mcp-entrez-bio

An MCP (Model Context Protocol) server for interacting with NCBI Entrez via Biopython.

Features

• Search PubMed with boolean queries (pubmed_esearch)
• Fetch PubMed abstracts as plain text (pubmed_efetch_abstracts)
• Automatic rate-limiting conforming to NCBI guidelines

Prerequisites

Provide your NCBI credentials via environment variables for higher rate limits (10 requests/s vs 3 requests/s without API key):

export NCBI_EMAIL="your_email@example.com"
export NCBI_API_KEY="your_api_key_here"  # Optional but recommended

Installation & Usage

Install using standard python tools or uv:

uv tool install .

Run the server directly via standard MCP stdio:

mcp-entrez