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:

# Required
PUBMED_API_KEY=your_ncbi_api_key_here
PUBMED_EMAIL=your.email@example.com

# Optional
CACHE_TTL=300
CACHE_MAX_SIZE=1000
RATE_LIMIT=3.0
LOG_LEVEL=info

Getting an NCBI API Key

1. Visit NCBI Account Settings
2. Sign in or create an account
3. Navigate to "API Key Management"
4. Create a new API key
5. Copy the key to your .env file

Usage

Available Tools

The server provides the following MCP tools:

1. search_pubmed

Search PubMed with advanced filtering options.

{
  "query": "machine learning healthcare",
  "max_results": 20,
  "date_range": "5y",
  "article_types": ["Journal Article", "Review"],
  "has_abstract": true
}

2. get_article_details

Get detailed information for specific PMIDs.

{
  "pmids": ["12345678", "87654321"],
  "include_abstracts": true,
  "include_citations": false
}

3. search_by_author

Search for articles by a specific author.

{
  "author_name": "Smith J",
  "max_results": 10,
  "include_coauthors": true
}

4. export_citations

Export citations in various formats.

{
  "pmids": ["12345678"],
  "format": "bibtex",
  "include_abstracts": false
}

5. find_related_articles

Find articles related to a specific PMID.

{
  "pmid": "12345678",
  "max_results": 10
}

6. search_mesh_terms

Search using MeSH terms.

{
  "term": "Machine Learning",
  "max_results": 20
}

7. analyze_research_trends

Analyze publication trends over time.

{
  "topic": "artific

... [View full README on GitHub](https://github.com/chrismannina/pubmed-mcp#readme)