agr-mcp-server

nuin/agr-mcp-server

3.2

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The Alliance of Genome Resources MCP Server provides programmatic access to genomic data, bioinformatics tools, and comparative genomics research capabilities.

Tools

  1. Gene Search

    Search for genes across multiple model organisms.

  2. Orthology Analysis

    Perform cross-species orthology analysis.

  3. Disease Associations

    Study gene-disease associations.

  4. Expression Analysis

    Analyze gene expression data.

  5. BLAST Sequence Analysis

    Perform BLAST searches for sequence analysis.

Alliance of Genome Resources MCP Server

🧬 Organized Alliance of Genome Resources MCP Server Implementation

A comprehensive Model Context Protocol (MCP) server providing programmatic access to the Alliance of Genome Resources genomic data, bioinformatics tools, and comparative genomics research capabilities.

📁 Project Structure

agr-mcp-server/
├── 🚀 src/                     # Core source code
│   ├── agr_server_enhanced.py  # Enhanced MCP server (30+ tools)
│   ├── agr_server_basic.py     # Basic MCP server (10 tools)
│   └── utils.py               # Utilities and configuration
│
├── 📚 examples/               # Usage examples and tutorials
│   ├── basic_examples.py      # Basic usage patterns
│   └── advanced_examples.py   # Advanced genomics workflows
│
├── 🧪 tests/                  # Test suite
│   └── test_agr_server.py     # Comprehensive tests
│
├── ⚙️ config/                # Configuration files
│   ├── development.yaml       # Development environment
│   ├── staging.yaml          # Staging environment
│   ├── production.yaml       # Production environment
│   └── mcp_client_config.json # MCP client configuration
│
├── 🛠️ scripts/               # Utility scripts
│   ├── agr_cli.py            # Command line interface
│   ├── health_check.py       # System health checker
│   ├── quick_start_demo.py   # Interactive demonstration
│   └── deploy.sh             # Deployment automation
│
├── 🐳 docker/               # Docker and deployment files
│   ├── Dockerfile            # Container configuration
│   └── docker-compose.yml    # Multi-service deployment
│
├── 📄 Documentation & Setup
│   ├── README.md             # Comprehensive documentation
│   ├── PROJECT_OVERVIEW.md   # Project summary
│   ├── requirements.txt      # Production dependencies
│   ├── requirements-dev.txt  # Development dependencies
│   ├── setup.py             # Package configuration
│   ├── Makefile             # Development automation
│   ├── .env.example         # Environment template
│   ├── .gitignore           # Git ignore patterns
│   └── LICENSE              # MIT License
│
└── 🔧 .github/              # CI/CD and automation
    └── workflows/
        └── ci.yml           # GitHub Actions pipeline

🚀 Quick Start

Navigate to the Project

cd /Users/nuin/Projects/alliance/agr-mcp-server

Basic Setup

# Create virtual environment
python3 -m venv venv
source venv/bin/activate

# Install dependencies
pip install -r requirements.txt

# Run interactive demo
python scripts/quick_start_demo.py

Try the Enhanced Server

# Start enhanced server (30+ tools)
python src/agr_server_enhanced.py

# Or use the CLI
python scripts/agr_cli.py search BRCA1
python scripts/agr_cli.py gene-info HGNC:1100

Health Check

python scripts/health_check.py

Development with Makefile

# Show all available commands
make help

# Complete development setup
make dev-setup

# Run tests
make test

# Run examples
make examples

# Deploy to development
make deploy-dev

⭐ Key Features

🔬 Core Genomics Functionality (30+ Tools)

  • Gene Search & Discovery across 8+ model organisms
  • Cross-Species Orthology and comparative analysis
  • Disease Associations and clinical relevance data
  • Expression Analysis with visualization-ready data
  • Molecular & Genetic Interactions
  • Allele & Variant Information
  • Functional Annotations (GO terms, pathways)
  • Literature Search with Textpresso integration
  • BLAST Sequence Analysis
  • JBrowse Genome Browser integration

🌍 Model Organisms Supported

  • Homo sapiens (Human) - HGNC identifiers
  • Mus musculus (Mouse) - MGI identifiers
  • Rattus norvegicus (Rat) - RGD identifiers
  • Danio rerio (Zebrafish) - ZFIN identifiers
  • Drosophila melanogaster (Fruit fly) - FlyBase identifiers
  • Caenorhabditis elegans (Roundworm) - WormBase identifiers
  • Saccharomyces cerevisiae (Baker's yeast) - SGD identifiers
  • Xenopus (Frog species) - Xenbase identifiers

🔧 Advanced Capabilities

  • AllianceMine data mining and complex queries
  • Expression Ribbons for visualization
  • Transgenic Models and construct data
  • Experimental Conditions and treatments
  • Pathway Analysis and biological networks
  • Literature Mining and citation management

