Simple PubMed

by andybrandt

67 stars

12.9k downloads

Not rated

GitHub

About

Access PubMed's medical research database via the Entrez API for biomedical literature search and analysis.

Details

Author: andybrandt
Repository: andybrandt/mcp-simple-pubmed
GitHub stars: 67
Downloads: 12,912
License: MIT License
Categories: Database, Other, Knowledge Base, AI, Design, Developer Tools, Search, Infrastructure
Tags: #mobile

- Search PubMed using keywords, MeSH terms, author names, and Boolean operators.
- Retrieve full text for open-access articles in PubMed Central.
- Access article abstracts and metadata via resource URIs.
- Pre-built MCP prompts for systematic reviews, PICO searches, and author searches.
- Returns an XML-ized version of full text for structured readability by AI.

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below
Plugin Name Simple PubMed

Command (node, npx, python, etc.) python
Arguments
- Argument 1 -m
- Argument 2 mcp_simple_pubmed
Environment
- PUBMED_EMAIL your-email@example.com
- PUBMED_API_KEY your-api-key
Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

From the repository

The server requires the following environment variables:

- PUBMED_EMAIL: Your email address (required by NCBI)
- PUBMED_API_KEY: Optional API key for higher rate limits

The standard rate limit is 3 requests / second. No rate limiting was implemented, as it is highly unlikely in the typical usage scenario that your AI would generate more traffic. If you need it, you can register for an API key which will give you 10 requests / second. Read about this on NCBI pages.

To install Simple PubMed for Claude Desktop automatically via Smithery:

npx -y @smithery/cli install mcp-simple-pubmed --client claude

pip install mcp-simple-pubmed

Add to your Claude Desktop configuration (claude_desktop_config.json):

(Mac OS)

{
  "mcpServers": {
    "simple-pubmed": {
      "command": "python",
      "args": ["-m", "mcp_simple_pubmed"],
      "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key" 
      }
    }
  }
}

(Windows)

{
  "mcpServers": {
    "simple-pubmed": {
      "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe",
      "args": [
        "-m",
        "mcp_simple_pubmed"
      ],
      "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key" 
      }
    }
  }
}

`Search PubMed`

Search the database using keywords, MeSH terms, author names, date ranges, and Boolean operators.

`Get Full Text`

Download full text when available (for open access articles in PubMed Central).

`Access Abstracts`

Retrieve article abstracts and metadata via resource URIs.

`Systematic Review Search`

Generate comprehensive search strategies with MeSH terms, synonyms, and date filters for systematic reviews.

`PICO Search`

Build clinical question searches using the PICO framework (Population, Intervention, Comparison, Outcome).

`Author Search`

Find all publications by a specific author with proper name formatting.

- Search PubMed - Search the database using keywords, MeSH terms, author names, date ranges, and Boolean operators
- Get Full Text - Download full text when available (for open access articles in PubMed Central)
- Access Abstracts - Retrieve article abstracts and metadata via resource URIs

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "simple pubmed": {
            "env": {
                "PUBMED_EMAIL": "your-email@example.com",
                "PUBMED_API_KEY": "your-api-key"
            },
            "args": [
                "-m",
                "mcp_simple_pubmed"
            ],
            "command": "python"
        }
    }
}

Linux

{
    "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key"
    },
    "args": [
        "-m",
        "mcp_simple_pubmed"
    ],
    "command": "python"
}

Macos

{
    "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key"
    },
    "args": [
        "-m",
        "mcp_simple_pubmed"
    ],
    "command": "python"
}

Windows

{
    "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key"
    },
    "args": [
        "-m",
        "mcp_simple_pubmed"
    ],
    "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
}

MCP Simple PubMed

An MCP server that provides access to PubMed articles through the Entrez API.

Features

Tools

- Search PubMed - Search the database using keywords, MeSH terms, author names, date ranges, and Boolean operators - Get Full Text - Download full text when available (for open access articles in PubMed Central) - Access Abstracts - Retrieve article abstracts and metadata via resource URIs

Prompts (New in v0.1.14)

MCP Prompts help you construct effective PubMed searches:

- Systematic Review Search - Generate comprehensive search strategies with MeSH terms, synonyms, and date filters for systematic reviews
- PICO Search - Build clinical question searches using the PICO framework (Population, Intervention, Comparison, Outcome)
- Author Search - Find all publications by a specific author with proper name formatting

These prompts guide the AI to build optimized PubMed queries, making it easier to conduct thorough literature searches.

Notes

Please note that the tool returns XML-ized version of full text. It is however more useful for AIs than a "human readable" text would have been as it gives them additional information about document's structure. At least, this is what Claude 3.5 Sonnet said he prefers.

Please also note that inability of this tool and possibly other tools to deliver a paper's full text may not be due to the fact that it is not available. When testing this tool I came across a paper that did not have full text on PubMed and when Claude accessed the publication URL (which we did get through DOI) using fetch he did get a "forbidden” error. However, I was able to access the very same page using a regular browser.

In other words if your AI assistant is not able to get the full text of a paper using this tool it is worth trying manually with a regular web browser.

Finally, this tool of course can’t give you access to paywalled/paid papers. You may be able to read them through your library access or – as a last resort – through a certain site that strives to make publicly funded research freely available.

Installation

Installing via Smithery

To install Simple PubMed for Claude Desktop automatically via Smithery:

npx -y @smithery/cli install mcp-simple-pubmed --client claude

Manual Installation

pip install mcp-simple-pubmed

Configuration

The server requires the following environment variables:

- PUBMED_EMAIL: Your email address (required by NCBI)
- PUBMED_API_KEY: Optional API key for higher rate limits

Usage with Claude Desktop

Add to your Claude Desktop configuration (claude_desktop_config.json):

(Mac OS)

{
  "mcpServers": {
    "simple-pubmed": {
      "command": "python",
      "args": ["-m", "mcp_simple_pubmed"],
      "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key" 
      }
    }
  }
}

(Windows)

{
  "mcpServers": {
    "simple-pubmed": {
      "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe",
      "args": [
        "-m",
        "mcp_simple_pubmed"
      ],
      "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key" 
      }
    }
  }
}

macOS SSL Certificate Fix

If you encounter SSL certificate verification errors on macOS (such as [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate in certificate chain), you need to install the proper certificate bundle:

/Applications/Python\ 3.13/Install\ Certificates.command

Replace 3.13 with your Python version number. This script comes with Python installations from python.org.

You can also run it from the Finder:

If you perform this change while Claude Desktop is open you will need to quit it and start it again for it to take effect.

License

MIT License

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About

Details

Jump to

Setting up with Highlight

From the repository

Search PubMed

Get Full Text

Access Abstracts

Systematic Review Search

PICO Search

Author Search

Claude Desktop / Cursor

Linux

Macos

Windows

MCP Simple PubMed

Features

Tools

Prompts (New in v0.1.14)

Notes

Installation

Installing via Smithery

Manual Installation

Configuration

Usage with Claude Desktop

macOS SSL Certificate Fix

License

Install

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`Search PubMed`

`Get Full Text`

`Access Abstracts`

`Systematic Review Search`

`PICO Search`

`Author Search`