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Pubmed

The PubMed MCP Server is a bridging service that provides AI assistants with access to the PubMed biomedical literature library via the Model Context Protocol (MCP), supporting literature search, metadata acquisition, and in - depth analysis functions.
Research and dataSearch tools#Literature search#Biomedicine#Metadata#AI analysis.Python
2.5 points
7.4K
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Overview

Installation

Content Details

Alternatives

What is the PubMed MCP Server?

The PubMed MCP Server is a bridging tool that allows AI assistants to search for scientific articles in PubMed, access their metadata, and conduct in - depth analysis through the Model Context Protocol (MCP).

How to use the PubMed MCP Server?

By configuring the AI assistant to support the MCP protocol, you can obtain the latest research papers on PubMed within seconds.

Applicable scenarios

Suitable for researchers, students, and anyone who needs quick access to research materials in the biomedical field.

Main features

Keyword search
Enter keywords to find relevant papers in PubMed.
Advanced search
Use multiple parameters for a more precise search.
Get paper metadata
Retrieve detailed paper metadata based on the PMID.
Download full - text PDF
Attempt to obtain the complete PDF version of the paper.
Deep analysis
Conduct a comprehensive text analysis of the selected paper.
Advantages
Quick access to the PubMed database
Support for multiple search methods
Provision of detailed paper metadata
Promotion of research in the biomedical field
Limitations
May not be able to obtain the full text of all papers
Dependence on the data availability of PubMed

How to use

Install dependencies
Ensure that Python 3.10+ and the FastMCP library are installed.
Start the server
Run the server script to start the service.
Configure the AI assistant
Add the PubMed MCP server address in the AI assistant settings.

Usage examples

Case 1: Search for papers related to CRISPR
Send a request to the AI assistant to find recent research on CRISPR.
Case 2: Get paper metadata
Enter the PMID number to get detailed information about a specific paper.

Frequently Asked Questions

How to install the PubMed MCP Server?
Can I download the full - text PDF of papers?
Is the PubMed MCP Server free to use?

Related resources

GitHub repository
Project source code and documentation
PubMed official website
The official website of PubMed
FastMCP documentation
FastMCP protocol documentation

Installation

Copy the following command to your Client for configuration
{
  "mcpServers": {
    "pubmed": {
      "command": "python",
      "args": ["-m", "pubmed-mcp-server"]
      }
  }
}

{
  "mcpServers": {
    "pubmed": {
      "command": "C:\\Users\\YOUR\\PATH\\miniconda3\\envs\\mcp_server\\python.exe",
      "args": [
        "D:\\code\\YOUR\\PATH\\PubMed-MCP-Server\\pubmed_server.py"
      ],
      "env": {},
      "disabled": false,
      "autoApprove": []
    }
  }
}

{
  "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": []
    }
  }
}
Note: Your key is sensitive information, do not share it with anyone.

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