pubmed-mcp: MCP Server for PubMed

PubMed is a free database maintained by the National Library of Medicine (NLM) at the National Institutes of Health (NIH), offering access to over 30 million citations for biomedical literature.

This is 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

Usage with Claude Code

Node.js v18 or higher is required. Claude Code typically installs Node.js during setup.

Adding pubmed-mcp in project scope

claude mcp add pubmed-mcp \
  --scope project -- \
  npx -y @ncukondo/pubmed-mcp \
  --email [email protected]

The -y option is used to skip the confirmation prompt during the initial installation.
The --scope project option installs the server in project scope, creating a .mcp.json file in the project root to store the MCP server settings.

If you omit --scope project, the server will be installed globally:

claude mcp add pubmed-mcp -- \
  npx -y @ncukondo/pubmed-mcp \
  --email [email protected]

You can also set the email address via the PUBMED_EMAIL environment variable. For better security, consider managing credentials in a .env file.

Adding pubmed-mcp with an API key

Specifying a PubMed API key relaxes PubMed’s request rate limits. Obtain an API key by creating an NCBI account and visiting the API Key Management page:

claude mcp add pubmed-mcp \
  --scope project -- \
  npx -y @ncukondo/pubmed-mcp \
  --email [email protected] \
  --api-key your-ncbi-api-key

Alternatively, set the API key via the PUBMED_API_KEY environment variable. For security reasons, it is recommended to store sensitive information like API keys in a .env file rather than in command line arguments or configuration files.

Enabling caching

Enabling caching returns cached results for identical requests, reducing the number of API calls.

Using command line arguments

claude mcp add pubmed-mcp \
  --scope project -- \
  npx -y @ncukondo/pubmed-mcp \
  --email [email protected] \
  --cache-dir ./pubmed-cache

Use --cache-dir to specify the cache directory, and --cache-ttl to set the cache time-to-live in seconds (default: 1 day / 86400 seconds):

claude mcp add pubmed-mcp \
  --scope project -- \
  npx -y @ncukondo/pubmed-mcp \
  --email [email protected] \
  --cache-dir ./pubmed-cache \
  --cache-ttl 3600

You can also configure caching via environment variables.

• PUBMED_CACHE_DIR: Directory path for caching responses
• PUBMED_CACHE_TTL: Cache time-to-live in seconds (default: 86400)

Configuration via JSON file

Instead of running commands, you can edit the JSON file directly.

• For project scope: edit .mcp.json in the project root.
• For global scope: edit ~/.claude.json.

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

Usage with Claude Desktop

1. Edit Configuration File

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

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

2. Configuration with Caching

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": [
        "-y",
        "@ncukondo/pubmed-mcp",
        "--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/pubmed-mcp

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

Requirements

System Requirements

• Node.js: >= 18
• npm: Latest version recommended

Environment Variables (Recommended)

• PUBMED_EMAIL: Email address recommended by NCBI
• PUBMED_API_KEY: API key for higher rate limits (optional)
• PUBMED_CACHE_DIR: Directory path for caching responses (optional)
• PUBMED_CACHE_TTL: Cache time-to-live in seconds (optional, default: 86400)

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 
cd mcp-server-pubmed
npm install

Development Commands

# Build
npm run build

# Development mode (watch)
npm run dev

# Run tests
npm test

# 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

MIT License