PubMed MCP Server

@JackKuo666

About PubMed MCP Server

🔍 Enable AI assistants to search, access, and analyze PubMed articles through a simple MCP interface.

#pubmed #mcp-server #biomedical-research

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "pubmed": {
      "command": "bash",
      "args": [
        "-c",
        "source /home/YOUR/PATH/mcp-server-pubmed/.venv/bin/activate && python /home/YOUR/PATH/pubmed-mcp-server.py"
      ],
      "env": {},
      "disabled": false,
      "autoApprove": []
    }
  }
}

Tools

No tools detected

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is PubMed MCP Server?

PubMed MCP Server provides a bridge between AI assistants and PubMed’s biomedical literature repository through the Model Context Protocol (MCP). It enables AI models to search for scientific articles, access metadata, and perform deep analysis programmatically.

How to use PubMed MCP Server?

Install Python 3.10+, FastMCP, and other dependencies (requests, beautifulsoup4). Clone the repository, run pip install -r requirements.txt, then start the server with python pubmed_server.py. For desktop clients, configure the MCP server JSON (examples for Claude Desktop and Cline are provided). Alternatively, install automatically via Smithery (commands for Claude, Cursor, Windsurf, CLine).

Key features of PubMed MCP Server

Search PubMed articles using keywords or advanced queries.
Fast retrieval of paper metadata.
Access detailed metadata for specific papers (by PMID).
Attempt to download full-text PDF content.
Perform comprehensive deep paper analysis.
Provide specialized research prompts for paper analysis.
Facilitate biomedical sciences research and analysis.

Use cases of PubMed MCP Server

Query recent PubMed articles on a topic (e.g., CRISPR).
Retrieve metadata for a known paper using its PMID.
Request a deep analysis of a specific paper’s content.
Support literature reviews and biomedical research workflows.

FAQ from PubMed MCP Server

What are the system requirements?

Python 3.10+, FastMCP library, and packages: asyncio, logging, requests, beautifulsoup4.

How do I install the server?

Clone the repository, install dependencies via pip install -r requirements.txt, and run python pubmed_server.py. Optionally, install via Smithery for automated client setup.

What tools does PubMed MCP Server provide?

Five tools: search_pubmed_key_words, search_pubmed_advanced, get_pubmed_article_metadata, download_pubmed_pdf, and deep_paper_analysis.

Can I download full-text PDFs?

The tool download_pubmed_pdf attempts to download the full-text PDF for a PubMed article, but availability depends on PubMed’s access policies.

Is authentication required?

No authentication is mentioned. The server uses public PubMed APIs and respects PubMed’s terms of service.

Frequently asked questions

What are the system requirements?

Python 3.10+, FastMCP library, and packages: asyncio, logging, requests, beautifulsoup4.

How do I install the server?

Clone the repository, install dependencies via `pip install -r requirements.txt`, and run `python pubmed_server.py`. Optionally, install via Smithery for automated client setup.

What tools does PubMed MCP Server provide?

Five tools: `search_pubmed_key_words`, `search_pubmed_advanced`, `get_pubmed_article_metadata`, `download_pubmed_pdf`, and `deep_paper_analysis`.

Can I download full-text PDFs?

The tool `download_pubmed_pdf` attempts to download the full-text PDF for a PubMed article, but availability depends on PubMed’s access policies.

Is authentication required?

No authentication is mentioned. The server uses public PubMed APIs and respects PubMed’s terms of service.

Comments

Basic information

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