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Tools

Nine tools for working with PubMed and NCBI data:

Tool	Description
pubmed_search_articles	Search PubMed with full query syntax, field-specific filters, date ranges, pagination, and optional brief summaries
pubmed_fetch_articles	Fetch full article metadata by PMIDs — abstract, authors, journal, MeSH terms, grants
pubmed_fetch_fulltext	Fetch full-text articles from PubMed Central, with optional Unpaywall fallback for non-PMC DOIs (HTML → Markdown or PDF → text)
pubmed_format_citations	Generate formatted citations in APA 7th, MLA 9th, BibTeX, or RIS
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 from PubMed Central (PMC), with an optional Unpaywall fallback for articles not in PMC.

• Accepts PMC IDs directly or PubMed IDs (auto-resolved to PMCIDs via ELink)
• PMC path returns complete article body organized by sections and subsections, plus optional references from back matter
• Unpaywall fallback (enabled by setting UNPAYWALL_EMAIL) resolves DOIs to legal open-access copies hosted by publishers or institutional repositories; extracts HTML landing pages to Markdown via Defuddle or PDFs to text via unpdf
• Discriminated output contract — source: "pmc" (structured sections) or source: "unpaywall" (single body + contentFormat metadata: html-markdown or pdf-text)
• Structured unavailable reasons (no-pmc-fallback-disabled, no-doi, no-oa, fetch-failed, parse-failed, service-error) so callers can retry or explain to users without parsing text
• 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_format_citations

Generate formatted citations for articles.

• Four citation styles: APA 7th, MLA 9th, BibTeX, RIS
• 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
• Similarity scores included for similar relationship type

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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
• Returns all available identifier mappings for each input ID

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) — zero deps, Workers-compatible

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

Self-Hosted / Local

Add the following to your MCP client configuration file.

{
  "mcpServers": {
    "pubmed": {
      "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": {
      "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": {
      "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
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	Delay between NCBI requests in ms	334 (100 with key)
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
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). Nine PubMed tools.
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/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.