PubMed MCP Server

by chrismannina

9 stars

384 downloads

Not rated

GitHub

About

A Model Context Protocol (MCP) server that enables AI assistants to search and analyze PubMed medical literature with advanced filtering, citations, and research tools.

Details

Author: chrismannina
GitHub stars: 9
Downloads: 384
Categories: Search

- Advanced PubMed search with date ranges, article types, authors, journals, and MeSH terms
- Retrieve detailed article information including abstracts, authors, and metadata
- Export citations in BibTeX, APA, MLA, Chicago, Vancouver, EndNote, and RIS formats
- Search by author with co‑author information
- Discover related articles and explore MeSH terms
- Analyze publication trends over time and compare multiple articles
- Built‑in caching and configurable rate limiting for respectful API usage

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 MCP Server

Command (node, npx, python, etc.)

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 mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

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 mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

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 mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

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 mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

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 mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

From the repository

Install Python 3.8+, obtain a free NCBI API key and a valid email, clone the repository, install dependencies (pip install -r requirements.txt), configure environment variables in a .env file, then run python -m src.main. Use an MCP client to call tools such as search_pubmed, get_article_details, and export_citations.

Claude Desktop / Cursor

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

{
    "mcpServers": {
        "pubmed mcp server": {
            "pubmed-mcp": {
                "command": "python",
                "args": [
                    "-m",
                    "src.main"
                ]
            }
        }
    }
}

McpServers

{
    "pubmed-mcp": {
        "command": "python",
        "args": [
            "-m",
            "src.main"
        ]
    }
}

PubMed MCP Server

A comprehensive Model Context Protocol (MCP) server for PubMed literature search and management. This server provides advanced search capabilities, citation formatting, and research analysis tools through the MCP protocol.

Features

- Advanced PubMed Search: Search with complex filters including date ranges, article types, authors, journals, and MeSH terms
- Article Details: Retrieve detailed information for specific PMIDs including abstracts, authors, and metadata
- Citation Export: Export citations in multiple formats (BibTeX, APA, MLA, Chicago, Vancouver, EndNote, RIS)
- Author Search: Find articles by specific authors with co-author information
- Related Articles: Discover articles related to a specific PMID
- MeSH Term Search: Search and explore Medical Subject Headings
- Journal Analysis: Get metrics and recent articles from specific journals
- Research Trends: Analyze publication trends over time
- Article Comparison: Compare multiple articles side by side
- Caching: Built-in caching for improved performance
- Rate Limiting: Respectful API usage with configurable rate limits

Installation

Prerequisites

- Python 3.8 or higher
- NCBI API key (free registration required)
- Valid email address for NCBI API identification

Quick Start

1. Clone the repository:

   git clone https://github.com/your-org/pubmed-mcp.git

   cd pubmed-mcp

2. Install dependencies:

   pip install -r requirements.txt

3. Set up environment variables:

   cp env.example .env

   # Edit .env with your NCBI API key and email

4. Run the server:

   python -m src.main

Development Installation

For development with additional tools:

make install-dev

Or manually:

pip install -r requirements.txt
pip install -e .
pip install black isort mypy flake8

Configuration

Create a .env file in the project root with the following variables:

```env

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Details

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Setting up with Highlight

From the repository

Claude Desktop / Cursor

McpServers

PubMed MCP Server

Features

Installation

Prerequisites

Quick Start

Development Installation

Configuration

Install

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