PubMed MCP Server - Remote Edition

A comprehensive Model Context Protocol (MCP) server for PubMed database access, optimized for deployment on render.com and other cloud platforms. This server provides advanced biomedical literature search, retrieval, and analysis capabilities through both local (stdio) and remote (SSE/HTTP) transports.

🚀 Features

🔧 Tools

• search_pubmed: Search PubMed with comprehensive summaries and metadata

• get_full_abstract: Retrieve complete abstracts by PMID

• get_full_text: Extract full text from PMC open access articles

• export_ris: Export citations in RIS format for reference managers

• get_citation_counts: Analyze citation metrics using NCBI elink API

• optimize_search_query: Transform natural language to optimized PubMed queries with MeSH terms

• find_similar_articles: Find similar articles using NCBI's similarity algorithm

• batch_process: Process multiple PMIDs with multiple operations efficiently

🌐 Deployment Modes

• Local Mode: Traditional stdio transport for Claude Desktop

• Remote Mode: SSE/HTTP transport for cloud deployment (render.com, etc.)

📋 Prerequisites

• Node.js v18.x or higher

• npm or yarn package manager

• (Optional) render.com account for cloud deployment

🎯 Installation & Usage

Option 1: Deploy to Render.com (Recommended for Remote Access)

1. Fork or clone this repository

2. Connect to Render.com

   • Sign up at render.com

   • Click "New +" → "Web Service"

   • Connect your GitHub repository

3. Configure Environment Variables in Render dashboard:

   NODE_ENV=production MCP_TRANSPORT=sse PORT=8000 HOST=0.0.0.0 LOG_LEVEL=info NCBI_EMAIL=your-email@example.com

4. Deploy

   • Render will automatically detect render.yaml and deploy

   • Your service URL will be: https://pubmed-mcp-server.onrender.com

5. Add to Claude Desktop

Add to your Claude Desktop configuration:

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

Option 2: Local Installation

1. Clone and install

2. Configure for Local Mode

Add to Claude Desktop configuration:

Option 3: Development Mode

⚙️ Configuration

Environment Variables

Transport Modes

Stdio Mode (Local)

• Traditional MCP transport for local Claude Desktop

• Activated by default or when MCP_TRANSPORT=stdio

• Communication via stdin/stdout

SSE Mode (Remote)

• HTTP/SSE transport for remote deployment

• Activated when MCP_TRANSPORT=sse or --remote flag

• Provides HTTP endpoints:

  • /sse - SSE connection endpoint

  • /health - Health check endpoint

  • /message - Client-to-server messaging

🔍 Example Usage

1. Query Optimization

2. Literature Search

3. Citation Analysis

4. Batch Processing

📊 API Limits

🛡️ Rate Limiting & Best Practices

1. NCBI Guidelines Compliance

   • Always provide a valid email address in NCBI_EMAIL

   • Respect API rate limits (3 requests/second without API key)

   • Use delays between requests (automatically handled)

2. Error Handling

   • Network connectivity issues

   • Invalid PMIDs or queries

   • API timeouts

   • Missing full text content

3. Performance Optimization

   • Use batch processing for multiple articles

   • Cache results when possible

   • Use query optimization for better search results

🏗️ Project Structure

🔧 Development

Build

Run Locally (stdio)

Run as Remote Server (SSE)

Clean Build

🚀 Deployment

Render.com

The repository includes a render.yaml file for automatic deployment:

1. Push your code to GitHub

2. Connect repository to Render

3. Render automatically deploys using render.yaml

4. Update environment variables in Render dashboard

Other Platforms

For deployment to other platforms (Heroku, AWS, DigitalOcean, etc.):

1. Set MCP_TRANSPORT=sse environment variable

2. Set PORT to platform-required value

3. Run npm run build && npm run start:remote

📖 MeSH Term Optimization

The server includes extensive medical term mappings:

• COVID-19 & Vaccines: covid, coronavirus, vaccination

• Cardiovascular: heart attack, myocardial infarction

• Cancer: tumor, oncology, carcinoma

• Mental Health: depression, anxiety

• Study Types: clinical trial, meta-analysis, RCT

• Treatment Types: therapy, surgery, medication

🤝 Contributing

1. Fork the repository

2. Create a feature branch

3. Make your changes

4. Test thoroughly (both local and remote modes)

5. Submit a pull request

📝 Version History

v1.0.2 (Current)

• ✨ Added remote/SSE transport support

• 🌐 Render.com deployment configuration

• 🔧 Environment variable configuration

• 📊 Health check endpoint

• ⚡ Dual mode support (stdio/SSE)

v1.0.1

• 🆕 Similar articles feature

• 📊 Citation analysis improvements

v1.0.0

• 🚀 Initial release

• 📖 Core PubMed functionality

📄 License

MIT License - see LICENSE file for details

🙋‍♂️ Support

For issues or questions:

1. Check existing GitHub issues

2. Create a new issue with detailed description

3. Include error messages and reproduction steps

🔗 Related Resources

• NCBI E-utilities Documentation

• PubMed Search Tips

• Model Context Protocol

• Render.com Docs

• Claude Desktop

🎯 Quick Start Checklist

• Clone repository

• Install dependencies (npm install)

• Build project (npm run build)

• Set NCBI_EMAIL environment variable

• Choose deployment mode (local or remote)

• Configure Claude Desktop

• Test with a simple search query

⚡ Performance Tips

1. Use query optimization for better search results

2. Batch process when analyzing multiple articles

3. Cache results to avoid redundant API calls

4. Monitor rate limits to prevent API throttling

5. Use specific PMIDs when possible for faster retrieval