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Unofficial bioRxiv MCP Server

Unofficial bioRxiv MCP Server

Model Context Protocol (MCP) server for accessing bioRxiv and medRxiv preprint servers (Cold Spring Harbor Laboratory). Provides access to 260,000+ preprints across 27 biological and 51 medical science categories.

Features

  • Single unified tool (biorxiv_info) with 7 methods

  • No API key required — uses the public bioRxiv API

  • Keyword search with client-side filtering over date-range browsing

  • Full preprint metadata retrieval by DOI (all versions)

  • Published preprint tracking (preprint → journal mapping)

  • Funder search by ROR ID (NIH, NSF, Wellcome, etc.)

  • Content and usage statistics (submissions, views, downloads)

  • Subject category listings for both bioRxiv and medRxiv

Related MCP server: medRxiv-MCP-Server

Installation

cd biorxiv-mcp-server
npm install
npm run build

Usage

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "command": "node",
      "args": ["/path/to/biorxiv-mcp-server/build/index.js"]
    }
  }
}

Tool: biorxiv_info

Single unified tool with multiple methods accessed via the method parameter.

Methods

1. search_preprints

Search preprints by keywords. Uses client-side filtering over the bioRxiv date-range API (no native keyword search endpoint). Scans up to 300 results across the date range.

{
  "method": "search_preprints",
  "query": "CRISPR gene editing",
  "server": "biorxiv",
  "date_from": "2025-01-01",
  "date_to": "2025-12-31",
  "category": "genetics",
  "limit": 30
}

Returns: doi, title, authors, abstract (500 chars), date, category, version, published status.

2. get_preprint_details

Get complete metadata for a specific preprint by DOI, including all versions.

{
  "method": "get_preprint_details",
  "doi": "10.1101/2024.01.15.575123",
  "server": "biorxiv"
}

Returns: all versions with doi, title, authors, full abstract, date, category, license, published status.

3. get_categories

List all available subject categories for bioRxiv (27) and medRxiv (51).

{
  "method": "get_categories"
}

4. search_published_preprints

Find preprints that have been formally published in peer-reviewed journals.

{
  "method": "search_published_preprints",
  "date_from": "2025-01-01",
  "publisher": "10.1038",
  "server": "biorxiv",
  "limit": 30
}

Common publisher DOI prefixes: 10.1038 (Nature), 10.1126 (Science), 10.1016 (Elsevier), 10.1371 (PLOS), 10.7554 (eLife), 10.1073 (PNAS).

5. search_by_funder

Find preprints by funding organization using ROR IDs. Data available from 2025-04-10 onwards.

{
  "method": "search_by_funder",
  "funder_ror_id": "021nxhr62",
  "server": "biorxiv",
  "limit": 30
}

Common ROR IDs: 021nxhr62 (NIH), 01cwqze88 (NSF), 02mhbdp94 (European Commission), 029chgv08 (Wellcome Trust), 05a28rw58 (HHMI), 006wxqw41 (MRC).

6. get_content_statistics

Get submission statistics (new papers, revisions, authors).

{
  "method": "get_content_statistics",
  "interval": "m"
}

Interval: "m" (monthly) or "y" (yearly).

7. get_usage_statistics

Get engagement statistics (views, downloads).

{
  "method": "get_usage_statistics",
  "interval": "m",
  "server": "biorxiv"
}

Example Queries with Claude

Once configured, you can ask Claude:

  • "Search bioRxiv for recent CRISPR preprints"

  • "Get details for preprint DOI 10.1101/2024.01.15.575123"

  • "What bioRxiv categories are available?"

  • "Find preprints published in Nature this month"

  • "Show NIH-funded preprints in cancer biology"

  • "What are the monthly submission statistics for bioRxiv?"

