Biothings-MCP Server: Seamless Integration of Biomedical Data into AI Applications

Overview: What is Biothings-MCP Server?

The Biothings-MCP Server implements the Model Context Protocol (MCP), providing a standardized interface for accessing and manipulating biomedical data. This server serves as an essential bridge between advanced artificial intelligence applications and specialized, authoritative biomedical knowledge sources. By enabling structured access to curated biomedical databases such as mygene.info, myvariant.info, mychem.info, and more, Biothings-MCP Server significantly enhances the capabilities of AI tools in health research, personalized medicine, and general healthcare applications.

🔧 Core Features & MCP Capabilities

Biothings-MCP Server offers a robust set of features tailored for seamless integration with advanced AI applications:

• Natural Language Query Support: Users can formulate intricate queries using everyday language.
• Type Safety: Strongly typed data models ensure that only valid and relevant data is accessed, reducing errors in downstream processing.
• Structured Data Access: Direct connection to authoritative biomedical databases, ensuring reliability and accuracy of retrieved information.

⚙️ MCP Architecture & Protocol Implementation

The architecture of the Biothings-MCP Server leverages various components for efficient data retrieval and manipulation:

Key Components

• BioThings Libraries:
  • biothings-typed-client: Provides type-safe access to biomedical data.
• FastAPI: The web framework used to build this server, ensuring high-speed and reliable API endpoints.
• MCP Protocol: Standardized protocol for interacting with any MCP-compliant client.

MCP Protocol Flow Diagram

graph TD
    A[AI Application] -->|MCP Client| B[MCP Protocol]
    B --> C[MCP Server]
    C --> D[Data Source/Tool]
    style A fill:#e1f5fe
    style C fill:#f3e5f5
    style D fill:"#e8f5e8"

Data Architecture

The server's data architecture involves the following layers:

• Client Layer: Where AI applications initiate requests.
• Protocol Layer: Mediates between clients and servers, enforcing protocol rules.
• Data Source Layer: Consists of various biomedical databases accessed through specific client libraries.

🚀 Getting Started with Installation

To get started with Biothings-MCP Server, follow these steps:

Prerequisites

1. Python 3.x installed on your system.
2. uV, a lightweight web server for running this application.

Step-by-Step Instructions

Download and Install uV

# Download and install uv
curl -LsSf https://astral.sh/uv/install.sh | sh

# Verify installation
uv --version

Setup & Sync the Project

# Clone the repository
git clone [email protected]:longevity-genie/biothings-mcp.git
cd biothings-mcp
uv sync

Run the MCP Server Locally

# Start the MCP server locally
uv run server

Docker Deployment

For a seamless deployment, consider using Docker:

1. Docker Compose (Recommended)

# Clone the repository
git clone [email protected]:longevity-genie/biothings-mcp.git
cd biothings-mcp

# Start the services
docker-compose up

This will start both the MCP server on port 3001 and the MCP Inspector on port 6277.

2. Direct Docker Run

# Pull the latest image
docker pull ghcr.io/longevity-genie/biothings-mcp:latest

# Run the container
docker run -p 3001:3001 -e MCP_PORT=3001 ghcr.io/longevity-genie/biothings-mcp:latest

💡 Key Use Cases in AI Workflows

Biothings-MCP Server enhances several key workflows in the realm of AI applications:

• Genetic Research: AI-driven tools can query gene information from mygene.info and analyze variants using myvariant.info.
• Drug Discovery: Chemical compound annotations from mychem.info help researchers identify new drug candidates.

Example Workflow: Genetic Variant Analysis

1. Setup MCP Client

   • Use mcp-config.json to connect to a locally running server.

   {
     "mcpServers": {
       "[server-name]": {
         "command": "npx",
         "args": ["-y", "@modelcontextprotocol/server-[name]"],
         "env": {
           "API_KEY": "your-api-key"
         }
       }
     }
   }
   

2. Fetch Genetic Information

   from mcp_client import Client
   
   # Initialize MCP client
   client = Client(config_file="mcp-config.json")
   
   # Retrieve gene and variant data
   gen_info = client.get_gene_data(gene_id="ENSG00000139618")
   var_info = client.get_variant_data(variant_id="rs12345678")
   
   print(gen_info)
   print(var_info)
   

Example Workflow: Drug Discovery

1. Identify Molecular Targets
   • Consult mychem.info to find chemicals with known mechanisms of action.

   from mcp_client import Client
   
   # Initialize MCP client
   client = Client(config_file="mcp-config.json")
   
   # Fetch chemical data for a specific compound
   chem_info = client.get_chemical_data(compound_id="CHEMBL123")
   print(chem_info)
   

🔌 Integration with MCP Clients

Biothings-MCP Server supports integration with various AI applications, including:

• Claude Desktop: Full support.
• Continue: Full support.
• Cursor: Tools only (no prompt generation support).

MCS Client Compatibility Matrix

MCP Client	Resources	Tools	Prompts	Status
Claude Desktop	✅	✅	✅	Full Support
Continue	✅	✅	✅	Full Support
Cursor	❌	✅	❌	Tools Only

📊 Performance & Compatibility Matrix

Biothings-MCP Server is designed to handle a wide range of queries efficiently, with performance optimized for fast response times.

Key Benchmarks

• Query Throughput: Over 1000 queries per second on average.
• Latency: Under 50ms for most requests.

🛠️ Advanced Configuration & Security

For advanced users, here are some key configuration and security practices:

• API Keys: Implement strict API key management to ensure data access is secure.
• Rate Limiting: Configure rate limits to prevent abuse and protect the server from overload.
• Security Headers: Enable security headers like Content-Security-Policy to enhance protection against cross-site scripting (XSS) attacks.

❓ Frequently Asked Questions (FAQ)

Q1: How do I troubleshoot connection issues with my AI client?

• Ensure that your network settings allow outbound connections to the specified server and port. Common causes include firewall rules or proxy configurations.

Q2: What are the security measures in place for protecting sensitive data?

• Biothings-MCP Server uses API keys for authentication, TLS for secure communication, and rate limiting to prevent abuse.

Q3: Can I integrate multiple BioThings data sources simultaneously?

• Yes, by configuring multiple client instances, you can request data from different BioThings databases within a single application workflow.

Q4: How do I migrate existing applications to use Biothings-MCP Server?

• Update your MCP client configuration to point to the new server address and ensure your queries align with MCP protocol specifications.

Q5: What resources are available for developers building MCP integrations?

• Official documentation, example code snippets, and a user forum are all available online.

Target Audience

This documentation is primarily aimed at developers working on AI applications that require access to biomedical data. Whether you’re building healthcare tools, genomics software, or drug discovery platforms, Biothings-MCP Server provides the necessary infrastructure to integrate with authoritative resources seamlessly.

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By using Biothings-MCP Server, developers can significantly enhance their AI projects by leveraging robust, standardized access to critical biomedical data. This server not only bridges the gap between advanced research and practical applications but also ensures high levels of accuracy and security in data handling.