MCP Server PubMed

MCP server for searching PubMed scientific articles using NCBI E-utilities API.

Features

• Search PubMed articles with flexible query parameters
• Fetch detailed article information including abstracts, authors, and DOI
• Built-in rate limiting (3 req/s without API key, 10 req/s with API key)
• Caching support for improved performance
• TypeScript implementation with full type safety

Installation

Via npx (Recommended)

No installation required! Use directly:

npx @ncukondo/mcp-server-pubmed --email [email protected]

Global Installation

npm install -g @ncukondo/mcp-server-pubmed

Local Installation

npm install @ncukondo/mcp-server-pubmed

Usage with Claude Code

1. Start the MCP Server

# Basic usage (email required)
npx @ncukondo/mcp-server-pubmed --email [email protected]

# With caching
npx @ncukondo/mcp-server-pubmed --email [email protected] --cache-dir ./cache --cache-ttl 3600

# With environment variables
[email protected] npx @ncukondo/mcp-server-pubmed

2. Connect with Claude Code

Start Claude Code and connect to the MCP server:

claude code --mcp @ncukondo/mcp-server-pubmed

Or set via environment variable:

export MCP_SERVERS="@ncukondo/mcp-server-pubmed"
claude code

Usage with Claude Desktop

1. Edit Configuration File

Edit Claude Desktop's configuration file (~/.claude/claude_desktop_config.json):

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": ["@ncukondo/mcp-server-pubmed"],
      "env": {
        "PUBMED_EMAIL": "[email protected]"
      }
    }
  }
}

2. Configuration with Caching

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": [
        "@ncukondo/mcp-server-pubmed",
        "--cache-dir",
        "./cache",
        "--cache-ttl",
        "3600"
      ],
      "env": {
        "PUBMED_EMAIL": "[email protected]",
        "PUBMED_API_KEY": "your-api-key"
      }
    }
  }
}

3. Configuration for Globally Installed Version

If you've installed globally:

npm install -g @ncukondo/mcp-server-pubmed

{
  "mcpServers": {
    "pubmed": {
      "command": "mcp-server-pubmed",
      "args": ["--cache-dir", "./pubmed-cache"],
      "env": {
        "PUBMED_EMAIL": "[email protected]"
      }
    }
  }
}

Direct JSON Configuration

Minimal Configuration

{
  "mcpServers": {
    "pubmed": {
      "command": "node",
      "args": ["/path/to/mcp-server-pubmed/dist/index.js"]
    }
  }
}

Full Configuration

{
  "mcpServers": {
    "pubmed": {
      "command": "node",
      "args": [
        "/path/to/mcp-server-pubmed/dist/index.js",
        "--cache-dir",
        "/path/to/cache",
        "--cache-ttl",
        "7200"
      ],
      "env": {
        "PUBMED_EMAIL": "[email protected]",
        "PUBMED_API_KEY": "your-ncbi-api-key"
      },
      "cwd": "/path/to/working/directory"
    }
  }
}

Requirements

System Requirements

• Node.js: >= 18
• npm: Latest version recommended
• Memory: Minimum 512MB, recommended 1GB+
• Network: Access to NCBI E-utilities API

Environment Variables (Recommended)

• PUBMED_EMAIL: Email address recommended by NCBI
• PUBMED_API_KEY: API key for higher rate limits (optional)

How to Use

Available Tools

search

Search PubMed articles with query parameters.

Parameters:

• query (required): Search query string
• max_results: Maximum number of results (default: 20)
• sort: Sort order for results

Example usage:

Search for "COVID-19 vaccine efficacy"

fetch_summary

Fetch detailed summary for specific PubMed articles.

Parameters:

• pmids (required): Array of PubMed IDs to fetch

Example usage:

Get detailed information for PMID 12345678

get_full_text

Get full text information for PubMed articles (when available).

Parameters:

• pmids (required): Array of PubMed IDs

MCP Server Development

Development Environment Setup

git clone <repository-url>
cd mcp-server-pubmed
npm install

Development Commands

# Build
npm run build

# Development mode (watch)
npm run dev

# Run tests
npm test

# Test UI
npm run test:ui

# Test (CI)
npm run test:run

Directory Structure

src/
├── index.ts          # Main server file
├── pubmed-api.ts     # PubMed API implementation
├── handlers/         # Request handlers
└── __tests__/        # Test files

Testing During Development

# Start server locally
npm run build
node dist/index.js

# Test with MCP client in another terminal
# Or use Claude Desktop config with "command": "node", "args": ["/absolute/path/to/dist/index.js"]

Debugging

# Start with debug mode
DEBUG=* node dist/index.js

# Debug with caching
DEBUG=* node dist/index.js --cache-dir ./debug-cache --cache-ttl 300

Packaging

# Build for distribution
npm run prepublishOnly

# Verify package
npm pack

Rate Limits

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

NCBI recommends including an email address in requests for better support.

Technical Specifications

• Runtime: Node.js (>=18)
• Language: TypeScript with ES2022 target
• Module System: ESM
• Build Tool: Vite
• Testing: Vitest
• MCP SDK: @modelcontextprotocol/sdk v1.17.1

License

ISC