PubMed Search

by gradusnikov

5 stars

259 downloads

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GitHub

About

Integrates with PubMed database via NCBI E-utilities API to search and retrieve academic papers, including titles, authors, journals, abstracts, and DOIs for biomedical research.

Details

Author: gradusnikov
Repository: gradusnikov/pubmed-search-mcp-server
GitHub stars: 5
Downloads: 259
License: BSD 3-Clause "New" or "Revised" License
Categories: AI, Developer Tools, Search, Infrastructure, Knowledge Base, API, Security

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 PubMed Search

Command (node, npx, python, etc.) mcp
Arguments
- Argument 1 dev
- Argument 2 pubmed_search_mcp_server.py
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": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "bash",
                "-c",
                "source /home/[user]/anaconda3/etc/profile.d/conda.sh && conda activate mcp && mcp run /home/[user]/pubmed-search-mpc-server/pubmed_search_mcp_server.py"
            ],
            "shell": true,
            "command": "wsl.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

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": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "bash",
                "-c",
                "source /home/[user]/anaconda3/etc/profile.d/conda.sh && conda activate mcp && mcp run /home/[user]/pubmed-search-mpc-server/pubmed_search_mcp_server.py"
            ],
            "shell": true,
            "command": "wsl.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

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": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "bash",
                "-c",
                "source /home/[user]/anaconda3/etc/profile.d/conda.sh && conda activate mcp && mcp run /home/[user]/pubmed-search-mpc-server/pubmed_search_mcp_server.py"
            ],
            "shell": true,
            "command": "wsl.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

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": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "bash",
                "-c",
                "source /home/[user]/anaconda3/etc/profile.d/conda.sh && conda activate mcp && mcp run /home/[user]/pubmed-search-mpc-server/pubmed_search_mcp_server.py"
            ],
            "shell": true,
            "command": "wsl.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

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": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "bash",
                "-c",
                "source /home/[user]/anaconda3/etc/profile.d/conda.sh && conda activate mcp && mcp run /home/[user]/pubmed-search-mpc-server/pubmed_search_mcp_server.py"
            ],
            "shell": true,
            "command": "wsl.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

From the repository

1. Start the server in development mode:

   mcp dev pubmed_search_mcp_server.py

2. or add the server to Claude Desktop app CLAUDE_DIRECTORY/claude_desktop_config.json. For example if you are using Windows Subsystem for Linux (WSL) it may look like this:

   "pubmed-search": {
               "command": "wsl.exe",
               "args": [
                   "bash",
                   "-c",
                   "source /home/[user]/anaconda3/etc/profile.d/conda.sh && conda activate mcp && mcp run /home/[user]/pubmed-search-mpc-server/pubmed_search_mcp_server.py"
               ]
           },

To install pubmed-search-mcp-server for Claude Desktop automatically via Smithery:

npx -y @smithery/cli install @gradusnikov/pubmed-search-mcp-server --client claude

1. Clone this repository:

   git clone <repository-url>

   cd pubmed-search-mcp-server

2. Install dependencies:

   pip install fastmcp requests python-dotenv

3. Create a .env file in the project root (if needed for configuration)

Claude Desktop / Cursor

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

{
    "mcpServers": {
        "pubmed search": {
            "env": {},
            "args": [
                "dev",
                "pubmed_search_mcp_server.py"
            ],
            "shell": false,
            "command": "mcp"
        }
    }
}

Linux

{
    "env": [],
    "args": [
        "dev",
        "pubmed_search_mcp_server.py"
    ],
    "shell": false,
    "command": "mcp"
}

Macos

{
    "env": [],
    "args": [
        "dev",
        "pubmed_search_mcp_server.py"
    ],
    "shell": false,
    "command": "mcp"
}

Windows

{
    "env": [],
    "args": [
        "bash",
        "-c",
        "source /home/[user]/anaconda3/etc/profile.d/conda.sh && conda activate mcp && mcp run /home/[user]/pubmed-search-mpc-server/pubmed_search_mcp_server.py"
    ],
    "shell": true,
    "command": "wsl.exe"
}

PubMedSearch MCP Server

A Model Content Protocol server that provides tools to search and retrieve academic papers from PubMed database.

Features

- Search PubMed by keywords in title/abstract or author names
- Retrieve detailed information including title, authors, journal, abstract, DOI and more

Installing via Smithery

To install pubmed-search-mcp-server for Claude Desktop automatically via Smithery:

npx -y @smithery/cli install @gradusnikov/pubmed-search-mcp-server --client claude

Installing Manually

1. Clone this repository:

   git clone <repository-url>
   cd pubmed-search-mcp-server

2. Install dependencies:

   pip install fastmcp requests python-dotenv

3. Create a .env file in the project root (if needed for configuration)

Usage

1. Start the server in development mode:

   mcp dev pubmed_search_mcp_server.py

2. or add the server to Claude Desktop app CLAUDE_DIRECTORY/claude_desktop_config.json. For example if you are using Windows Subsystem for Linux (WSL) it may look like this:

   "pubmed-search": {
               "command": "wsl.exe",
               "args": [
                   "bash",
                   "-c",
                   "source /home/[user]/anaconda3/etc/profile.d/conda.sh && conda activate mcp && mcp run /home/[user]/pubmed-search-mpc-server/pubmed_search_mcp_server.py"
               ]
           },

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About

Details

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Setting up with Highlight

From the repository

Claude Desktop / Cursor

Linux

Macos

Windows

PubMedSearch MCP Server

Features

Installing via Smithery

Installing Manually

Usage

Install

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