pubmed-mcp-server

<div align="center"> <h1>@cyanheads/pubmed-mcp-server</h1> <p><b>Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.</b> <div>11 Tools • 1 Resource • 1 Prompt</div> </p> </div>

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Public Hosted Server: https://pubmed.caseyjhand.com/mcp

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Tools

11 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_europepmc_fetch | Fetch complete Europe PMC records — including the untruncated abstract — by source + epmcId, the only identifier many preprint, patent, and Agricola records carry | | 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
• Character budgets keep context size predictable: maxCharacters caps body text per article (PMC sections and subsections, or the Unpaywall body), maxCharactersPerSection caps a single PMC section, and overflowMode picks between truncate (fill sections in document order) and outline (split the budget evenly so every heading survives with an excerpt). Budgets run after the semantic filters, and a truncation object reports per-article and per-section character counts whenever anything was shortened
• 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
• abstractSnippet is capped at 400 characters to keep a page bounded; abstractTruncated says whether it was cut, and pubmed_europepmc_fetch returns the whole abstract for the records worth reading in full
• Disabled when EUROPEPMC_ENABLED=false; tool is not registered in that case

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pubmed_europepmc_fetch

Fetch complete Europe PMC records by source + epmcId, the detail counterpart to pubmed_europepmc_search.

• Returns the full, untruncated abstract as display-ready plain text — markup stripped, HTML entities decoded
• Addressed by the source and epmcId of a search hit, the only identifier preprint (PPR), patent (PAT), and Agricola (AGR) records reliably carry — pubmed_fetch_articles needs a PMID and pubmed_fetch_fulltext needs a PMCID, PMID, or DOI
• Up to 25 records per call, resolved in a single Europe PMC request
• Pairs unresolved requests back to the caller in notFound instead of failing the batch
• 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

1. Navigate into the directory:

cd pubmed-mcp-server

1. 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). Eleven 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.