PubMed MCP: Documentation
Updated:
Connection
Repo: github.com/cyanheads/pubmed-mcp-server (126★). Install: npx -y pubmed-mcp-server (stdio) or a Streamable HTTP mode. No auth needed for basic search; an optional NCBI_API_KEY raises the rate limit on E-utilities calls.
Tools
Search PubMed and Europe PMC (search_pubmed) with MeSH-term support, fetch article metadata and abstract by PMID/DOI, extract full text via PMC or Unpaywall (get_full_text), a MeSH-term lookup to refine a query.
Agent flow
"Find studies on this topic from the last 3 years, filtered by publication type", "find the full text of this paper by DOI", "look up the right MeSH term for precise medical search".
Pricing
Completely free — PubMed E-utilities and Europe PMC are public; a free NCBI_API_KEY lifts some rate limits.
Note
A community project (cyanheads), not officially affiliated with NCBI/NLM. Full text isn't available for every article — it depends on publisher policy and PMC/Unpaywall coverage.