@cyanheads/pubmed-mcp-server

MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata and open-access full text (PMC + Unpaywall), generate citations, explore MeSH terms, and discover related research.

★ 106 stars↓ 4k/wkupdated 1d agogithub ↗

What it does

PubMed MCP server provides unified access to PubMed, PubMed Central, and Europe PMC, offering ten integrated tools for biomedical literature research. Search capabilities include full NCBI query syntax with field-specific filtering, date ranges, and publication type selection. The server chains multiple full-text sources—NCBI PMC, Europe PMC, and Unpaywall—to retrieve articles that may not be available through any single API. It generates formatted citations in multiple standards (APA 7th, MLA 9th, BibTeX, RIS), explores MeSH vocabulary with tree structures, and discovers article relationships including cited-by and reference lists. ID conversion between DOIs, PMIDs, and PMCIDs is supported throughout.

Who it's for

Biomedical researchers conducting literature reviews, academic investigators needing structured access to peer-reviewed publications, and developers embedding PubMed discovery into AI-assisted research workflows. Also useful for clinicians and subject-matter experts integrating evidence synthesis into Claude-powered applications.

Common use cases

Search PubMed with field-specific filters (author, journal, MeSH terms, publication date, and publication type)
Retrieve full-text articles from PMC, Europe PMC preprints, or Unpaywall open-access sources
Generate formatted citations in multiple styles for bibliography compilation
Discover related articles, cited-by references, or reference lists for a given PMID
Convert between DOI, PMID, and PMCID identifiers and resolve partial bibliographic citations

Setup pitfalls

Requires outbound network access to NCBI E-utilities, Europe PMC, and optionally Unpaywall APIs—network restrictions may block retrieval
Set UNPAYWALL_EMAIL env var to enable Unpaywall full-text access; disable Europe PMC with EUROPEPMC_ENABLED=false if needed
File system read and write access enabled—ensure appropriate sandboxing or permissions for the deployment context
NCBI API has rate limits; heavy usage may require registering an API key with NCBI for higher request quotas