bioRxiv Skill

This skill provides access to the bioRxiv preprint repository using the official bioRxiv API.

When to Use

• User asks for recent biology preprints
• User wants papers from specific bioRxiv categories (bioinformatics, genomics, etc.)
• User needs paper metadata (title, authors, DOI, date, category)
• User asks for preprints from a specific date range

Quick Start

List Available Collections

python scripts/biorxiv.py --list

Fetch Recent Papers

# Default: bioinformatics papers
python scripts/biorxiv.py --collection bioinformatics

# Other collections
python scripts/biorxiv.py --collection genomics
python scripts/biorxiv.py --collection neuroscience
python scripts/biorxiv.py --collection microbiology

# Specific date range
python scripts/biorxiv.py --collection bioinformatics --start 2026-03-01 --end 2026-03-09

# Limit results
python scripts/biorxiv.py --collection bioinformatics --limit 10

Output as JSON

python scripts/biorxiv.py --collection bioinformatics --json

Available Collections

• bioinformatics
• genomics
• molecular-biology
• cell-biology
• genetics
• evolutionary-biology
• ecology
• neuroscience
• plant-biology
• microbiology
• immunology
• cancer-biology
• biochemistry
• biophysics
• structural-biology
• systems-biology
• synthetic-biology
• developmental-biology
• computational-biology

API Notes

Official bioRxiv API

• Base URL: https://api.biorxiv.org/details/biorxiv/{start_date}/{end_date}/{cursor}
• No authentication required
• Returns up to 100 papers per call
• Supports category filtering via query parameter

API Endpoints

• /details/biorxiv/[start]/[end]/[cursor] — Paper metadata
• /pub/[start]/[end]/[cursor] — Published articles only

Usage Patterns

Summarize Recent Papers

1. Fetch papers from desired collection
2. Parse titles and abstracts
3. Group by theme if multiple
4. Provide concise summary

Find Papers by Topic

1. Search across multiple relevant collections
2. Filter by keywords in titles
3. Return most relevant results