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PubMed MCP Server

by codingaslu

Healthcare & BioPubMedBioPythonEntrezAsynchronousSearch

This MCP server searches PubMed for article abstracts using BioPython's Entrez module. It leverages the FastMCP framework to provide asynchronous search capabilities for PubMed.

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Last updated: N/A

What is PubMed MCP Server?

The PubMed MCP Server is an MCP server that allows users to search PubMed for article abstracts. It utilizes BioPython's Entrez module and the FastMCP framework to provide asynchronous search capabilities.

How to use PubMed MCP Server?

  1. Clone the repository. 2. Install dependencies using uv add -r requirements.txt. 3. Configure your Entrez email in main.py. 4. Start the server using uv run main.py. 5. Configure your MCP client to connect to the server using the provided config.json example. 6. Use the search_pubmed tool with a query and maximum results to retrieve abstracts.

Key features of PubMed MCP Server

  • Search PubMed for articles

  • Retrieve abstracts of articles

  • Asynchronous operation to avoid blocking

  • Uses BioPython's Entrez module

Use cases of PubMed MCP Server

  • Researching scientific literature

  • Automated abstract retrieval for analysis

  • Integrating PubMed search into other applications

  • Quickly finding relevant articles based on keywords

FAQ from PubMed MCP Server

What is the default query for the search_pubmed tool?

The default query is "endocarditis".

What is the default maximum number of results for the search_pubmed tool?

The default maximum number of results is 10.

What is the purpose of setting the Entrez email?

Setting the Entrez email is required by NCBI to identify the user and is important for responsible use of the Entrez API.

What is the role of the FastMCP framework?

The FastMCP framework provides the infrastructure for creating and managing asynchronous microservice-based applications, enabling the PubMed MCP server to handle requests efficiently.

What license is this project under?

This project is licensed under the MIT License.