BioC PMC MCP Server

A Model Context Protocol (MCP) server for accessing PMC Open Access articles in BioC format. This package provides seamless integration with AI assistants and research tools through the MCP protocol.

✨ Features

• 🔬 PMC Article Access - Access full-text articles from PMC Open Access collection
• 📦 Batch Download - Download multiple articles with concurrency control
• 🎯 Multiple ID Support - Support for both PubMed ID and PMC ID
• 📄 Format Flexibility - Support for XML and JSON formats
• 🌐 Encoding Options - Unicode and ASCII encoding support
• ⚡ Fast Response - 30-second timeout with optimized performance
• 🛡️ Robust Error Handling - Comprehensive error management
• 📊 Detailed Logging - Debug-friendly logging system
• 🔧 Easy Integration - Simple MCP protocol implementation

🚀 Quick Start

Installation

npm install -g bioc-pmc-mcp

Usage

As a Global Command

bioc-pmc-mcp

As an MCP Server

The server will start and listen for MCP protocol messages via stdio.

Integration with Claude Desktop

To use this MCP server with Claude Desktop, add the following to your Claude Desktop configuration file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "bioc-pmc-mcp": {
        "command": "npx",
        "args": ["-y", "bioc-pmc-mcp"]
    }
  }
}

After adding this configuration, restart Claude Desktop and you'll be able to access PMC articles directly through the MCP interface.

Development Installation

cd bioc-pmc-mcp
npm install
npm start

📖 Usage

MCP Tool Integration

The server provides four tools for accessing PMC articles:

1. get_article - Get Single Article

Parameters:

• id (string, required): PubMed ID or PMC ID (e.g., 17299597 or PMC1790863)
• format (string, optional): Data format ("xml" or "json"), default "json"
• encoding (string, optional): Encoding format ("unicode" or "ascii"), default "unicode"

Example:

{
  "name": "get_article",
  "arguments": {
    "id": "17299597",
    "format": "json",
    "encoding": "unicode"
  }
}

2. batch_download - Batch Download Articles

Parameters:

• ids (array, required): Array of article IDs
• format (string, optional): Data format, default "json"
• encoding (string, optional): Encoding format, default "unicode"
• concurrency (number, optional): Number of concurrent requests, default 5
• delay (number, optional): Delay between requests in milliseconds, default 100

Example:

{
  "name": "batch_download",
  "arguments": {
    "ids": ["17299597", "PMC1790863"],
    "format": "json",
    "encoding": "unicode",
    "concurrency": 3,
    "delay": 200
  }
}

3. get_article_info - Get Article Information

Parameters:

• id (string, required): PubMed ID or PMC ID

Example:

{
  "name": "get_article_info",
  "arguments": {
    "id": "17299597"
  }
}

4. validate_id - Validate Article ID

Parameters:

• id (string, required): Article ID to validate

Example:

{
  "name": "validate_id",
  "arguments": {
    "id": "17299597"
  }
}

Response Format:

{
  "success": true,
  "id": "17299597",
  "format": "json",
  "encoding": "unicode",
  "data": {
    // BioC format article data
  }
}

🔧 Technical Details

• Timeout: 30 seconds
• Headers: Automatic Content-Type and User-Agent
• Error Handling: Distinguishes between network, API, and timeout errors
• Logging: Detailed request and response logging
• Concurrency Control: Configurable concurrent request limits
• Rate Limiting: Configurable delays between requests

🛠️ Error Handling

The server handles the following error types:

• Timeout Errors: Requests exceeding 30 seconds
• Network Errors: Unable to connect to API server
• API Errors: Server returning error status codes (404, 400, 500+)
• Parameter Errors: Missing required parameters or incorrect types
• ID Validation Errors: Invalid article ID formats

🧪 Testing

Run the test suite:

npm test

This will test:

• API connectivity
• Parameter validation
• Error handling
• Batch download functionality

📁 Project Structure

├── server.js              # Main server file
├── package.json           # Project configuration and dependencies
├── README.md             # Project documentation
├── LICENSE               # MIT License
├── INSTALLATION.md       # Installation guide
├── CLAUDE_INTEGRATION.md # Claude Desktop integration guide
├── mcp-config-example.json # MCP configuration example
└── test/
    └── test-api.js       # Test suite