bioRxiv Connector

bioRxiv Connector#

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

What You Can Do#

With this connector, Claude can help you:

  • Search for preprints by topic, author, or keywords

  • Track cutting-edge research before journal publication

  • Find preprints that have been published in peer-reviewed journals

  • Discover research funded by specific organizations

  • Monitor publication trends and submission statistics

  • Identify emerging research topics and collaborations

Data Source: bioRxiv and medRxiv APIs (Cold Spring Harbor Laboratory)

MCP Endpoint: https://mcp.deepsense.ai/biorxiv/mcp Coverage: 260,000+ preprints across 26 biological science categories and 40+ medical science categories

IMPORTANT: Preprints on bioRxiv and medRxiv have NOT undergone peer review. They should not be reported as established information.

Getting Started#

Adding the Connector to Claude#

  1. Open Claude’s Connector Settings

    • In Claude Desktop, select your profile icon in the bottom left

    • Navigate to Settings → Connectors

  2. Find the bioRxiv Connector

    • Browse the available connectors catalogue

    • Search for “bioRxiv” or find it under Research connectors

  3. Enable the Connector

    • Click on the bioRxiv Connector

    • Click “Enable” or “Add Connector”

    • The connector will be activated immediately

    • No authentication required - the connector works immediately after enabling

  4. Verify the Connection

    • Ask Claude: “Find recent CRISPR preprints on bioRxiv”

    • Claude should use the bioRxiv connector to search

Available Tools#

1. Search Preprints#

What it does: Searches for preprints by keywords, topics, or authors across bioRxiv and medRxiv.

Use it for:

  • Finding research on specific topics

  • Discovering latest preprints in your field

  • Searching by author names

  • Filtering by subject category

  • Tracking research over time periods

Example queries:

  • “Find recent preprints on CRISPR gene editing”

  • “Search for COVID-19 research on medRxiv from 2020”

  • “Show me neuroscience preprints from the last month”

  • “Find preprints about immunotherapy in cancer biology”

  • “Search for machine learning applications in biology”

What Claude will do:

  1. Search bioRxiv or medRxiv by your keywords

  2. Apply filters for date range or category if specified

  3. Return matching preprints with:

    • DOI (Digital Object Identifier)

    • Title and authors

    • Abstract

    • Posting date

    • Category/subject area

    • Version number (if revised)

    • Publication status (if published in a journal)

    • Download and view metrics

  4. Indicate total matches available

2. Get Preprint Details#

What it does: Retrieves complete information for a specific preprint by its DOI.

Use it for:

  • Reading full abstracts and methodology

  • Finding author contact information

  • Checking version history and revisions

  • Accessing PDF downloads

  • Verifying publication status

  • Getting supplementary materials

Example queries:

  • “Get details for preprint DOI 10.1101/2023.01.01.123456”

  • “Show me the full information for this bioRxiv paper”

  • “Has this preprint been published in a journal?”

  • “Find the corresponding author email for this preprint”

  • “Get the PDF link for DOI 10.1101/2022.12.15.520567”

What Claude will do:

  1. Retrieve complete preprint metadata

  2. Provide full title, abstract, and author list with affiliations

  3. Show version history if the preprint has been revised

  4. Include publication outcome:

    • Journal name if published

    • Published article DOI

    • Publication date

  5. Provide access links:

    • PDF URL

    • HTML URL (if available)

    • Supplementary materials

  6. Show license and copyright information

3. Get Categories#

What it does: Lists all available subject categories for bioRxiv and medRxiv.

Use it for:

  • Discovering available research areas

  • Choosing categories for focused searches

  • Understanding field organization

  • Browsing research by discipline

Example queries:

  • “What categories are available on bioRxiv?”

  • “List all medical research areas on medRxiv”

  • “Show me the subject categories for life sciences”

What Claude will do:

  1. Retrieve category lists for bioRxiv and/or medRxiv

  2. Provide bioRxiv categories (26 total):

    • Animal Behavior and Cognition, Biochemistry, Bioengineering, Bioinformatics, Biophysics, Cancer Biology, Cell Biology, Developmental Biology, Ecology, Evolutionary Biology, Genetics, Genomics, Immunology, Microbiology, Molecular Biology, Neuroscience, and more

  3. Provide medRxiv categories (40+ total):

    • Addiction Medicine, Allergy and Immunology, Cardiovascular Medicine, Epidemiology, Infectious Diseases, Oncology, Public Health, and more

  4. Help you select appropriate categories for searches

4. Search Published Preprints#

What it does: Finds preprints that have been formally published in peer-reviewed journals, with optional filtering by publisher.

Use it for:

  • Tracking publication outcomes

  • Verifying preprint quality through peer review

  • Finding the journal version of preprints

  • Calculating preprint-to-publication timelines

  • Identifying journals that publish from preprint servers

  • Filtering by specific publisher or journal

Search options:

  • Search all published preprints by date range

  • Filter by specific publisher using DOI prefix (e.g., ‘10.1038’ for Nature)

  • Include full details (authors, abstract) or summary only

  • Search bioRxiv, medRxiv, or both servers

Example queries:

  • “Find preprints that were published in journals last month”

  • “Show me which COVID-19 preprints got published”

  • “Track publication outcomes for neuroscience preprints”

  • “What preprints from 2022 have been peer-reviewed?”

