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NCBI Gene MCP Server

by mohammadnajeeb
GitHub
Python
MIT License
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NCBI Gene MCP Client

🧬 MCP client for fetching gene and protein metadata from NCBI Entrez API

This project provides a Model Context Protocol (MCP) client that interfaces with the NCBI Entrez API to fetch detailed information about genes and proteins. It's designed to be used both as a standalone command-line tool and as an MCP server for integration with MCP-compatible clients.

🚀 Features

  • Gene Search: Search for genes using flexible queries
  • Gene Information: Fetch detailed gene metadata by NCBI Gene ID
  • Protein Information: Fetch protein details by NCBI Protein ID
  • Symbol Search: Search genes by symbol with optional organism filtering
  • Rate Limiting: Built-in respect for NCBI API rate limits
  • MCP Server: JSON-RPC server for MCP protocol integration
  • CLI Interface: Easy-to-use command-line interface

📦 Installation

From Source (Development)

# Clone the repository git clone <repository-url> cd ncbi_gene_mcp_client # Install in development mode pip install -e .

From PyPI (when available)

pip install ncbi_gene_mcp_client

🔧 Usage

Command Line Interface

After installation, you can use the CLI commands:

Demo (Quick Start)
ncbi-gene-client demo
Search for genes
ncbi-gene-client search-genes "BRCA1" ncbi-gene-client search-genes "breast cancer" --max-results 10
Get gene information by ID
ncbi-gene-client gene-info 672 # BRCA1 gene
Search by gene symbol
ncbi-gene-client search-symbol BRCA1 --organism human ncbi-gene-client search-symbol TP53
Get protein information
ncbi-gene-client protein-info <protein_id>
ncbi-gene-client --email your@email.com --api-key YOUR_API_KEY demo

Python API

from ncbi_gene_mcp_client.main import NCBIGeneMCPClientBridge # Initialize the client client = NCBIGeneMCPClientBridge( email="your@email.com", # Recommended by NCBI api_key="your_api_key" # Optional, for higher rate limits ) # Search for genes results = client.search_genes("BRCA1[gene] AND human[organism]") print(f"Found {results.count} genes") # Get detailed gene information gene_info = client.fetch_gene_info("672") # BRCA1 print(f"Gene: {gene_info.name}") print(f"Description: {gene_info.description}") print(f"Organism: {gene_info.organism}") # Search by gene symbol genes = client.search_by_gene_symbol("BRCA1", organism="human") for gene in genes: print(f"{gene.name}: {gene.description}")

MCP Server

Run as an MCP server for integration with MCP-compatible clients:

ncbi-gene-mcp-server

The MCP server provides the following tools:

  • search_genes: Search for genes using a query
  • fetch_gene_info: Get detailed gene information by ID
  • fetch_protein_info: Get protein information by ID
  • search_by_gene_symbol: Search genes by symbol with optional organism filter

🧪 Examples

from ncbi_gene_mcp_client.main import NCBIGeneMCPClientBridge client = NCBIGeneMCPClientBridge() # Search for BRCA1 gene results = client.search_genes("BRCA1") print(f"Found {results.count} results") # Get details for the first result if results.ids: gene_info = client.fetch_gene_info(results.ids[0]) print(f"Gene: {gene_info.name}") print(f"Chromosome: {gene_info.chromosome}")
# Search for genes related to a disease results = client.search_genes("diabetes[disease] AND human[organism]") for gene_id in results.ids[:5]: # First 5 results gene = client.fetch_gene_info(gene_id) print(f"{gene.name}: {gene.description}")

Example 3: Cross-species Gene Comparison

# Compare BRCA1 across species for organism in ["human", "mouse", "rat"]: genes = client.search_by_gene_symbol("BRCA1", organism=organism) if genes: gene = genes[0] print(f"{organism}: {gene.name} on chromosome {gene.chromosome}")

📊 Data Models

GeneInfo

{ "gene_id": "672", "name": "BRCA1", "description": "BRCA1 DNA repair associated", "organism": "Homo sapiens", "chromosome": "17", "map_location": "17q21.31", "gene_type": "protein-coding", "other_aliases": ["BRCAI", "BRCC1", "BROVCA1"], "summary": "This gene encodes a 190 kD nuclear phosphoprotein..." }

SearchResult

{ "count": 1, "ids": ["672"], "query_translation": "BRCA1[gene]" }

⚙️ Configuration

NCBI API Guidelines

It's recommended to provide your email address when using the NCBI API:

client = NCBIGeneMCPClientBridge(email="your@email.com")

For higher rate limits, you can also provide an API key:

client = NCBIGeneMCPClientBridge( email="your@email.com", api_key="your_ncbi_api_key" )

