biorxiv-mcp-server

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Overview

bioRxiv and medRxiv preprints, metadata and full text. Search by keyword and author, browse a date interval (optionally by subject), fetch any preprint by DOI, and see which preprints went on to journal publication.

Tools

Tool	Description
biorxiv_get_preprint	Fetch full metadata, abstract, revision history, and journal crosswalk for one or more preprints by DOI
biorxiv_list_recent	List preprints posted or updated within a date interval, with optional server, category, and funder filters
biorxiv_search_preprints	Search preprints by keyword and/or author via EuropePMC for relevance ranking, enriched with bioRxiv/medRxiv metadata
biorxiv_get_published_version	Resolve a preprint DOI to its journal publication record (journal DOI, name, published date), or a journal article's DOI to the preprint it was posted as
biorxiv_list_published_versions	List preprints that appeared as journal articles within a journal publication-date interval, whenever they were posted, optionally from one publisher
biorxiv_get_fulltext	Retrieve a preprint's full text as best-effort Markdown extracted from its rendered HTML article page
biorxiv_list_categories	List valid subject category strings for bioRxiv and medRxiv

Capability reference

biorxiv_get_preprint _tool

• Takes DOIs bare or pasted (https://doi.org/…, doi:…, a biorxiv.org/medrxiv.org article URL, a vN or .full suffix), scoped to biorxiv, medrxiv, or both (default both)
• Accepts up to 200 entries and looks up the first 10 distinct DOIs; the rest come back in unprocessed[] to pass in another call. A repeated DOI is looked up once, and every list keeps input order
• Each preprint returns its full revision history in revisions[] — title, authors, category, license, awards, jatsxmlUrl, publishedJournalDoi once accepted, and the server it was found on (biorxiv or medrxiv, ready to pass back as server). Funder names are omitted because the upstream API misattributes them
• The abstract sits on the latest revision only: the upstream API keeps one abstract per preprint. An earlier revision's own abstract is on its article page, through biorxiv_get_fulltext with version
• A DOI that fails lands in failed[] with a reason (not_found, invalid_doi_format, upstream_unavailable, rate_limited) and a retryable flag; not_found only when every attempted server answered

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biorxiv_list_recent _tool

• Takes a start_date/end_date interval, server (default both), and optional category (a value from biorxiv_list_categories) and bioRxiv-only funder (a ROR ID) filters; a filter that cannot be applied raises invalid_category or invalid_funder
• Pages of 30 advance with an integer cursor, tracked per server ({ biorxiv: { cursor, total }, medrxiv: { cursor, total } }); a cursor past the last page is marked exhausted: true, and a server that did not answer is named in failed[]
• Abstracts are omitted by default; include_abstract: true adds them. Each is the preprint's latest-revision abstract, even on a row for an earlier revision

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biorxiv_search_preprints _tool

• Takes query and/or author, optional date_from/date_to and server (default both); up to 100 results per page (default 25; a larger limit returns 100 with a notice), paged with cursor_mark
• EuropePMC ranks the matches (it indexes new preprints within 1–2 days of posting) and the bioRxiv/medRxiv API enriches them with the same fields as biorxiv_get_preprint; a record left with EuropePMC metadata only carries enriched: false and an enrichment_error (service_error, rate_limited, not_found), with partial_results set
• Abstracts are included by default; include_abstract: false drops them for a response about a third the size

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biorxiv_get_published_version _tool

• Takes one DOI and server (default both): a preprint DOI (10.1101/, 10.64898/), or a journal article's DOI, which resolves to the preprint it was posted as (10.1016/j.cell.2020.01.001 → 10.1101/614172); 10.64898/ DOIs resolve through the preprint's own journal DOI
• Returns the preprint DOI, journal DOI, journal name, published date, corresponding-author institution, and the server that answered; if no server answers it raises a retryable upstream_unavailable or rate_limited, never doi_not_found
• Cold Spring Harbor Laboratory Press journal DOIs (10.1101/gr.…, gad.…, lm.…) share the preprint prefix and cannot be resolved by DOI

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biorxiv_list_published_versions _tool

• Takes a start_date/end_date interval of journal publication dates and server (default both); each row matches the record biorxiv_get_published_version returns, and may be a preprint posted years earlier
• Returns limit rows per server (default 25, up to the API's 100-row page) from an integer cursor, continued at each server's nextCursor; a cursor past the last row is marked exhausted: true, and a server that did not answer is named in failed[]
• Optional publisher, a journal DOI prefix (10.7554 for eLife), lists only the bioRxiv preprints published under it; server: "both" queries bioRxiv alone, and server: "medrxiv" or a prefix the API does not recognize raises invalid_publisher. These rows carry no journal name, authors, or abstract
• Abstracts are omitted by default; include_abstract: true adds them

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biorxiv_get_fulltext _tool

• Takes a DOI, server (default both), and an optional version (or a vN suffix; the two must agree, and a version the preprint lacks raises version_not_found); returns Markdown extracted from the rendered HTML article page, naming the answering server
• Table cells are not on the page: each table keeps its caption, and omittedTables names it with the URL that serves its cells
• Pages via offset/limit characters (default 20,000), reporting totalChars, remainingChars, hasMore, and wordCount; PDF-only preprints and blocked pages raise fulltext_unavailable, routing to biorxiv_get_preprint

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biorxiv_list_categories _tool