  • "Search medRxiv for COVID-19 vaccine preprints"

Important Notes

  • Preprints are NOT peer-reviewed — results should not be cited as established fact

  • Keyword search is client-side (bioRxiv API only supports date-range browsing), so narrow date ranges improve relevance

  • DOI format: 10.1101/YYYY.MM.DD.NNNNNN (bioRxiv prefix is always 10.1101)

  • Funder data only available from April 10, 2025 onwards

Data Source

  • Database: bioRxiv / medRxiv (Cold Spring Harbor Laboratory)

  • Preprints: 260,000+ across biology and medicine

  • Categories: 27 bioRxiv + 51 medRxiv subject areas

  • API: https://api.biorxiv.org/

  • Rate limits: No published limits, respectful usage encouraged

License

MIT

Available Tools

1 tool
biorxiv_infoB

Unified bioRxiv/medRxiv preprint database access. 260K+ preprints. Methods: search_preprints (keyword search with date range filtering), get_preprint_details (full metadata by DOI), get_categories (list subject categories), search_published_preprints (find preprints published in journals), search_by_funder (find preprints by funding org ROR ID), get_content_statistics (submission stats), get_usage_statistics (views/downloads stats).

ParametersJSON Schema
NameRequiredDescriptionDefault
doiNoPreprint DOI e.g. "10.1101/2024.01.15.575123" (for get_preprint_details)
limitNoMaximum results to return (default 30)
queryNoSearch keywords (for search_preprints — client-side filter against title/abstract)
cursorNoPagination offset (default 0)
methodYesThe bioRxiv operation to perform.
serverNoWhich server to query (default "biorxiv")
date_toNoEnd date YYYY-MM-DD (optional, defaults to today)
categoryNoSubject category filter (optional)
intervalNoTime interval for stats: "m" (monthly) or "y" (yearly)
date_fromNoStart date YYYY-MM-DD (optional)
publisherNoPublisher DOI prefix e.g. "10.1038" for Nature (for search_published_preprints)
funder_ror_idNoROR ID e.g. "021nxhr62" for NIH (for search_by_funder)

TDQS

B3.2/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description must disclose behavioral traits. It does not mention read-only nature, rate limits, authentication, data freshness, or what happens on errors. The only behavioral fact is the scale ('260K+ preprints'), but this does not convey operational behavior. The description relies on the schema for parameter details but adds no transparency about side effects or execution context.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is compact: a purpose statement, a scale fact, and a structured method list. It front-loads the core purpose and uses a clear enumeration. While the method list is long, each item is a concise phrase. No redundant fluff or unnecessary details, making it efficient for scanning.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a tool with 7 methods and 12 parameters, the description provides a high-level map of capabilities but lacks depth. It does not specify return formats, example usage, or decision trees for method selection. Given no output schema, the description only partially suffices; an agent would need to rely on the schema and method names to infer correctness.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, and parameter descriptions already include method mappings (e.g., doi is 'for get_preprint_details'). The tool description lists methods but does not elaborate on parameter syntax or relationships beyond what the schema provides. Thus it adds marginal value, meeting the baseline for high schema coverage.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly identifies the resource (bioRxiv/medRxiv preprint database) and the action (unified access), then enumerates specific methods such as 'search_preprints' and 'get_preprint_details', which indicates the tool's scope. It does not explicitly distinguish from sibling tools (none provided), but the method list clarifies purpose. The verb 'access' is somewhat generic, but the method names add specificity.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description lists all available methods with brief parentheticals (e.g., 'keyword search with date range filtering' for search_preprints), implying when each might be used. However, it lacks explicit guidance on choosing between similar methods (e.g., search_preprints vs search_published_preprints) or when this tool is not appropriate. No exclusions or alternative tools are mentioned.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. 1 tool updatev1.0.0
    • First observedbiorxiv_info

TDQS

A3.6/5.0
Disambiguation5/5

With only one tool, there is no possibility of confusing it with other tools. The tool's description clearly enumerates its methods, so an agent can understand its purpose without ambiguity.

Naming Consistency5/5

The single tool name 'biorxiv_info' is clear and follows a consistent naming style. Since there are no other tools to contrast with, consistency is trivially high.

Tool Count3/5

A single tool is borderline for a server, but given the narrow scope of bioRxiv/medRxiv access, it can be acceptable. However, it feels thin compared to servers that expose separate tools for distinct operations.

Completeness5/5

The tool bundles methods covering search, metadata retrieval, category listing, publication status, funder lookup, and statistics. This provides broad coverage of preprint database operations, with no obvious dead ends.

Maintenance

ActivityInactive
ResponsivenessSyncing

Resources

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