pubmed-mcp-server

Overview

The pubmed-mcp-server provides deep integration with PubMed and NCBI's E-utilities API, enabling users to search articles, fetch metadata and full text, generate citations, explore MeSH terms, and discover related research. Built on TypeScript with a well-structured codebase that supports both STDIO and HTTP transport methods. The server implements proper rate limiting for NCBI API requests and includes fallback mechanisms like Unpaywall for full text retrieval. It's actively maintained with clear documentation and examples for multiple deployment scenarios.

Try asking AI

After installing, here are 3 things you can ask your AI assistant:

• pubmed_search_articles

  Search PubMed with full query syntax and filters

  Try:Find articles about CRISPR gene editing published in the last 5 yearsTry:Search for clinical trials related to Alzheimer's treatmentTry:Find papers by author 'Smith JB' in Nature journal
• pubmed_fetch_articles

  Fetch full article metadata by PubMed IDs

  Try:Get details for PMID: 12345678Try:Fetch metadata for articles with PMIDs 123, 456, and 789Try:Show me full information for PMID: 87654321
• pubmed_fetch_fulltext

  Fetch full-text articles from PubMed Central with Unpaywall fallback

  Try:Get the full text for PMID: 12345678Try:Fetch article content for PMC12345Try:Retrieve the full text for DOI: 10.1234/example
• pubmed_format_citations

  Generate formatted citations in APA, MLA, BibTeX, or RIS

  Try:Generate APA 7th citation for PMID: 12345678Try:Format these PMIDs in MLA 9th style: 123, 456, 789Try:Create BibTeX citations for articles with IDs 12345 and 67890
• pubmed_find_related

  Find similar articles, citing articles, or references for a given PMID

  Try:Find articles similar to PMID: 12345678Try:Show me papers that cite PMID: 87654321Try:Get references for article with PMID: 11111111
• pubmed_spell_check

  Spell-check biomedical queries using NCBI's ESpell service

  Try:Check spelling for 'diabetus mellitus' search termTry:Correct 'myocardial infarcion' for my searchTry:Verify 'neorodegenerative diseases' query
• pubmed_lookup_mesh

  Search and explore MeSH vocabulary with tree numbers and scope notes

  Try:Find MeSH term for 'COVID-19'Try:Show details for 'Breast Neoplasms' MeSH termTry:Explore 'Diabetes Mellitus' in MeSH vocabulary
• pubmed_lookup_citation

  Resolve partial bibliographic references to PubMed IDs via ECitMatch

  Try:Find PMID for: Nature 2023; 590(7846): 123-456Try:Match reference: Smith JB, et al. Lancet. 2022; 400(10345): 78-90Try:Resolve citation: JAMA 2021; 326(12): 1156
• pubmed_convert_ids

  Convert between DOI, PMID, and PMCID using PMC ID Converter

  Try:Convert DOI 10.1234/example to PMIDTry:Find PMCID for PMID: 12345678Try:Convert these PMIDs to DOIs: 123, 456, 789

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Installation

{
  "mcpServers": {
    "pubmed": {
      "type": "streamable-http",
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

bunx @cyanheads/pubmed-mcp-server@latest

npx -y @cyanheads/pubmed-mcp-server@latest

docker run -i --rm ghcr.io/cyanheads/pubmed-mcp-server:latest

{
  "mcpServers": {
    "pubmed": {
      "command": "bunx",
      "args": ["@cyanheads/pubmed-mcp-server@latest"]
    }
  }
}

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