PubMed MCP server

This MCP server provides an interface to search and fetch articles from PubMed, a database containing over 35 million citations for biomedical literature from MEDLINE, life science journals, and online books. It utilizes the pubmedclient Python package to handle search and fetch operations.

Installation

Prerequisites

Before installing the PubMed MCP server, ensure that:

• You have uv installed on your system
• The uvx command is available in your PATH

Configuration

Add the PubMed MCP server to your Claude Desktop configuration by modifying your claude_desktop_config.json file:

{
    "mcpServers": {
        "pubmedmcp": {
            "command": "uvx",
            "args": ["pubmedmcp@latest"],
            "env": {
                "UV_PRERELEASE": "allow",
                "UV_PYTHON": "3.12"
            }
        }
    }
}

PATH Configuration

Since Claude's PATH may differ from your system PATH, you may need to specify the PATH in your configuration file to ensure uvx is accessible:

{
    "mcpServers": {
        "pubmedmcp": {
            "command": "uvx",
            "args": ["pubmedmcp@latest"],
            "env": {
                "UV_PRERELEASE": "allow",
                "UV_PYTHON": "3.12"
            }
        }
    },
    "PATH": "/usr/local/bin:/usr/bin:/bin"
}

Usage

Once configured, Claude can access PubMed through this MCP server. You can:

• Search for biomedical literature using PubMed's database
• Fetch specific articles by their identifiers
• Access article metadata and content

Example Queries

Ask Claude to:

• "Find recent research papers about COVID-19 vaccines"
• "Summarize the latest findings on Alzheimer's disease treatments"
• "Get me the abstract for PubMed ID 12345678"
• "What are the key conclusions from recent studies on gut microbiome and mental health?"

The MCP server will handle the PubMed searches behind the scenes and provide Claude with the relevant biomedical literature.

How to add this MCP server to Cursor

There are two ways to add an MCP server to Cursor. The most common way is to add the server globally in the ~/.cursor/mcp.json file so that it is available in all of your projects.

If you only need the server in a single project, you can add it to the project instead by creating or adding it to the .cursor/mcp.json file.

Adding an MCP server to Cursor globally

To add a global MCP server go to Cursor Settings > MCP and click "Add new global MCP server".

When you click that button the ~/.cursor/mcp.json file will be opened and you can add your server like this:

{
    "mcpServers": {
        "cursor-rules-mcp": {
            "command": "npx",
            "args": [
                "-y",
                "cursor-rules-mcp"
            ]
        }
    }
}

Adding an MCP server to a project

To add an MCP server to a project you can create a new .cursor/mcp.json file or add it to the existing one. This will look exactly the same as the global MCP server example above.

How to use the MCP server

Once the server is installed, you might need to head back to Settings > MCP and click the refresh button.

The Cursor agent will then be able to see the available tools the added MCP server has available and will call them when it needs to.

You can also explictly ask the agent to use the tool by mentioning the tool name and describing what the function does.