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 Articles#

What it does: Finds preprints that have been formally published in peer-reviewed journals.

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

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?”

What Claude will do:

  1. Search for preprints with published versions

  2. Return both preprint and journal information:

    • Preprint DOI and title

    • Authors and abstract

    • Journal published in

    • Published article DOI

    • Publication date

    • Time from preprint to publication

  3. Show which preprints achieved peer-reviewed publication

  4. Indicate total published articles available

5. Search bioRxiv Publications#

What it does: Tracks bioRxiv-specific publication outcomes with simplified data (bioRxiv only, not medRxiv).

Use it for:

  • Analyzing bioRxiv publication patterns

  • Getting streamlined publication data

  • Tracking publication rates by category

  • Understanding field validation through peer review

Example queries:

  • “Show me recent bioRxiv papers that got published”

  • “Track publication outcomes for cancer biology preprints”

  • “Find bioRxiv preprints published in the last 3 months”

What Claude will do:

  1. Search bioRxiv publications (simpler than full search)

  2. Return streamlined information:

    • bioRxiv DOI

    • Published DOI

    • Title

    • Category

    • Preprint date

    • Published date

  3. Calculate time to publication

  4. Filter by date range or recent activity

6. Search by Publisher#

What it does: Finds preprints by the journal or publisher that eventually published them.

Use it for:

  • Tracking specific journal’s preprint pipeline

  • Finding preprints in top-tier journals

  • Analyzing journal acceptance patterns

  • Identifying research quality indicators

Example queries:

  • “Find preprints published in Nature”

  • “Show me papers that appeared in Cell”

  • “What preprints did PLOS ONE publish?”

  • “Search for preprints published by Science journal”

What Claude will do:

  1. Search by publisher or journal name (Nature, Cell, PLOS, Science, etc.)

  2. Return preprints published in that journal:

    • Preprint and published DOIs

    • Title and authors

    • Publication timeline

    • Category information

  3. Show journal acceptance patterns

  4. Indicate total preprints published by that journal

7. Search by Funder#

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

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”

  • “Show me research funded by the Wellcome Trust”

  • “What preprints acknowledge NSF funding?”

  • “Search for Bill & Melinda Gates Foundation research”

  • “Find Howard Hughes Medical Institute studies”

What Claude will do:

  1. Search by funder name or ROR ID (NIH, NSF, Wellcome Trust, ERC, etc.)

  2. Return funded preprints with:

    • Preprint information

    • Funder acknowledgments

    • Grant numbers (if available)

    • Research topics and categories

  3. Show research outputs by funder

  4. Indicate funding patterns and priorities

8. Get Statistics#

What it does: Retrieves submission and usage statistics for bioRxiv and medRxiv.

Use it for:

  • Understanding preprint growth trends

  • Comparing bioRxiv vs medRxiv volume

  • Identifying popular research categories

  • Analyzing field adoption of preprints

  • Tracking research output over time

Example queries:

  • “Show me bioRxiv submission statistics”

  • “How many preprints are on medRxiv?”

  • “What are the trending categories on bioRxiv?”

  • “Track preprint growth over the last year”

What Claude will do:

  1. Retrieve server statistics

  2. Provide:

    • Total preprints posted

    • Submissions by month/year

    • Downloads and abstract views

    • Category distributions

    • Growth trends over time

  3. Compare bioRxiv vs medRxiv if requested

  4. Show popular categories and emerging trends

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 Articles 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: 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 “NIH” or “National Institutes of Health”

  2. Filter by date range (2020-2021)

  3. Search for “COVID-19” or related terms

  4. Return NIH-funded preprints with:

    • Grant acknowledgments

    • Research topics

    • Publication outcomes

  5. Use Search Published Articles to track peer-review success

Need Help?#

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

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