PubMed MCP Server

Install

Works with Claude Code, VS Code, Codex, Cursor, Windsurf, Claude Desktop. Read the repository before you give any tool access to your data.

npx agentmarket install connector/cyanheads-pubmed-mcp-server

About

Use cases: deep-research

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Permissions

What this server can do and what it asks for, from its tool list, install config and code. Checked Oct 25, 2026.

Tools

11 read · 0 write · 0 deleteRead-only

Secrets

1 (API keys, tokens or passwords)

Install scripts

None found

Runs as

Node.js package

Tools (11)

As the server listed them on Oct 25, 2026. Descriptions are the server’s own words; hidden characters are shown as [U+…].

• pubmed_convert_idsPubmed Convert Idsread-only

  Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Only resolves articles indexed in PubMed Central — for articles not in PMC, use pubmed_search_articles instead.

• pubmed_europepmc_fetchPubmed Europepmc Fetchread-only

  Fetch complete Europe PMC records — including the full, untruncated abstract — addressed as `records: [{ source, epmcId }]`, an array even for one record. Pairs with `pubmed_europepmc_search`, which returns bounded `abstractSnippet` values and flags cut ones with `abstractTruncated: true`; copy each hit's `source` and `epmcId` into `records` here to read the whole abstract. This is the retrieval path for preprint (`PPR`), patent (`PAT`), and Agricola (`AGR`) records, which frequently carry no PMID and no DOI, so `pubmed_fetch_articles` and `pubmed_fetch_fulltext` cannot address them. Up to 25 …

• pubmed_europepmc_searchPubmed Europepmc Searchread-only

  Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`. Abstracts arrive as a bounded `abstractSnippet` with `abstractTruncated` marking the cut ones — pass a hit to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]` for the complete abstract.

• pubmed_fetch_articlesPubmed Fetch Articlesread-only

  Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms, linked retraction, erratum, and comment notices, and databank accessions such as trial registration IDs; grants and the members of a collective author are opt-in (`includeGrants`, `includeInvestigators`). Set `maxResponseCharacters` to bound the whole response: articles past the ceiling are deferred whole and listed in `deferred.ids` for a follow-up call.

• pubmed_fetch_fulltextPubmed Fetch Fulltextread-only

  Fetch full-text articles from PubMed Central as structured sections — the body, then back matter such as acknowledgments, declarations, and appendices — with tables and references. When PMC misses, transparently falls back to Europe PMC `fullTextXML` (structured JATS for records with a PMC counterpart), then to Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text. Name articles by `pmcids` (PMC IDs directly), `pmids` (PubMed IDs, auto-resolved), `dois` (DOIs, auto-resolved to PMC via the ID Converter; preprints and EPMC-only OA fall through to the…

• pubmed_find_relatedPubmed Find Relatedread-only

  Find articles related to a source article — similar content (similar), articles citing this one (cited_by), or articles this one cites (references). Uses NCBI ELink as the primary source; falls back to Europe PMC then OpenAlex when NCBI is unavailable.

• pubmed_format_citationsPubmed Format Citationsread-only

  Get formatted citations for PubMed articles in one or more formats (apa, mla, bibtex, ris, vancouver). Pass a single format as a string or multiple as an array. Retractions, errata, and expressions of concern NCBI links to an article come back in `notices`; Vancouver and APA also cite a retraction in the reference itself.

• pubmed_lookup_citationPubmed Lookup Citationread-only

  Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or a four-digit year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.

• pubmed_lookup_meshPubmed Lookup Meshread-only

  Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms, plus pagination via offset for paging past the maxResults cap.

• pubmed_search_articlesPubmed Search Articlesread-only

  Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), and pagination via offset for paging through large result sets.

• pubmed_spell_checkPubmed Spell Checkread-only

  Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin `pubmed_search_articles` result, or when a drug, gene, disease, or author name may be misspelled. Corrections are applied in place, so field tags, operators, spacing, and gene symbols stay as written (`alzhiemer diseese treatmnt outcomse` → `alzheimer disease treatment outcomes`). Words in all capitals, with digits or non-ASCII letters, or differing only in case are never changed, nor is a single letter swapped for another (`q fever`, the initial in `smith q`), words after a num…

Signals

Stars

162

Forks

24

Open issues

8

Weekly downloads

1,577

Last commit

Oct 23, 2026 (6 days ago)

Last release

Oct 26, 2026 (4 days ago)

Last package publish

Oct 23, 2026 (6 days ago)

From GitHub (fetched Oct 24, 2026) and the package registry.

Details

Registry name

io.github.cyanheads/pubmed-mcp-server

Version

2.11.1

Auth

Auth not stated

Packages

npm @cyanheads/pubmed-mcp-servernpm @cyanheads/pubmed-mcp-server

License

Apache-2.0

Repository

github.com/cyanheads/pubmed-mcp-server

First seen

Oct 24, 2026

Last checked

Oct 26, 2026

Source

Official MCP Registrygithub-graphql