  • “Find preprints published in Nature” (publisher=‘10.1038’)

  • “Show me papers that appeared in PLOS journals” (publisher=‘10.1371’)

Common publisher DOI prefixes:

  • ‘10.1038’ - Nature Publishing Group

  • ‘10.1126’ - Science/AAAS

  • ‘10.1016’ - Elsevier

  • ‘10.1371’ - PLOS

  • ‘10.7554’ - eLife

  • ‘10.1073’ - PNAS

What Claude will do:

  1. Search for preprints with published versions

  2. Optionally filter by publisher DOI prefix

  3. Return both preprint and journal information:

    • Preprint DOI and title

    • Authors and abstract (if include_details=True)

    • Journal published in

    • Published article DOI

    • Publication date

    • Time from preprint to publication

  4. Show which preprints achieved peer-reviewed publication

  5. Support pagination for large result sets

5. Search by Funder#

What it does: Finds preprints by funding source or grant organization using ROR IDs.

Use it for:

  • Tracking research funded by specific organizations

  • Analyzing funder research portfolios

  • Identifying funding opportunities

  • Understanding funder research priorities

  • Competitive intelligence on funded research

Example queries:

  • “Find NIH-funded preprints” (ROR ID: ‘021nxhr62’)

  • “Show me research funded by the Wellcome Trust” (ROR ID: ‘029chgv08’)

  • “What preprints acknowledge NSF funding?” (ROR ID: ‘01cwqze88’)

  • “Search for European Commission research” (ROR ID: ‘02mhbdp94’)

  • “Find Howard Hughes Medical Institute studies” (ROR ID: ‘05a28rw58’)

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

What Claude will do:

  1. Search by funder ROR ID (requires date range)

  2. Return funded preprints with:

    • Preprint information (DOI, title, authors, abstract)

    • Funder acknowledgments

    • Research topics and categories

  3. Show research outputs by funder

  4. Indicate funding patterns and priorities

  5. Filter by category if specified

6. Get Content Statistics#

What it does: Retrieves submission statistics for bioRxiv - tracking new papers, revisions, authors, and cumulative totals.

Use it for:

  • Understanding preprint growth trends

  • Analyzing submission patterns (new vs revised)

  • Tracking author participation over time

  • Monitoring platform growth

  • Generating submission trend reports

Example queries:

  • “Show me bioRxiv submission statistics”

  • “How many new preprints are posted monthly?”

  • “Track bioRxiv growth over the last year”

  • “Compare new submissions vs revisions”

What Claude will do:

  1. Retrieve content statistics by interval (monthly or yearly)

  2. Provide per period:

    • New papers posted

    • Revised papers updated

    • New authors joining

    • Cumulative papers total

    • Cumulative authors total

    • Time period (YYYY-MM or YYYY)

  3. Show historical data from bioRxiv inception to present

  4. Enable trend analysis and growth tracking

7. Get Usage Statistics#

What it does: Retrieves engagement statistics for bioRxiv - tracking views, downloads, and reader activity.

Use it for:

  • Analyzing readership trends

  • Tracking engagement metrics (views, downloads)

  • Comparing abstract vs full-text vs PDF engagement

  • Understanding usage patterns over time

  • Monitoring platform adoption

Example queries:

  • “Show me bioRxiv usage statistics”

  • “How many downloads does bioRxiv get monthly?”

  • “Track abstract views over time”

  • “Compare PDF downloads vs full-text views”

What Claude will do:

  1. Retrieve usage statistics by interval (monthly or yearly)

  2. Provide per period:

    • Abstract page views

    • Full-text HTML views

    • PDF downloads

    • Cumulative abstract views

    • Cumulative full-text views

    • Cumulative PDF downloads

    • Time period (YYYY-MM or YYYY)

  3. Show historical data from bioRxiv inception to present

  4. Enable engagement trend analysis

Usage Examples#

Example 1: Literature Review#

You: “I’m researching CRISPR applications in cancer therapy. Find recent preprints on this topic.”

Claude will:

  1. Use Search Preprints with keywords “CRISPR cancer therapy”

  2. Filter by recent posting dates

  3. Apply relevant categories (Cancer Biology, Molecular Biology)

  4. Return matching preprints with abstracts

  5. Use Get Preprint Details for promising results

  6. Use Search Published Preprints to check if any have been peer-reviewed

Example 2: Tracking Publication Outcomes#

You: “Has the preprint DOI 10.1101/2023.05.15.540789 been published in a journal?”

Claude will:

  1. Use Get Preprint Details to retrieve full information

  2. Check publication status field

  3. If published, provide:

    • Journal name

    • Published article DOI

    • Publication date

    • Time from preprint to publication

  4. Provide links to both preprint and published versions

Example 3: Finding Papers Published in Top Journals#

You: “Show me preprints that were published in Nature in the last year”

Claude will:

  1. Use Search Published Preprints with:

    • publisher=‘10.1038’ (Nature DOI prefix)

    • date_from and date_to for last year

    • server=‘biorxiv’ or ‘medrxiv’ as appropriate

  2. Return preprints published in Nature journals with:

    • Preprint and published DOIs

    • Publication timeline

    • Research topics

  3. Show acceptance patterns and time to publication

Example 4: Funding Analysis#

You: “What COVID-19 research has the NIH funded? Show me preprints from 2020-2021.”

Claude will:

  1. Use Search by Funder with:

    • funder_ror_id=‘021nxhr62’ (NIH)

    • date_from=‘2020-01-01’, date_to=‘2021-12-31’

  2. Return NIH-funded preprints with grant acknowledgments and research topics

  3. Use Search Published Preprints to track which ones achieved peer-review

  4. Analyze publication outcomes and research impact

Example 5: Analyzing Platform Growth#

You: “How has bioRxiv grown over time? Show me submission and usage trends.”

Claude will:

  1. Use Get Content Statistics with interval=‘monthly’

  2. Display new papers, revisions, and author participation trends

  3. Use Get Usage Statistics with interval=‘monthly’

  4. Show abstract views, downloads, and engagement metrics

  5. Compare growth patterns and identify emerging trends

Need Help?#

For issues or questions about the bioRxiv Connector, see our Troubleshooting Guide.

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