Rate Limiting

The client automatically handles NCBI's rate limiting requirements:

  • Without API key: 3 requests per second
  • With API key: 10 requests per second

🧪 Testing

Run the test suite:

# Install test dependencies pip install -e ".[dev]" # Run tests pytest # Run with coverage pytest --cov=ncbi_gene_mcp_client # Run integration tests (requires internet) pytest -m integration

🔍 Development

Setting up for development

# Clone and install in development mode git clone <repository-url> cd ncbi_gene_mcp_client pip install -e ".[dev]" # Run linting flake8 ncbi_gene_mcp_client/ mypy ncbi_gene_mcp_client/ # Format code black ncbi_gene_mcp_client/

Project Structure

ncbi_gene_mcp_client/ ├── ncbi_gene_mcp_client/ │ ├── __init__.py │ ├── main.py # Main client class │ ├── bridge.py # NCBI API bridge │ ├── models.py # Data models │ ├── mcp_server.py # MCP server implementation │ └── cli.py # Command-line interface ├── tests/ │ ├── __init__.py │ └── test_main.py # Test suite ├── pyproject.toml # Project configuration ├── README.md # This file └── LICENSE # MIT License

📝 NCBI Resources

📄 License

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

👨‍💻 Author

Mohammad Najeeb
📧 mona00002@uni-saarland.de

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Features

  • Feature 1: Description of feature 1
  • Feature 2: Description of feature 2
  • Feature 3: Description of feature 3
  • MCP Integration: Full Model Context Protocol server implementation

API Methods

Core Methods

  • method1(): Description of method1
  • method2(): Description of method2
  • method3(): Description of method3

Configuration

The package uses a configuration class for settings:

from ncbi_gene_mcp_client.main import NCBIGeneMCPClientConfig, NCBIGeneMCPClientBridge config = NCBIGeneMCPClientConfig( base_url="https://api.example.com", api_key="your_api_key", timeout=30.0 ) bridge = NCBIGeneMCPClientBridge(config)

MCP Server Configuration

To use the MCP server with an MCP client, configure it as follows:

{ "mcpServers": { "ncbi_gene_mcp_client": { "command": "ncbi_gene_mcp_client-server", "env": {} } } }

The server will automatically handle:

  • JSON-RPC communication
  • Tool discovery and invocation
  • Error handling and reporting

Development

Setup Development Environment

# Install in development mode with dev dependencies pip install -e .[dev] # Run tests pytest # Format code black ncbi_gene_mcp_client/ # Type checking mypy ncbi_gene_mcp_client/

Project Structure

ncbi_gene_mcp_client/ ├── pyproject.toml # Package configuration ├── README.md # This file ├── LICENSE # MIT License ├── ncbi_gene_mcp_client/ # Main package │ ├── __init__.py # Package initialization │ ├── main.py # Core functionality │ └── mcp_server.py # MCP server implementation └── tests/ # Test files ├── __init__.py └── test_main.py # Tests for main functionality

License

MIT License - see LICENSE file for details.

Contributing

  1. Fork the repository
  2. Create a feature branch
  3. Make your changes
  4. Add tests
  5. Run the test suite
  6. Submit a pull request

Support

For issues and questions, please use the GitHub issue tracker.

Install Server
A
security – no known vulnerabilities
A
license - permissive license
A
quality - confirmed to work

How are these scores calculated?

remote-capable server

The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.

Tools

MCP server that interfaces with the NCBI Entrez API to fetch detailed information about genes and proteins, enabling gene searches, gene/protein metadata retrieval, and symbol searching with organism filtering.

  1. 🚀 Features
    1. 📦 Installation
      1. From Source (Development)
      2. From PyPI (when available)
    2. 🔧 Usage
      1. Command Line Interface
      2. Python API
      3. MCP Server
    3. 🧪 Examples
      1. Example 1: Basic Gene Search
      2. Example 2: Disease Gene Search
      3. Example 3: Cross-species Gene Comparison
    4. 📊 Data Models
      1. GeneInfo
      2. SearchResult
    5. ⚙️ Configuration
      1. NCBI API Guidelines
      2. Rate Limiting
    6. 🧪 Testing
      1. 🔍 Development
        1. Setting up for development
        2. Project Structure
      2. 📝 NCBI Resources
        1. 📄 License
          1. 👨‍💻 Author
            1. 🤝 Contributing
              1. Features
                1. API Methods
                  1. Core Methods
                  2. Configuration
                2. MCP Server Configuration
                  1. Development
                    1. Setup Development Environment
                    2. Project Structure
                  2. License
                    1. Contributing
                      1. Support

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