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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.

• Accepts exactly one of pmcids (direct PMC IDs), pmids (PubMed IDs, auto-resolved), or dois (auto-resolved to PMC via the ID Converter; preprints and EPMC-only OA fall through to Europe PMC / Unpaywall)
• NCBI PMC and Europe PMC both return structured JATS; output records origin via viaSource: "pmc" | "europepmc" | "unpaywall"
• Europe PMC layer (enabled by default; disable with EUROPEPMC_ENABLED=false) recovers PMC-counterpart records that NCBI PMC EFetch missed, and resolves DOI input to PMC counterparts when one exists. EPMC's fullTextXML is PMC-keyed, so preprints (PPR), patents (PAT), and Agricola (AGR) are reachable via pubmed_europepmc_search for metadata but have no full text via this chain.
• Unpaywall layer (enabled by setting UNPAYWALL_EMAIL) resolves DOIs to legal OA copies; extracts HTML landing pages to Markdown via Defuddle or PDFs to text via unpdf
• Discriminated output contract — source: "pmc" (structured sections, regardless of whether it came from PMC or EPMC) or source: "unpaywall" (best-effort body + contentFormat: html-markdown or pdf-text)
• Structured unavailable reasons (not-found, no-pmc-fallback-disabled, no-epmc-fulltext, no-doi, no-oa, fetch-failed, parse-failed, service-error) so callers can retry or explain to users without parsing text
• Each unavailable entry carries idType (pmid / pmcid / doi) and triedTiers — per-tier outcomes (not-attempted, miss, no-fulltext, service-error, …) in execution order, so callers can see which stage failed and why
• Section filtering by title (case-insensitive match, e.g. ["methods", "results"]) and configurable max sections apply to PMC output
• Up to 10 articles per request

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pubmed_europepmc_search

Search Europe PMC (EBI/EMBL-EBI), a broader open-access biomedical corpus than PubMed alone.

• Surfaces records PubMed search can't reach — preprints (source: PPR), patents (source: PAT), Agricola (source: AGR), plus everything in PubMed (MED) and PMC (PMC). On recent queries this can mean dozens of relevant hits with zero PubMed overlap.
• Default sources ["MED", "PMC", "PPR"]; pass sources to include PAT / AGR
• Cursor-based pagination via cursorMark (unlike pubmed_search_articles, which uses offset) — * for the first page, return nextCursorMark for the next
• Output discriminator on source plus optional pmid / pmcId / doi cross-walking
• Disabled when EUROPEPMC_ENABLED=false; tool is not registered in that case

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pubmed_format_citations

Generate formatted citations for articles.

• Five citation styles: APA 7th, MLA 9th, BibTeX, RIS, Vancouver (ICMJE/NLM)
• Request multiple styles per article in a single call
• Hand-rolled formatters — zero external dependencies, fully Workers-compatible
• Up to 50 articles per request
• Reports formatted counts and unavailable PMIDs for partial-result handling

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pubmed_find_related

Find articles related to a source article via ELink.

• Three relationship types: similar (content similarity), cited_by, references
• Results enriched with title, authors, publication date, and source via ESummary
• Results returned in NCBI's relevance order

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pubmed_spell_check

Spell-check a biomedical query using NCBI's ESpell.

• Returns the original query, corrected query, and whether a suggestion was found
• Useful for query refinement before searching

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pubmed_lookup_mesh

Search and explore the MeSH (Medical Subject Headings) vocabulary.

• Search MeSH terms by name with exact-heading matching
• Detailed records with tree numbers, scope notes, and entry terms by default
• Useful for building precise PubMed queries with controlled vocabulary

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pubmed_lookup_citation

Resolve partial bibliographic references to PubMed IDs via NCBI ECitMatch.

• Match citations by journal, year, volume, first page, and/or author name
• More fields = better match accuracy; at least one field required
• Batch up to 25 citations per request
• Deterministic matching — more reliable than free-text search for known references
• Returns explicit matched, not_found, and ambiguous statuses with recovery detail

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pubmed_convert_ids

Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.

• Batch up to 50 IDs per request
• Accepts DOIs, PMIDs, or PMCIDs (all IDs must be the same type)
• Only resolves articles indexed in PubMed Central
• Per-ID success/error reporting — partial batches return resolved mappings alongside structured errors for unresolvable IDs, not a batch-level failure

Resource and prompt

Type	Name	Description
Resource	pubmed://database/info	PubMed database metadata via EInfo (field list, record count, last update)
Prompt	research_plan	Generate a structured 4-phase biomedical research plan outline

Features

Built on @cyanheads/mcp-ts-core:

• Declarative tool definitions — single file per tool, framework handles registration and validation
• Unified error handling across all tools
• Pluggable auth (none, jwt, oauth)
• Swappable storage backends: in-memory, filesystem, Supabase, Cloudflare KV/R2/D1
• Structured logging with optional OpenTelemetry tracing
• Runs locally (stdio/HTTP) or on Cloudflare Workers from the same codebase

PubMed-specific:

• Complete NCBI E-utilities integration (ESearch, EFetch, ESummary, ELink, ESpell, EInfo, ECitMatch) plus PMC ID Converter
• Sequential request queue with configurable delay for NCBI rate limit compliance
• NCBI-specific XML parser with isArray hints for PubMed's inconsistent XML structure
• Hand-rolled citation formatters (APA, MLA, BibTeX, RIS, Vancouver) — zero deps, Workers-compatible

Agent-friendly output:

• Provenance on every response — source labels, license fields, best-effort warnings on Unpaywall results, and effective-query echo on searches so agents can reason about trust
• Graceful partial failure — batch tools return per-item success/error rows instead of failing the request, with structured status codes and actionable next-step text
• Discriminated output contracts — source: "pmc" | "unpaywall", typed unavailable reasons, viaSource and triedTiers fields — callers branch on data, not string parsing

Getting started

Public Hosted Instance

A public instance is available at https://pubmed.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "type": "streamable-http",
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

Self-Hosted / Local

Add the following to your MCP client configuration file.

