Pubmed MCP server

PubMed — Biomedical Literature

The U.S. National Library of Medicine's PubMed. ~37 million biomedical and life-science citations going back to 1781. The canonical biomedical literature database — used by every clinician, researcher, and grant officer. MeSH (Medical Subject Headings) tagging makes structured search powerful. Free, no auth.

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Why this matters for AI agents

For biomedical research, drug efficacy questions, clinical guidelines, or systematic literature review, PubMed is the canonical first stop. Where Semantic Scholar is broader but less curated, PubMed is biomedical-focused with MeSH structure that supports precise queries.

Common flows:

• Topic search. "Recent papers on GLP-1 agonists for cardiovascular outcomes" → search with MeSH terms or keywords.
• Specific paper. PMID lookup → full record (title, abstract, authors, MeSH tags).
• Author affiliation / contact. getsummary's authors[] stays plain name strings (unchanged); a separate authordetails[] array, index-aligned with authors[], adds {name, affiliations[], emails[]} — affiliations is the text verbatim from the efetch XML record, and emails is whatever email address(es) a plain regex finds inside that text (empty array when the record carries none — no guessing or enrichment beyond what NCBI indexed). searchpubmed still returns bare author name strings only, with no authordetails; call get_summary on its PMIDs for affiliation/contact detail.
• Author profile. Papers by a specific author (with disambiguation challenges).
• Citation tracking. Cross-reference with Crossref for DOIs and citation networks.
• Evidence landscape. Count clinical trials, randomized trials, systematic reviews, meta-analyses, observational studies, and case reports for one query with pubmedevidencelandscape.
• Publication momentum. Use pubmedpublicationtrend for exact annual PubMed counts across a bounded window.
• Integrity check. Use pubmedintegritycheck before relying on one PMID to surface NLM-indexed retractions, expressions of concern, errata, updates, and related notices.

Auth

None. NCBI E-utilities (PubMed's API) is free. Without an API key, calls are throttled to 3/sec; with a free NCBI API key (https://www.ncbi.nlm.nih.gov/account/), 10/sec. Pass via _apiKey.

MeSH terms

PubMed's secret weapon is MeSH (Medical Subject Headings) — a controlled vocabulary applied to every paper by NLM librarians. Allows precise queries:

• [mh] exact MeSH heading
• [majr] major heading (the paper is about this)
• [ti] title
• [au] author

Example: glucagon-like peptide-1[mh] AND cardiovascular diseases[majr] AND 2023:2024[dp] finds papers majoring on cardiovascular outcomes for GLP-1 agonists in 2023-2024.

Common pitfalls

Shortened. The full README is on GitHub.