Skip to main content
Glama

PubMed MCP Server

by ncukondo
GitHub
TypeScript
OverviewInspectNewSchemaRelated ServersReviewsScore
Need Help?View Source CodeReport Issue

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 your@email.com

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 your@email.com

You can also set the email address via the PUBMED_EMAIL environment variable.

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 your@email.com \ --api-key your-ncbi-api-key

Alternatively, set the API key via the PUBMED_API_KEY environment variable.

Enabling caching

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

claude mcp add pubmed-mcp \ --scope project npx \ -y @ncukondo/pubmed-mcp \ --email your@email.com \ --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 your@email.com \ --cache-dir ./pubmed-cache \ --cache-ttl 3600

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": "your@email.com" } } } }

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": "your-email@example.com" } } } }

2. Configuration with Caching

{ "mcpServers": { "pubmed": { "command": "npx", "args": [ "-y", "@ncukondo/pubmed-mcp", "--cache-dir", "./cache", "--cache-ttl", "3600" ], "env": { "PUBMED_EMAIL": "your-email@example.com", "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": "your-email@example.com" } } } }

Requirements

System Requirements

  • Node.js: >= 18
  • npm: Latest version recommended
  • PUBMED_EMAIL: Email address recommended by NCBI
  • PUBMED_API_KEY: API key for higher rate limits (optional)

How to Use

Available Tools

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

This server cannot be installed

-
security - not tested
F
license - not found
-
quality - not tested

How are these scores calculated?

remote-capable server

The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.

Enables searching and retrieving scientific articles from PubMed using NCBI E-utilities API with features like rate limiting and caching.

  1. Features
    1. Usage with Claude Code
      1. Adding pubmed-mcp in project scope
      2. Adding pubmed-mcp with an API key
      3. Enabling caching
      4. Configuration via JSON file
    2. Usage with Claude Desktop
      1. 1. Edit Configuration File
      2. 2. Configuration with Caching
      3. 3. Configuration for Globally Installed Version
    3. Requirements
      1. System Requirements
      2. Environment Variables (Recommended)
    4. How to Use
      1. Available Tools
    5. MCP Server Development
      1. Development Environment Setup
      2. Development Commands
      3. Directory Structure
      4. Testing During Development
      5. Debugging
      6. Packaging
    6. Rate Limits
      1. Technical Specifications
        1. License

          Related MCP Servers

          • MCP Scholarly Server

            adityak74
            A
            security
            A
            license
            A
            quality
            Enables users to search for academic articles on platforms like arXiv using specific keywords, with plans to integrate more scholarly databases in the future.
            Last updated -
            2
            139
            Python
            MIT License
            • Apple

          • Academic Paper Search MCP Server

            afrise
            A
            security
            A
            license
            A
            quality
            Enables real-time search and retrieval of academic paper information from multiple sources, providing access to paper metadata, abstracts, and full-text content when available, with structured data responses for integration with AI models that support tool/function calling.
            Last updated -
            3
            58
            Python
            AGPL 3.0

          • PubMed Enhanced Search

            leescot
            -
            security
            F
            license
            -
            quality
            Enables search and retrieval of academic papers from PubMed database with advanced features like MeSH term lookup, publication statistics, and PICO-based evidence search.
            Last updated -
            5
            Python
            • Apple

          • Semantic Scholar MCP Server

            JackKuo666
            -
            security
            F
            license
            -
            quality
            Provides tools for accessing the Semantic Scholar API to search papers, retrieve paper and author details, and fetch citations and references through the Model Context Protocol.
            Last updated -
            23
            Python
            • Apple
            • Linux

          View all related MCP servers

          New MCP Servers

          MCP directory API

          We provide all the information about MCP servers via our MCP API.

          curl -X GET 'https://glama.ai/api/mcp/v1/servers/ncukondo/pubmed-mcp'

          If you have feedback or need assistance with the MCP directory API, please join our Discord server