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

Or with npx (no Bun required):

{
  "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"
      }
    }
  }
}

Or with Docker:

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "type": "stdio",
      "command": "docker",
      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/pubmed-mcp-server:latest"]
    }
  }
}

For Streamable HTTP, set the transport and start the server:

MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp

Prerequisites

• Bun v1.3.2 or higher.
• Optional: NCBI API key for higher rate limits (10 req/s vs 3 req/s).

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/pubmed-mcp-server.git

2. Navigate into the directory:

cd pubmed-mcp-server

3. Install dependencies:

bun install

Configuration

All configuration is validated at startup via Zod schemas in src/config/server-config.ts. Key environment variables:

Variable	Description	Default
MCP_TRANSPORT_TYPE	Transport: stdio or http	stdio
MCP_HTTP_PORT	HTTP server port	3010
MCP_HTTP_ENDPOINT_PATH	HTTP endpoint path where the MCP server is mounted	/mcp
MCP_PUBLIC_URL	Public origin override for TLS-terminating reverse-proxy deployments (landing page, Server Card, RFC 9728 metadata).	none
MCP_AUTH_MODE	Authentication: none, jwt, or oauth	none
MCP_LOG_LEVEL	Log level (debug, info, warning, error, etc.)	info
MCP_GC_PRESSURE_INTERVAL_MS	Opt-in Bun-only forced-GC pressure loop (ms). Drains the per-request McpServer/McpSessionTransport cycle under sustained low-traffic HTTP. Recommended starting point if heap growth is observed: 60000.	0 (disabled)
LOGS_DIR	Directory for log files (Node.js only).	<project-root>/logs
STORAGE_PROVIDER_TYPE	Storage backend: in-memory, filesystem, supabase, cloudflare-kv/r2/d1	in-memory
NCBI_API_KEY	NCBI API key for higher rate limits (10 req/s vs 3 req/s)	none
NCBI_ADMIN_EMAIL	Contact email sent with NCBI requests (recommended by NCBI)	none
NCBI_REQUEST_DELAY_MS	Minimum gap between NCBI request starts in ms	334 (100 with key)
NCBI_MAX_CONCURRENT	Max concurrent in-flight NCBI requests	8
NCBI_MAX_RETRIES	Retry attempts for failed NCBI requests	6
NCBI_TIMEOUT_MS	Per-request HTTP timeout in ms	30000
NCBI_TOTAL_DEADLINE_MS	Total deadline across all retry attempts for one NCBI call, in ms	60000
UNPAYWALL_EMAIL	Contact email for Unpaywall. When set, pubmed_fetch_fulltext falls back to Unpaywall open-access copies for non-PMC DOIs	none
UNPAYWALL_TIMEOUT_MS	Per-request HTTP timeout for Unpaywall lookups and content fetches, in ms	20000
EUROPEPMC_ENABLED	Enable Europe PMC search tool and the pubmed_fetch_fulltext JATS fallback chain. Set false to disable all EPMC calls and skip tool registration.	true
EUROPEPMC_EMAIL	Optional contact email sent with Europe PMC requests (EBI courtesy).	none
EUROPEPMC_REQUEST_DELAY_MS	Minimum gap between Europe PMC request starts in ms	200
EUROPEPMC_MAX_RETRIES	Retry attempts for failed Europe PMC requests	3
EUROPEPMC_TIMEOUT_MS	Per-request HTTP timeout for Europe PMC calls, in ms	20000
OTEL_ENABLED	Enable OpenTelemetry	false

Running the server

Local development

• Build and run the production version:

  # One-time build
  bun run rebuild
  
  # Run the built server
  bun run start:http
  # or
  bun run start:stdio
  

• Run checks and tests:

  bun run devcheck  # Lints, formats, type-checks, and more
  bun run test      # Runs the test suite
  

Project structure

Directory	Purpose
src/mcp-server/tools	Tool definitions (*.tool.ts). Ten tools across PubMed, PMC, and Europe PMC.
src/mcp-server/resources	Resource definitions. Database info resource.
src/mcp-server/prompts	Prompt definitions. Research plan prompt.
src/services/ncbi	NCBI E-utilities service layer — API client, queue, parser, formatter.
src/services/europe-pmc	Europe PMC service — search + fullTextXML JATS retrieval. Reuses the NCBI JATS parser.
src/services/unpaywall	Unpaywall service — DOI → OA location resolution and content fetch (HTML/PDF).
src/config	Server-specific environment variable parsing and validation with Zod.
tests/	Unit and integration tests, mirroring the src/ structure.

Development guide

See CLAUDE.md for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for logging, ctx.state for storage
• Register new tools and resources in the createApp() arrays

Contributing

Issues and pull requests are welcome. Run checks and tests before submitting:

bun run devcheck
bun run test

License

This project is licensed under the Apache 2.0 License. See the LICENSE file for details.