bioRxiv

MCP server claude life-sciences

The bioRxiv Connector gives Claude access to bioRxiv and medRxiv preprint servers, hosting research papers in biological and medical sciences posted before peer review.

Homepage: https://claude.com/resources/tutorials/using-the-biorxiv-and-medrxiv-connector-in-claude
Remote URL: https://hcls.mcp.claude.com/biorxiv/mcp
Transport: streamable-http

Tools (7)

Extracted live via the executor SDK.

search_preprints
Search bioRxiv/medRxiv preprints. Returns DOI, title, authors, abstract preview, category.
WHEN TO USE:
- Literature review and research discovery
- Finding recent research in specific fields
- Tracking new submissions by date or category
SEARCH METHODS (use only ONE):
- Date range: date_from + date_to (e.g., '2024-01-01' to '2024-06-30') - RECOMMENDED
- Recent days: recent_days=30 (last 30 days)
- Recent count: recent_count=50 (searches last ~90 days, returns up to 'limit' results)
IMPORTANT: All searches use date ranges internally. recent_count searches a 90-day window. If no search method specified, defaults to last 60 days.
SERVERS:
- 'biorxiv': Biological sciences (default)
- 'medrxiv': Medical/health sciences
CATEGORIES (27 available): biochemistry, bioinformatics, cancer biology, cell biology, genetics, genomics, immunology, microbiology, molecular biology, neuroscience, and 17 more. Use get_categories tool for full list.
LIMITATIONS:
- NO keyword/text search - filter by category and date only
- Results are NOT peer-reviewed preprints
EXAMPLES:
- Last 30 days of neuroscience: recent_days=30, category='neuroscience'
- Cancer biology Q1 2024: date_from='2024-01-01', date_to='2024-03-31', category='cancer biology'
PAGINATION: Use cursor for next page (cursor=100 for results 100-199)
RELATED: get_preprint (full details by DOI), get_categories (list all categories)
get_preprint
Get complete metadata for a specific preprint by DOI.
WHEN TO USE:
- You have a DOI and need full details
- Need abstract, authors, PDF URL, funding info
- Checking if preprint was published in a journal
RETURNS: title, all authors, corresponding author + institution, full abstract, category, license, version, PDF URL, web URL, funding details, published DOI (if available)
DOI FORMATS (all accepted):
- '10.1101/2024.01.15.123456'
- ''
SERVERS:
- 'biorxiv': For bioRxiv preprints (DOI contains biorxiv dates like 2024.01.15)
- 'medrxiv': For medRxiv preprints
IMPORTANT: Preprints are NOT peer-reviewed
RELATED: search_preprints (find DOIs), search_published_articles (find journal version)
get_categories
List all 27 bioRxiv subject categories for filtering searches.
WHEN TO USE:
- Before search_preprints to see valid category values
- To understand research area classifications
RETURNS: Category names and API-compatible format (e.g., 'cancer biology' -> 'cancer_biology')
FULL LIST: animal behavior and cognition, biochemistry, bioengineering, bioinformatics, biophysics, cancer biology, cell biology, clinical trials, developmental biology, ecology, epidemiology, evolutionary biology, genetics, genomics, immunology, microbiology, molecular biology, neuroscience, paleontology, pathology, pharmacology and toxicology, physiology, plant biology, scientific communication and education, synthetic biology, systems biology, zoology
search_published_preprints
Find preprints that have been published in peer-reviewed journals.
WHEN TO USE:
- Track which preprints became journal articles
- Find the peer-reviewed version of a preprint
- Analyze preprint-to-publication patterns
- Filter articles by whether they were published by a specific journal
SEARCH METHODS (use only ONE):
- Date range: date_from + date_to
- Recent count: recent_count=50
- Recent days: recent_days=30
FILTERS:
- include_details: True for full metadata (slower), False for summary (faster)
- publisher: Filter by DOI prefix (e.g., '10.1038' for Nature) - see below
COMMON PUBLISHER PREFIXES:
- '10.1038' - Nature Publishing Group
- '10.1126' - Science/AAAS
- '10.1016' - Elsevier
- '10.1371' - PLOS
- '10.7554' - eLife
- '10.1073' - PNAS
EXAMPLE: Find recently published medRxiv papers: server='medrxiv', recent_days=30
search_by_funder
Search for preprints funded by a specific organization using ROR ID.
WHEN TO USE:
- Track research output from specific funding bodies
- Analyze funder-specific publication patterns
- Monitor grant-funded research areas
REQUIRES: funder_ror_id (9-character ROR ID)
COMMON FUNDER ROR IDS:
- '021nxhr62' - NIH (National Institutes of Health)
- '01cwqze88' - NSF (National Science Foundation)
- '02mhbdp94' - European Commission
- '029chgv08' - Wellcome Trust
- '05a28rw58' - HHMI (Howard Hughes Medical Institute)
- '006wxqw41' - MRC (Medical Research Council UK)
- '00f54p054' - BBSRC (UK)
- '01s5ya894' - Chan Zuckerberg Initiative
Find more ROR IDs at:
RETURNS: DOI, title, authors, abstract preview, category (same as search_preprints)
IMPORTANT: Date range required. Earliest date is 2025-04-10 (funder metadata inception)
SERVERS: 'biorxiv' or 'medrxiv'
get_content_statistics
Get bioRxiv submission statistics over time.
WHEN TO USE:
- Analyze bioRxiv growth trends
- Track submission patterns (new vs revised papers)
- Generate platform statistics reports
RETURNS (per month/year): new_papers, revised_papers, new_authors, cumulative_papers, cumulative_authors, period (YYYY-MM or YYYY)
INTERVALS: 'monthly' (default) or 'yearly'
NOTE: Returns all historical data from bioRxiv inception to present
get_usage_statistics
Get bioRxiv usage/engagement statistics over time.
WHEN TO USE:
- Analyze readership trends
- Track engagement metrics (views, downloads)
- Compare abstract vs full-text vs PDF engagement
RETURNS (per month/year): abstract_views, full_text_views, pdf_downloads, cumulative_abstract, cumulative_full_text, cumulative_pdf, period (YYYY-MM or YYYY)
INTERVALS: 'monthly' (default) or 'yearly'
NOTE: Returns all historical data from bioRxiv inception to present