• No API call — a static list of 25 bioRxiv and 51 medRxiv categories, limited to the ones the listing API filters on
• Use it to pick a category for biorxiv_list_recent

Features

Built on @cyanheads/mcp-ts-core: stdio and Streamable HTTP transports, pluggable auth (none / jwt / oauth), swappable storage (in-memory, filesystem, Supabase, Cloudflare KV/R2/D1), structured logging with optional OpenTelemetry tracing.

bioRxiv-specific:

• BiorxivApiService wraps api.biorxiv.org (details, publications, and crosswalk endpoints) and EuropePmcService wraps EuropePMC search, both with retry and exponential backoff
• BiorxivFullTextService extracts Markdown from the article pages on www.biorxiv.org / www.medrxiv.org
• Every upstream retry ladder runs on what is left of the tool call's one 50 s budget, so a hung origin ends before a client's 60 s request timeout — in a classified, retryable error, or, when the step that hung is optional, in a result that says what is missing
• Queries biorxiv and medrxiv in parallel when server="both", each result naming the server that answered; a lookup by DOI stops waiting once the server holding that DOI answers
• Polite User-Agent header including a mailto address (BIORXIV_MAILTO env var) per Cold Spring Harbor Lab API guidelines
• Pairs with pubmed-mcp-server (post-publication), openalex-mcp-server (citation analytics), and crossref-mcp-server (DOI metadata)

Agent-friendly output:

• Graceful partial failure — per-DOI and per-server failures land in failed[] with a typed reason and retryable flag instead of aborting the call
• Rate-limit transparency — a 429 surfaces as reason: "rate_limited" with the parsed retryAfter wait, distinct from upstream_unavailable
• Typed enrichment status — biorxiv_search_preprints results carry enriched plus a typed enrichment_error (service_error / rate_limited / not_found)
• Clean titles and abstracts — export markup and symbol placeholders ({beta}, [≥]) are resolved to plain text

Getting started

Public Hosted Instance

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

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

Self-Hosted / Local

Add the following to your MCP client configuration file.

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["@cyanheads/biorxiv-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info",
        "BIORXIV_MAILTO": "[email protected]"
      }
    }
  }
}

Or with npx (no Bun required):

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@cyanheads/biorxiv-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info",
        "BIORXIV_MAILTO": "[email protected]"
      }
    }
  }
}

Or with Docker:

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

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

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

Prerequisites

• Bun v1.4.0 or higher (or Node.js v24+).

Installation

1. Clone the repository:

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

2. Navigate into the directory:

cd biorxiv-mcp-server

3. Install dependencies:

bun install

4. Configure environment:

cp .env.example .env
# optionally set BIORXIV_MAILTO for polite API access

Configuration

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

Variable	Description	Default
BIORXIV_MAILTO	Email address for the User-Agent header; optional but recommended.	—
BIORXIV_API_BASE_URL	Override the bioRxiv API base URL.	https://api.biorxiv.org
EUROPEPMC_API_BASE_URL	Override the EuropePMC base URL.	https://www.ebi.ac.uk/europepmc/webservices/rest
BIORXIV_WEB_BASE_URL	Override the bioRxiv website base URL (full-text HTML source for biorxiv_get_fulltext).	https://www.biorxiv.org
MEDRXIV_WEB_BASE_URL	Override the medRxiv website base URL (full-text HTML source for biorxiv_get_fulltext).	https://www.medrxiv.org
MCP_TRANSPORT_TYPE	Transport: stdio or http.	stdio
MCP_HTTP_PORT	HTTP server port.	3010
MCP_HTTP_ENDPOINT_PATH	HTTP endpoint path.	/mcp
MCP_AUTH_MODE	Auth mode: 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
LOG_TOOL_FAILURE_PAYLOADS	Log each failed tool call's arguments and result, redacted by key name and capped at LOG_TOOL_FAILURE_PAYLOAD_MAX_BYTES (default 16384). A secret inside a free-form value is not redacted.	false
OTEL_ENABLED	Enable OpenTelemetry instrumentation.	false

See .env.example for the full list of optional overrides.

Running the server

Local development

• Build and run:

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

• Run checks and tests:

  bun run devcheck   # Lint, format, typecheck, security
  bun run test       # Vitest test suite
  bun run lint:mcp   # Validate MCP definitions against spec
  

Docker

docker build -t biorxiv-mcp-server .
docker run --rm -e [email protected] -p 3010:3010 biorxiv-mcp-server

The Dockerfile defaults to HTTP transport, stateless session mode, and logs to /var/log/biorxiv-mcp-server. OpenTelemetry peer dependencies are installed by default — build with --build-arg OTEL_ENABLED=false to omit them.

Project structure

Directory	Purpose
src/index.ts	createApp() entry point — registers tools and initializes services.
src/config	Server-specific environment variable parsing and validation with Zod.
src/mcp-server/tools	Tool definitions (*.tool.ts). Seven tools across bioRxiv and medRxiv.
src/services/biorxiv	BiorxivApiService — details, publications, and crosswalk endpoint wrappers with retry.
src/services/biorxiv-fulltext	BiorxivFullTextService — rendered HTML article page fetch and Markdown extraction.
src/services/europe-pmc	EuropePmcService — preprint keyword/author search endpoint wrapper.
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 request-scoped logging, ctx.state for tenant-scoped storage
• Register new tools via the barrel in src/mcp-server/tools/definitions/index.ts
• Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields

Contributing

Issues are welcome. Run checks and tests before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.