biorxiv-database

Search bioRxiv preprints by keywords, authors, dates, and categories, returning structured JSON metadata.

6|Updated Dec 30, 2025
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill biorxiv-database-pur3v4d3r
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: biorxiv-database
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/biorxiv-database
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill biorxiv-database-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

bioRxiv is a major repository of life sciences preprints, but discovering relevant papers across keywords, authors, dates, and categories can be slow and manual. This skill provides a fast, structured way to search the bioRxiv database, return rich metadata (titles, abstracts, DOIs, authors, categories), and optionally download PDFs for deeper analysis.

Core Features & Use Cases

  • Keyword and author searches: Find papers by keywords, authors, and date ranges, with optional category filters.
  • Metadata extraction and export: Return structured data including title, abstract, DOI, date, authors, and category; supports JSON output for downstream workflows.
  • PDF retrieval: Download full-text PDFs for selected papers to enable offline analysis and citation review.
  • Use Case: A literature reviewer gathers all papers on a topic within a date window and exports metadata for a synthesized review.

Quick Start

Ask me to search bioRxiv for papers by keywords and date range, then download the resulting PDFs if needed.

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, authors, and date ranges?

You can search bioRxiv preprints by providing keywords, author names, and specific date ranges to retrieve structured metadata. The tool processes these parameters to return matching papers with titles, abstracts, DOIs, and category details.

Can I download full-text PDFs for bioRxiv papers after retrieving their metadata?

Yes, you can download full-text PDFs for selected bioRxiv papers after retrieving their metadata. This functionality enables offline analysis and citation review directly from the queried search results.

What structured data fields are returned when querying the bioRxiv database?

Querying the bioRxiv database returns structured JSON data containing DOIs, titles, abstracts, authors, and categories. This structured output supports direct integration into downstream data analysis workflows.

Does the bioRxiv search tool require Python and the requests package to run?

Yes, the bioRxiv search tool requires a Python environment and depends on the requests package to function. It provides a ready-to-run CLI that uses this dependency to query the API and fetch preprint data.

How do I filter bioRxiv preprint searches by specific life sciences categories?

You can filter bioRxiv preprint searches by applying category filters alongside your keyword and date range queries. The CLI supports these options to narrow down results to specific life sciences fields.

What is the best way to export bioRxiv metadata for a systematic literature review?

The best way to export bioRxiv metadata for a literature review is using the tool's JSON output format. Querying by date windows and keywords yields structured data with DOIs and abstracts, ready for downstream synthesis.