PubMed MCP Server

A Model Context Protocol (MCP) server for accessing and processing biomedical literature from PubMed. It provides a standardized interface for applications to search, retrieve metadata, download PDFs, and analyze PubMed articles.

Overview

This server implements the MCP standard, allowing AI assistants and other clients to interact with PubMed data programmatically. It is hosted on the Apify platform and is based on the original open-source project from JackKuo666/PubMed-MCP-Server.

Key Features

The server exposes five main tools:

• search_pubmed_key_words: Search PubMed articles using simple keywords.
• search_pubmed_advanced: Perform more complex, field-specific searches.
• get_pubmed_article_metadata: Fetch detailed metadata (title, authors, abstract, journal, etc.) for a specific article by its PubMed ID (PMID).
• download_pubmed_pdf: Download the full-text PDF of an available article.
• deep_paper_analysis: Run an in-depth analysis on a specified paper.

How to Use

Connection

MCP clients connect to the server at the following URL:

https://mcp-servers--pubmed-mcp-server.apify.actor/mcp

Client Configuration

Add the server configuration to your MCP client (e.g., Claude Desktop, Cline). You must provide a valid Apify API token.

{
  "mcpServers": {
    "pubmed": {
      "url": "https://mcp-servers--pubmed-mcp-server.apify.actor/mcp",
      "headers": {
        "Authorization": "Bearer YOUR_APIFY_TOKEN"
      }
    }
  }
}

Note: Replace YOUR_APIFY_TOKEN with your actual token from the Apify Console. For general guidance on connecting to MCP servers, see the official docs at mcp.apify.com.

Input/Output

The tools typically accept parameters like search queries or PubMed IDs (PMIDs) as input. Outputs are structured JSON data containing:

• Search results: Lists of articles with identifiers, titles, and snippets.
• Article metadata: Comprehensive details including authors, publication date, journal, MeSH terms, and the abstract.
• PDF content: The binary PDF file for downloadable articles.
• Analysis results: Structured insights from the deep_paper_analysis tool.

References & Links

• Official MCP Documentation: mcp.apify.com
• Apify Platform Docs: docs.apify.com/platform
• Apify MCP Server Docs: docs.apify.com/platform/integrations/mcp
• Source GitHub Repository: github.com/apify/mcp-servers
• Developer Community: Discord

Server Claim: To claim or manage this server, contact ai@apify.com.