoritative gene-disease assertion

Methodology Support

Gene Curator adapts to your curation approach through:

• Configurable Schemas: Define evidence fields, validation rules, and scoring logic
• Pluggable Scoring Engines: Built-in support for ClinGen SOP v11, GenCC, and custom algorithms
• Dynamic Forms: UI automatically adapts to your methodology's requirements
• Flexible Workflows: Customize stages, transitions, and approval processes

Default Login Credentials (Development)

• Admin: [email protected] / admin123
• Curator: [email protected] / curator123
• Viewer: [email protected] / viewer123

Architecture

gene-curator/
├── backend/                 # FastAPI + PostgreSQL backend
│   ├── app/api/v1/         # REST API endpoints
│   ├── app/scoring/        # Pluggable scoring engines
│   └── app/tests/          # Test suite
├── frontend/               # Vue 3 + Vite application
│   ├── src/components/     # UI components
│   └── src/stores/         # State management
└── database/sql/           # PostgreSQL schema definitions

Documentation

• API Documentation: http://localhost:8051/docs (interactive OpenAPI)
• Architecture Details: See CLAUDE.md for development guidelines
• Schema Specifications: See plan/SCHEMA_SPECIFICATIONS.md

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

• ClinGen Consortium: For establishing the Gene-Disease Validity Standard Operating Procedures
• GenCC: For the Gene Curation Coalition standards and guidelines
• Scientific Community: For the principles of verifiable, attributable, and replicable genetic curation
• Vue.js & FastAPI Communities: For excellent frameworks that enable rapid development

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Gene Curator - Supporting the future of genetic curation through flexible, methodology-agnostic architecture.