💻 Usage Examples

Command Line Interface

# Search for genes
python scripts/agr_cli.py search BRCA1 --limit 10

# Get comprehensive gene information  
python scripts/agr_cli.py gene-info HGNC:1100

# Find orthologs across species
python scripts/agr_cli.py orthologs HGNC:1100

# Get disease associations
python scripts/agr_cli.py diseases HGNC:1100

# Search literature
python scripts/agr_cli.py literature "BRCA1 mutations"

# BLAST sequence search
python scripts/agr_cli.py blast ATCGATCGATCG --program blastn

Python API Usage

from src.agr_server_enhanced import EnhancedAGRClient

client = EnhancedAGRClient()

# Search for genes
results = await client.search_genes("BRCA1")

# Get gene information
gene_info = await client.get_gene_info("HGNC:1100")

# Find orthologs
orthologs = await client.find_orthologs("HGNC:1100")

🧪 Testing & Quality

# Run comprehensive tests
python -m pytest tests/test_agr_server.py -v

# Check code quality
make lint

# Run security scan
make security

# Performance test
make test-cov

🐳 Docker Deployment

# Build and run with Docker
cd docker/
docker build -t agr-mcp-server .
docker run -p 8000:8000 agr-mcp-server

# Or use docker-compose
docker-compose up -d

📊 Monitoring & Health

# System health check
python scripts/health_check.py

# Monitor logs (if running with Docker)
docker logs agr-mcp-server

# Check system status
make health-check

⚙️ Configuration

Environment Variables

# Copy and edit environment template
cp .env.example .env

# Key settings
AGR_BASE_URL=https://www.alliancegenome.org/api
AGR_TIMEOUT=30
LOG_LEVEL=INFO

Environment-Specific Configs

  • Development: config/development.yaml
  • Staging: config/staging.yaml
  • Production: config/production.yaml

🤖 Claude Integration

Claude Code Integration

Add the AGR MCP server to Claude Code by updating your configuration file:

Configuration Location:

  • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
  • Linux: ~/.config/claude/claude_desktop_config.json
  • Windows: %APPDATA%\Claude\claude_desktop_config.json

Configuration:

{
  "mcpServers": {
    "agr-genomics-enhanced": {
      "command": "python3",
      "args": ["/Users/nuin/Projects/alliance/agr-mcp-server/src/agr_server_enhanced.py"],
      "cwd": "/Users/nuin/Projects/alliance/agr-mcp-server",
      "env": {
        "VIRTUAL_ENV": "/Users/nuin/Projects/alliance/agr-mcp-server/venv"
      }
    }
  }
}

Usage Examples with Claude Code:

# Natural language queries Claude can now handle:
"Search for BRCA1 genes across all species"
"Find disease associations for TP53"
"Get orthology information for HGNC:1100"
"BLAST this DNA sequence: ATCGATCGATCG"
"Show me expression data for the CFTR gene"

Claude Desktop Integration

Use the same configuration as Claude Code above. After updating the config file, restart Claude Desktop to load the MCP server.

Available Tools: 30+ genomics tools including gene search, disease associations, orthology analysis, BLAST searches, and expression data across 8 model organisms.

🌐 Alliance Integration

This MCP server integrates with the full Alliance ecosystem:

🎯 Use Cases

Research Applications

  • Comparative Genomics: Cross-species gene function analysis
  • Disease Research: Gene-disease association studies
  • Drug Discovery: Target identification and validation
  • Systems Biology: Pathway and network analysis

AI/ML Integration

  • Training Data: Large-scale genomics datasets
  • Feature Engineering: Gene annotations and functional data
  • Knowledge Graphs: Structured biological knowledge
  • Predictive Modeling: Gene function and disease prediction

📞 Support & Resources

  • Project Location: /Users/nuin/Projects/alliance/agr-mcp-server/
  • Documentation: See README.md for comprehensive guides
  • Examples: Check examples/ directory for usage patterns
  • CLI Help: Run python scripts/agr_cli.py --help
  • Health Check: Run python scripts/health_check.py
  • AGR Support: Contact

🏗️ Development

Getting Started

# Clone/navigate to project
cd /Users/nuin/Projects/alliance/agr-mcp-server

# Setup development environment
make dev-setup

# Run examples
make examples

# Start development server
make server-enhanced

Development Commands

make help            # Show all available commands
make test            # Run tests
make lint            # Code quality checks
make format          # Format code
make docs            # Build documentation
make clean           # Clean build artifacts

📈 Production Features

  • High Performance: Async/await architecture, connection pooling
  • Reliability: Comprehensive error handling, health monitoring
  • Security: Input validation, rate limiting, security scanning
  • Scalability: Multi-instance deployment, load balancing
  • Monitoring: Health checks, logging, metrics

🎉 Status: Ready for Use!

✅ FULLY IMPLEMENTED & ORGANIZED

  • Complete MCP server with 30+ genomics tools
  • Organized project structure for maintainability
  • Production-ready deployment options
  • Comprehensive testing and quality assurance
  • Full documentation and examples
  • Multi-environment configuration
  • CI/CD pipeline and automation

Ready for immediate use in genomics research, AI/ML applications, and clinical bioinformatics workflows! 🧬