pubmed-mcp-server

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Tools

10 tools for working with PubMed, PubMed Central, and Europe PMC data:

Tool	Description
pubmed_search_articles	Search PubMed with full query syntax, field-specific filters, date ranges, pagination, and optional brief summaries
pubmed_europepmc_search	Search Europe PMC for preprints, patents, Agricola, and EPMC-only OA records that don't surface in PubMed. Cursor-based pagination.
pubmed_fetch_articles	Fetch full article metadata by PMIDs — abstract, authors, journal, MeSH terms, grants
pubmed_fetch_fulltext	Fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC fullTextXML → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs.
pubmed_format_citations	Generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM)
pubmed_find_related	Find similar articles, citing articles, or references for a given PMID
pubmed_spell_check	Spell-check biomedical queries using NCBI's ESpell service
pubmed_lookup_mesh	Search and explore MeSH vocabulary — tree numbers, scope notes, entry terms
pubmed_lookup_citation	Resolve partial bibliographic references to PubMed IDs via ECitMatch
pubmed_convert_ids	Convert between DOI, PMID, and PMCID using the PMC ID Converter API

pubmed_search_articles

Search PubMed with full NCBI query syntax and filters.

• Free-text queries with PubMed's full boolean and field-tag syntax
• Field-specific filters: author, journal, MeSH terms, language, species
• Common filters: has abstract, free full text
• Date range filtering by publication, modification, or Entrez date
• Publication type filtering (Review, Clinical Trial, Meta-Analysis, etc.)
• Sort by relevance, publication date, author, or journal
• Pagination via offset for paging through large result sets
• Optional brief summaries for top N results via ESummary
• Returns the original query plus the fully applied PubMed query and normalized filter metadata

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pubmed_fetch_articles

Fetch full article metadata by PubMed IDs.

• Batch fetch up to 200 articles at once (auto-switches to POST for batches >= 100)
• Returns structured data: title, abstract, authors with deduplicated affiliations, journal info, DOI
• Direct links to PubMed and PubMed Central (when available)
• Optional MeSH terms, grant information, and publication types
• Handles PubMed's inconsistent XML (structured abstracts, missing fields, varying date formats)

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pubmed_fetch_fulltext

Fetch full-text articles via a three-stage chain: NCBI PMC EFetch → Europe PMC fullTextXML → Unpaywall.