MCP server for NCBI Entrez using Biopython
Project description
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
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