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PubMed MCP Server

@codingaslu

代码仓库

基本信息

分类

数据与分析

传输方式

stdio

作者

codingaslu

关于 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 asynchronous search capabilities for PubMed.

PubMed MCP Server 配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

{
  "mcpServers": {
    "pubmed-mcp-server-codingaslu": {
      "command": "uv",
      "args": [
        "run",
        "main.py"
      ]
    }
  }
}

PubMed MCP Server 工具

工具列表暂未提供

当前收录暂时没有可展示的工具列表，不代表服务没有工具。请查阅项目文档了解支持的能力。

工具是从 README 中自动提取的。维护者可以在 ## Tools 标题下列出工具,即可填充这部分内容。

概览

What is PubMed MCP Server?

The PubMed MCP Server is a Model Context Protocol (MCP) server that searches PubMed for article abstracts using BioPython's Entrez module and the FastMCP framework. It provides asynchronous search capabilities for researchers and developers who need to retrieve PubMed data through MCP‑compatible clients.

How to use PubMed MCP Server?

Clone the repository, install dependencies with uv add -r requirements.txt, set a valid email address in main.py (Entrez.email), then start the server with uv run main.py. Configure your MCP client with the path to uv and the server directory as specified in the config.json example. Use the search_pubmed tool with parameters query (default "endocarditis") and max_results (default 10).

Key features of PubMed MCP Server

  • Searches PubMed for articles by query term.
  • Retrieves abstracts of returned articles.
  • Asynchronous execution via asyncio.to_thread.
  • Built on the FastMCP framework.
  • Configurable maximum number of results.
  • Simple Python‑based setup with uv.

Use cases of PubMed MCP Server

  • Automating literature reviews by programmatically fetching PubMed abstracts.
  • Integrating PubMed search results into AI‑powered research assistants.
  • Building MCP‑enabled tools that require live biomedical literature data.
  • Batch‑retrieving abstracts for multiple search queries in parallel.

常见问题

1

What does the PubMed MCP Server do?

It allows MCP‑compatible clients to search PubMed and retrieve article abstracts asynchronously using a single tool (`search_pubmed`).

2

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.

3

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.

4

What are the default search parameters?

The search tool uses a default query of `"endocarditis"` and a default `max_results` of 10. Both can be overridden when calling the tool.

5

Does the server have any data storage or authentication?

No. The server does not store data locally; it queries PubMed’s public API. No authentication is required beyond the valid email address.

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