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Pubmed MCP Server

Search biomedical literature, retrieve full text and metadata, resolve identifiers, analyze citations, and format references over MCP.

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Install Pubmed MCP Server

Pick your client, then add it in one click or paste the config.

STDIONode.js
~/Library/Application Support/Claude/claude_desktop_config.json
claude_desktop_config.json
{
  "mcpServers": {
    "pubmed-mcp-server-2": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ]
    }
  }
}

Settings → Developer → Edit Config, merge this into mcpServers, then fully quit and reopen Claude Desktop.

Install not yet sandbox-tested— we haven't run this command through our automated sandbox yet. Not a red flag; we're working through the catalog.

Overview

pubmed-mcp-server connects MCP clients to PubMed, PubMed Central, Europe PMC, NIH iCite, Unpaywall, and related NCBI services for biomedical literature research. It supports article search, metadata and full-text retrieval, citation metrics, MeSH lookup, identifier conversion, citation resolution, and reference formatting. Run it as a stdio process, a local Streamable HTTP server, or use the hosted endpoint at https://pubmed.caseyjhand.com/mcp. Reach for it when an agent needs structured literature discovery, open-access text retrieval, or citation-aware research workflows.

Use cases

  • Search PubMed with structured biomedical filters
  • Retrieve open-access article full text
  • Resolve partial references to PMIDs
  • Compare citation metrics across articles
  • Format references for research documents

Key features

  • PubMed and Europe PMC search
  • Metadata and full-text retrieval
  • MeSH lookup and query spell checking
  • NIH iCite citation metrics
  • APA, MLA, BibTeX, RIS, and Vancouver formatting
  • PMID, PMCID, and DOI conversion

Tools12

What Pubmed MCP Server lets your agent do. Expand a tool for its parameters.

Self-reported~350 tokens of context

Security & health

What it can reach and how reliably it runs — from our own checks, not the maintainer’s claims.

ActiveLast checked 1d ago

Recent health check succeeded.

12/12 checks healthy over the last 47d

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 11d ago via OSV.dev · @cyanheads/pubmed-mcp-server (npm)

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

GitHub stars165Stargazers on the source repository.
npm downloads14kPackage downloads in the last 30 days.
Last commit9d agoMost recent push to the default branch.
Tools exposed12Callable tools this server registers over MCP.
Directory activity8 viewsConfig copies, upvotes, and views on AllMCPs.

How Pubmed MCP Server works

What pubmed-mcp-server does

pubmed-mcp-server exposes biomedical literature workflows through the Model Context Protocol. It searches PubMed using full query syntax, structured filters, date ranges, and optional result summaries. It also searches Europe PMC for records beyond PubMed’s coverage, including preprints, patents, Agricola entries, and open-access material.

Article retrieval can include abstracts, authors, journals, publication types, MeSH terms, grants, databank accessions, investigator lists for collective authors, and linked retraction or correction notices. Full text can be requested with a PMID, PMCID, or DOI. Citation-oriented functions provide NIH iCite metrics, related articles, citing articles, references, citation formatting, and partial-reference resolution.

How it works

The server communicates with MCP clients over stdio or Streamable HTTP. It can run locally or be accessed through the hosted MCP endpoint at https://pubmed.caseyjhand.com/mcp. The available MCP surface includes 12 tools, one database-information resource, and a research_plan prompt for generating a structured four-phase biomedical research plan.

Full-text retrieval tries PMC first, then Europe PMC, and finally Unpaywall when configured with an email address. Responses identify the source tier and can report truncation, unavailable records, deferred content, and other typed results. Europe PMC search uses cursor pagination and can be disabled through configuration.

Setup and configuration

Install the package with the npm-based MCP configuration used by the provided client install links, or run the project through its Docker package. Client setup options are available for Claude Desktop, Cursor, and VS Code. The server can also be configured as a local Streamable HTTP service rather than a stdio process.

Set UNPAYWALL_EMAIL to enable the Unpaywall fallback during full-text retrieval. EUROPEPMC_ENABLED=false disables the Europe PMC search and fetch tools. No API key is required for the documented PubMed, Europe PMC, PMC, iCite, and identifier-resolution operations.

Tools and capabilities

  • pubmed_search_articles searches PubMed, applies filters, reports the effective query, and can return match counts or brief summaries.
  • pubmed_fetch_articles retrieves metadata for up to 200 PMIDs per call, including notices and optional grants or investigators.
  • pubmed_fetch_fulltext retrieves available full text using PMIDs, PMCIDs, or DOIs, with response-size and section controls.
  • pubmed_europepmc_search and pubmed_europepmc_fetch search and retrieve Europe PMC records, including complete abstracts.
  • pubmed_fetch_citation_metrics returns iCite measures such as Relative Citation Ratio, NIH percentile, citation counts, and clinical citations.
  • pubmed_format_citations produces APA 7, MLA 9, BibTeX, RIS, or Vancouver references.
  • pubmed_find_related, pubmed_spell_check, pubmed_lookup_mesh, pubmed_lookup_citation, and pubmed_convert_ids support discovery, query correction, vocabulary lookup, citation matching, and DOI/PMID/PMCID conversion.

Limitations and notes

Full-text availability depends on PMC, Europe PMC, or Unpaywall coverage and licensing. Unpaywall fallback requires UNPAYWALL_EMAIL. Tool limits apply: full-text requests process the first 10 of up to 50 identifiers, citation formatting accepts up to 50 PMIDs, and Europe PMC fetch accepts up to 25 records per call. NIH iCite does not identify retractions, so article notices should be checked separately with pubmed_fetch_articles.

Read the full README View source on GitHub

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Frequently Asked Questions about Pubmed MCP Server

pubmed-mcp-server is an MCP server that connects AI clients to PubMed, Europe PMC, PMC, NIH iCite, and related NCBI services. Its main tools search literature, fetch article metadata and full text, retrieve citation metrics, format citations, resolve identifiers, look up MeSH terms, and find related or citing articles.

Install it through the npm-based MCP configuration or Docker package, then register it with an MCP client as a stdio process or Streamable HTTP service. Direct install links are provided for Claude Desktop, Cursor, and VS Code.

Yes, pubmed-mcp-server has a Cursor installation link and can run there over its standard MCP configuration. It also supports Claude Desktop and VS Code, as well as local stdio or Streamable HTTP deployment.

It accepts a PMID, PMCID, or DOI and checks PMC first, then Europe PMC, then Unpaywall. Set `UNPAYWALL_EMAIL` to enable the final fallback; results identify the source used and can report unavailable or truncated content.

Yes, `pubmed_format_citations` formats PMID records as APA 7, MLA 9, BibTeX, RIS, or Vancouver references. It also includes linked retraction, erratum, and expression-of-concern notices when available.

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