Skills biorxiv-database
🧬

biorxiv-database

Safe 🌐 Network access📁 Filesystem access

Search bioRxiv preprints by keywords, authors, and dates

Also available from: davila7

Researchers waste hours manually searching bioRxiv for relevant preprints. This skill automates literature discovery with precise filtering by keywords, authors, date ranges, and scientific categories.

Supports: Claude Codex Code(CC)
🥉 76 Bronze
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Go to Settings → Capabilities → Skills → Upload skill

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Test it

Using "biorxiv-database". Search for COVID-19 vaccine papers from 2021

Expected outcome:

  • Found 342 papers matching your criteria
  • Top result: 'mRNA vaccine efficacy against variants' by Smith et al.
  • DOI: 10.1101/2021.03.15.123456
  • Published: March 15, 2021
  • Abstract: We analyzed vaccine effectiveness...
  • PDF available for download

Using "biorxiv-database". Find neuroscience papers by author 'Yong' from 2024

Expected outcome:

  • Found 8 papers
  • Recent: 'Neural circuit mapping in vivo' by Yong et al.
  • Date: 2024-08-20
  • Category: neuroscience
  • PDF ready for download

Security Audit

Safe
v4 • 1/17/2026

The static analyzer flagged 248 issues, but all are false positives. Markdown documentation backticks were misidentified as shell command execution. The Python script is a straightforward bioRxiv API client that makes legitimate requests to https://api.biorxiv.org, saves results to files, and optionally supports API key authentication. No malicious intent, data exfiltration, or suspicious behavior patterns found.

4
Files scanned
1,425
Lines analyzed
2
findings
4
Total audits

Risk Factors

🌐 Network access (1)
scripts/biorxiv_search.py:23
📁 Filesystem access (1)
scripts/biorxiv_search.py:255
Audited by: claude View Audit History →

Quality Score

64
Architecture
100
Maintainability
87
Content
21
Community
100
Security
91
Spec Compliance

What You Can Build

Literature review for thesis

Search recent preprints in your field, download relevant papers, and track citations for comprehensive literature reviews.

Monitor competitor research

Track publications by specific authors or labs to stay updated on competing research in your field.

Trend analysis in life sciences

Analyze publication patterns over time to identify emerging research trends and hotspots.

Try These Prompts

Basic keyword search 
Search bioRxiv for preprints about CRISPR gene editing published in the last 30 days and save results to crispr_recent.json
Author tracking 
Find all preprints by author 'Zhang F' from 2023-2024 and download the PDFs
Category filtering 
Search for machine learning papers in the neuroscience category from the last 6 months, include abstracts
Systematic review 
Search bioRxiv for papers matching keywords: 'single-cell RNA-seq', 'spatial transcriptomics', 'multi-omics' published between 2022-2024, filter by bioinformatics category, and export complete metadata

Best Practices

  • Use category filters to narrow results and improve search precision
  • Implement caching to avoid repeated API calls for the same queries
  • Respect rate limits by adding delays between bulk operations

Avoid

  • Avoid searching without date ranges - this returns excessive results
  • Do not make concurrent requests - this violates bioRxiv's rate limits
  • Never hardcode DOIs in scripts - always use search results dynamically

Frequently Asked Questions

Does this search medRxiv preprints too?
No, this skill only searches bioRxiv for life sciences preprints. MedRxiv requires separate API access.
How many papers can I download at once?
The API returns up to 100 papers per search. Download PDFs one at a time with 0.5s delays between requests.
Can I search full text content?
Searches only scan titles, abstracts, and author names. Full-text search requires downloading PDFs separately.
What date formats are accepted?
Use YYYY-MM-DD format (e.g., 2024-01-15). You can also use --days-back for relative dates.
Are published papers included?
Results include all bioRxiv preprints regardless of publication status. Check the 'published' field for journal information.
How do I cite papers found through this tool?
Each result includes DOI, authors, title, and date. Use the DOI to generate proper citations in your reference manager.

Developer Details

Author

K-Dense-AI

License

MIT

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/biorxiv-database

Ref

main

File structure

📁 references/

📄 api_reference.md

📁 scripts/

📄 biorxiv_search.py

📄 SKILL.md