PubMed MCP Server

An MCP (Model Context Protocol) server that provides tools for searching and retrieving biomedical literature from PubMed via the NCBI E-utilities API.

Features

Tool	Description
search_pubmed	Search PubMed with a query string, returns article summaries
fetch_article	Fetch full metadata and abstract for a specific PMID
fetch_abstract	Get just the abstract text for a PMID
verify_citation	Check if a PMID matches a given title (returns similarity score)
search_by_title	Find the correct PMID for a given article title

Installation

From PyPI

pip install suppevo-pubmed-mcp

From source

git clone https://github.com/gomezmera/suppevo-pubmed-mcp.git
cd suppevo-pubmed-mcp/pubmed
pip install -e .

Configuration

NCBI API Key (recommended)

An API key increases your rate limit from 3 requests/sec to 10 requests/sec.

1. Create a free NCBI account at NCBI
2. Go to Account Settings and generate an API key
3. Set the environment variable:

export NCBI_API_KEY="your-api-key-here"

Or add it to a .env file in your home directory (~/.env):

NCBI_API_KEY=your-api-key-here

The server will automatically load it from ~/.env if present.

Running the Server

Standalone

# If installed via pip
suppevo-pubmed-mcp

# Or run directly with FastMCP
fastmcp run server.py

With Kiro

Add to your .kiro/settings/mcp.json:

{
  "mcpServers": {
    "pubmed": {
      "command": "python",
      "args": ["/path/to/suppevo-pubmed-mcp/pubmed/server.py"],
      "env": {
        "NCBI_API_KEY": "your-api-key-here"
      }
    }
  }
}

Or if installed from PyPI:

{
  "mcpServers": {
    "pubmed": {
      "command": "uvx",
      "args": ["suppevo-pubmed-mcp"],
      "env": {
        "NCBI_API_KEY": "your-api-key-here"
      }
    }
  }
}

With Claude Desktop

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "pubmed": {
      "command": "uvx",
      "args": ["suppevo-pubmed-mcp"],
      "env": {
        "NCBI_API_KEY": "your-api-key-here"
      }
    }
  }
}

Usage Examples

Once connected to an MCP client, you can use natural language:

• "Search PubMed for vitamin D supplementation meta-analysis 2024"
• "Fetch the full details for PMID 30415628"
• "Verify that PMID 17846391 is about vitamin D supplementation and total mortality"
• "Find the PMID for the article titled 'Effect of zinc supplementation on C-reactive protein'"
• "Get the abstract for PMID 25927176"

Query Syntax

The search_pubmed tool supports PubMed's full query syntax:

# Basic search
vitamin D supplementation

# Field-specific
curcumin AND inflammation[Title]

# Author search
Prasad AS[Author] AND zinc

# Date range
omega-3 AND cardiovascular[Title] AND 2020:2024[dp]

# MeSH terms
"Zinc/therapeutic use"[MeSH]

Rate Limits

Configuration	Rate Limit
Without API key	3 requests/second
With API key	10 requests/second

The server automatically throttles requests to stay within limits. NCBI may temporarily block IPs that exceed these limits.

Development

# Clone and install in development mode
git clone https://github.com/gomezmera/suppevo-pubmed-mcp.git
cd suppevo-pubmed-mcp/pubmed
pip install -e .

# Run the server
python server.py

Publishing

See RELEASING.md for instructions on publishing to PyPI.

License

MIT