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biorxiv-database

Fetch bioRxiv preprint metadata as structured JSON with DOIs and abstracts.

15|2|Updated Dec 17, 2025
Search Tags:#metadata#preprints#pdf-download#biorxiv#literature-search#doi
One-click install
npx skills add https://github.com/rubensliv/k-dense-ai --skill biorxiv-database-rubensliv
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: biorxiv-database
Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/biorxiv-database
Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill biorxiv-database-rubensliv

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

bioRxiv hosts a huge stream of life sciences preprints. This skill helps researchers quickly discover, filter, and retrieve metadata for relevant papers, enabling faster literature reviews and data curation.

Core Features & Use Cases

  • Keyword and author driven searches across bioRxiv, with optional date-range and category filters.
  • Retrieve structured metadata including titles, abstracts, DOIs, authors, dates, licenses, and categories; supports DOI lookup and PDF download links.
  • Use Case: A researcher wants to compile a dataset of 50 genomics papers published in 2023–2024, with DOIs and direct PDF URLs for quick access.

Quick Start

Use this skill to search bioRxiv for papers on a topic and export a JSON file containing key metadata and direct PDF URLs.

Frequently Asked Questions about biorxiv-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search bioRxiv preprints by keywords and date ranges?▼

You can search bioRxiv preprints by keywords, authors, date ranges, and categories to retrieve structured JSON metadata including DOIs, titles, abstracts, and authors for literature reviews.

What's the best way to download bioRxiv PDFs for a literature review?▼

The best way to download bioRxiv PDFs is to fetch metadata containing direct PDF URLs through the bioRxiv API, then use those links to programmatically download the full text articles.

Can I filter bioRxiv metadata by category and author for systematic reviews?▼

Yes, you can filter bioRxiv metadata by specific life sciences categories and author names, returning structured JSON with titles, abstracts, DOIs, and dates suitable for systematic reviews.

Does Python requests library handle bioRxiv API rate limits?▼

The Python requests library executes bioRxiv API queries while the script handles rate limits and basic error conditions, ensuring stable metadata retrieval for literature review pipelines.

What metadata fields are returned when fetching bioRxiv preprints?▼

Fetching bioRxiv preprints returns structured JSON metadata containing DOIs, titles, abstracts, authors, publication dates, licenses, categories, and direct PDF download URLs for each article.

When should I use bioRxiv API searches instead of other literature databases?▼

Use bioRxiv API searches when you need rapid access to life sciences preprints before peer review, retrieving structured JSON metadata for trend analyses and meta-analyses across biological domains.

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