pubmed-mcp-server

Public Hosted Server: https://pubmed.caseyjhand.com/mcp

Overview

Biomedical literature from PubMed, PubMed Central, and Europe PMC. Search it, fetch metadata and full text, resolve identifiers and partial citations, format references, and ground queries in MeSH vocabulary. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.

Tools

Resources

Prompts

Capability reference

pubmed_search_articles tool

• Full PubMed query syntax plus filters (author, journal, MeSH, publication type, language, species, abstract, free full text) and publication/modification/Entrez date ranges
• Up to 1,000 results per page and offsets up to 9,998, or maxResults: 0 for the match count alone; summaryCount adds briefs for up to 50 hits
• Reports totalCount, the effectiveQuery PubMed ran, and the appliedFilters
• Rejects blank filter values, impossible dates, and reversed date ranges before PubMed is called

pubmed_fetch_articles tool

• Up to 200 PMIDs per call; misses are listed in unavailablePmids
• Abstract, authors, journal, DOI, publication types, linked retraction/erratum/comment notices, and links; MeSH terms on by default, grants via includeGrants, and the members of a collective author (its InvestigatorList, thousands on some consortium trials) via includeInvestigators
• recordType separates journal articles from Bookshelf chapters and books; opt-in maxResponseCharacters defers overflow to deferred.ids

pubmed_fetch_fulltext tool

• pmcids, pmids, and dois in any mix, up to 50 distinct identifiers per call: the first 10 are fetched and the rest returned in overLimit for a follow-up call. Each is tried against PMC, then Europe PMC, then Unpaywall (needs UNPAYWALL_EMAIL); an article several of them name is fetched and returned once, and viaSource names the tier that answered
• source: "pmc" returns sections (the body, then back matter such as acknowledgments, declarations, and appendices), tables, and figures; source: "unpaywall" returns a best-effort HTML or PDF text body
• Misses carry a typed reason and triedTiers; sections, maxCharacters, overflowMode, and maxResponseCharacters bound the response, and truncation reports what was cut

pubmed_europepmc_search tool

• Adds preprints (PPR), patents (PAT), and Agricola (AGR) to MED and PMC; defaults to MED, PMC, PPR
• Cursor pagination via cursorMark / nextCursorMark, up to 100 per page; abstracts arrive as 400-character snippets
• Not registered when EUROPEPMC_ENABLED=false

pubmed_europepmc_fetch tool

• Up to 25 records per call, addressed by a search hit's source + epmcId, with the full abstract; unresolved ids land in notFound; opt-in maxResponseCharacters defers overflow to deferred.records
• Not registered when EUROPEPMC_ENABLED=false

pubmed_format_citations tool

• Up to 50 PMIDs per call, in any mix of apa, mla, bibtex, ris, and vancouver
• Bookshelf records cite as edited books, each chapter dated by its own last revision or contribution date; PMIDs that can't be fetched are reported as unavailable
• Retractions, errata, and expressions of concern NCBI links to an article come back as notices and are shown ahead of its citations; Vancouver adds a Retraction in: / Erratum in: note and APA a retraction parenthetical

pubmed_find_related tool

• similar, cited_by, or references, up to 50 per page with offset pagination
• Falls back to Europe PMC, then OpenAlex, and names the provider that answered; fails as all_providers_failed if none can

pubmed_spell_check tool

• Returns original, corrected, and hasSuggestion, fixing every misspelled token in one call
• Run it after a zero-hit or thin search, then retry pubmed_search_articles with corrected

pubmed_lookup_mesh tool

• Descriptors by name or free-text term, with an exact heading match pinned first; up to 50 per page, continued via nextOffset
• Records carry meshId; includeDetails (default on) adds tree numbers, scope notes, and entry terms

pubmed_lookup_citation tool

• Up to 25 partial citations per call; a journal or a four-digit year is required, and volume, first page, and author sharpen the match
• Each is matched independently and comes back matched, not_found, or ambiguous, with recovery detail

pubmed_convert_ids tool

• Up to 50 ids per call, all of one declared idType (doi, pmid, pmcid); only PMC-indexed articles resolve
• One success or error row per id, in order, so a partial batch never fails

pubmed://database/info resource

• Live EInfo call for the pubmed database, returned as application/json
• count, lastUpdate, and fields[], whose names are the search tags pubmed_search_articles accepts

research_plan prompt

• Arguments: title, goal, and keywords required; organism and includeAgentPrompts optional
• Returns a four-phase research plan; includeAgentPrompts: "true" adds an agent-guidance block under each of its nine sub-steps, two of which point at tools: the literature review names pubmed_search_articles and pubmed_lookup_mesh, and the interpretation step names pubmed_search_articles

Features

Built on @cyanheads/mcp-ts-core: stdio and Streamable HTTP transports, pluggable auth (none / jwt / oauth), swappable storage (in-memory, filesystem, Supabase, Cloudflare KV/R2/D1), structured logging with optional OpenTelemetry tracing.

PubMed-specific:

• NCBI E-utilities (ESearch, EFetch, ESummary, ELink, ESpell, EInfo, ECitMatch) and the PMC ID Converter, with Europe PMC, OpenAlex, and Unpaywall filling the gaps
• Shared NCBI request queue: paced request starts, capped concurrency, a cooldown that holds every caller a