What are the required dependencies?

Python 3.8 or higher, the `mcp[cli]` package, and BioPython. Dependencies are managed via `uv` and a `requirements.txt` file.

How do I configure the Entrez email?

You must set a valid email address in `main.py` by assigning it to `Entrez.email`. This is required by NCBI’s Entrez usage policy.

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PubMed MCP Server

This repository contains an MCP server that searches PubMed for article abstracts using BioPython's Entrez module. It leverages the FastMCP framework

Local serverstdioPython

What is the PubMed MCP Server?

This repository contains an MCP server that searches PubMed for article abstracts using BioPython's Entrez module. It leverages the FastMCP framework to provide

The short version

Search PubMed: — Query for articles based on a search term
Retrieve Abstracts: — Fetch abstracts of articles returned from PubMed
Asynchronous Operation: — Uses asynchronous execution (via asyncio.to_thread) to avoid blocking the server

What it needs from you

Python 3.8 or higher - mcp[cli] - BioPython

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

Recorded tools

Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.

Tool	What it does
query	The search term for PubMed (default is "endocarditis").
max_results	Maximum number of articles to retrieve (default is 10).

Configuration

Python 3.8 or higher - mcp[cli] - BioPython

Example prompts to try

“Use PubMed to Tool.”
“Use PubMed to Parameters.”
“Use PubMed to query.”

Frequently asked questions

This repository contains an MCP server that searches PubMed for article abstracts using BioPython's Entrez module. It leverages the FastMCP framework to provide Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.