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PubMed MCP Server

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About PubMed MCP Server

Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.

#mcp#pubmed#pubmed-parser#ncbi#ai-agents#ai-tools#pubmed-api#model-context-protocol#mcp-server#bio-medical-research

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server@latest"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info",
        "NCBI_API_KEY": "your-key-here"
      }
    }
  }
}

Tools

10

Search PubMed with full query syntax, field-specific filters, date ranges, pagination, and optional brief summaries

Search Europe PMC for preprints, patents, Agricola, and EPMC-only OA records that don't surface in PubMed. Cursor-based pagination.

Fetch full article metadata by PMIDs — abstract, authors, journal, MeSH terms, grants

Fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs.

Generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM)

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

Spell-check biomedical queries using NCBI's ESpell service

Search and explore MeSH vocabulary — tree numbers, scope notes, entry terms

Resolve partial bibliographic references to PubMed IDs via ECitMatch

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

Overview

What is PubMed MCP Server?

A biomedical literature retrieval server that integrates PubMed, Europe PMC, and Unpaywall into MCP. It offers 10 tools for searching articles, fetching metadata and full text, formatting citations, exploring MeSH terms, and converting identifiers. Designed for researchers, clinicians, and AI agents needing structured access to life‑science publications.

How to use PubMed MCP Server?

Use the public hosted instance at https://pubmed.caseyjhand.com/mcp via Streamable HTTP with any MCP client, or self‑host locally using bunx @cyanheads/pubmed-mcp-server@latest in stdio mode. One‑click install buttons are available for Claude Desktop, Cursor, and VS Code.

Key features of PubMed MCP Server

  • Search PubMed with full boolean and field‑tag syntax
  • Search Europe PMC for preprints, patents, and Agricola
  • Fetch full‑text articles via a three‑stage retrieval chain
  • Generate citations in APA, MLA, BibTeX, RIS, and Vancouver
  • Resolve partial citations and convert between DOI, PMID, PMCID

Use cases of PubMed MCP Server

  • Rapid literature search with field‑specific filters and date ranges
  • Batch retrieval of article metadata and full text for systematic reviews
  • Citation formatting and bibliography generation in multiple styles
  • AI‑assisted research planning with the research_plan prompt
  • Building biomedical search tools with provenance‑aware output

FAQ from PubMed MCP Server

What’s the difference between pubmed_search_articles and pubmed_europepmc_search?

pubmed_search_articles uses NCBI E‑utilities and returns only PubMed‑indexed articles. pubmed_europepmc_search queries Europe PMC and also covers preprints, patents, and Agricola records not found in PubMed.

How does full‑text retrieval work?

pubmed_fetch_fulltext tries NCBI PMC EFetch first, falls back to Europe PMC fullTextXML, then to Unpaywall for legal OA copies. The source of each result is marked (pmc, europepmc, or unpaywall). Unpaywall requires setting UNPAYWALL_EMAIL.

What citation styles are available?

APA 7th, MLA 9th, BibTeX, RIS, and Vancouver (ICMJE/NLM). All formatters are hand‑rolled with zero external dependencies.

How do I run the server locally?

Add it to your MCP client config with "command": "bunx", "args": ["@cyanheads/pubmed-mcp-server@latest"] and set "MCP_TRANSPORT_TYPE": "stdio". Alternatively, use the public HTTP endpoint.

What are the batch size limits?

Fetch articles: up to 200. Full text: up to 10. Citations: up to 50. ID conversion: up to 50. Citation lookup: up to 25. Larger requests return per‑item results with structured errors, not batch failures.

Frequently asked questions

What’s the difference between `pubmed_search_articles` and `pubmed_europepmc_search`?

`pubmed_search_articles` uses NCBI E‑utilities and returns only PubMed‑indexed articles. `pubmed_europepmc_search` queries Europe PMC and also covers preprints, patents, and Agricola records not found in PubMed.

How does full‑text retrieval work?

`pubmed_fetch_fulltext` tries NCBI PMC EFetch first, falls back to Europe PMC `fullTextXML`, then to Unpaywall for legal OA copies. The source of each result is marked (`pmc`, `europepmc`, or `unpaywall`). Unpaywall requires setting `UNPAYWALL_EMAIL`.

What citation styles are available?

APA 7th, MLA 9th, BibTeX, RIS, and Vancouver (ICMJE/NLM). All formatters are hand‑rolled with zero external dependencies.

How do I run the server locally?

Add it to your MCP client config with `"command": "bunx", "args": ["@cyanheads/pubmed-mcp-server@latest"]` and set `"MCP_TRANSPORT_TYPE": "stdio"`. Alternatively, use the public HTTP endpoint.

What are the batch size limits?

Fetch articles: up to 200. Full text: up to 10. Citations: up to 50. ID conversion: up to 50. Citation lookup: up to 25. Larger requests return per‑item results with structured errors, not batch failures.

Comments

Basic information

Category

Data & Analytics

License

Apache-2.0

Transports

stdio

Author

cyanheads

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