PubMed MCP Server

What is PubMed MCP Server?

A comprehensive Model Context Protocol (MCP) server for PubMed literature search and management. It provides advanced search capabilities, citation formatting, and research analysis tools, integrating with the PubMed API through NCBI E‑utilities. Designed for researchers, developers, and anyone needing programmatic access to PubMed.

How to use PubMed MCP Server?

Install Python 3.8+, obtain a free NCBI API key and a valid email, clone the repository, install dependencies (pip install -r requirements.txt), configure environment variables in a .env file, then run python -m src.main. Use an MCP client to call tools such as search_pubmed, get_article_details, and export_citations.

Key features of PubMed MCP Server

• Advanced PubMed search with date ranges, article types, authors, journals, and MeSH terms
• Retrieve detailed article information including abstracts, authors, and metadata
• Export citations in BibTeX, APA, MLA, Chicago, Vancouver, EndNote, and RIS formats
• Search by author with co‑author information
• Discover related articles and explore MeSH terms
• Analyze publication trends over time and compare multiple articles
• Built‑in caching and configurable rate limiting for respectful API usage

Use cases of PubMed MCP Server

• Automate literature searches with complex filters for systematic reviews
• Fetch and format citations for reference management tools
• Analyze research trends by topic over a specified number of years
• Compare multiple articles side‑by‑side for literature analysis
• Integrate PubMed search capabilities into AI assistants and research workflows

FAQ from PubMed MCP Server

What API key is required?

A free NCBI API key is required. Obtain it from NCBI Account Settings under “API Key Management”.

What are the runtime dependencies?

Python 3.8 or higher, an NCBI API key, and a valid email for NCBI API identification.

Does the server store any data locally?

It uses built‑in caching (configurable TTL and max size) for improved performance, but no persistent storage of user data is described.

Are there any rate limits?

The server includes configurable rate limiting to ensure respectful API usage. The default rate limit parameter is RATE_LIMIT=3.0.

Can I run the server in a container?

Yes, a Dockerfile and Docker Compose configuration are provided. Build with make docker-build and run with make docker-run or via docker-compose.