biorxiv-database

# bioRxiv Database ## Overview This skill provides efficient Python-based tools for searching and retrieving preprints from the bioRxiv database. It enables comprehensive searches by keywords, authors, date ranges, and categories, returning structured JSON metadata that includes titles, abstracts, DOIs, and citation information. The skill also supports PDF downloads for full-text analysis. ## When to Use This Skill Use this skill when: - Searching for recent preprints in specific research areas - Tracking publications by particular authors - Conducting systematic literature reviews - Analyzing research trends over time periods - Retrieving metadata for citation management - Downloading preprint PDFs for analysis - Filtering papers by bioRxiv subject categories ## Core Search Capabilities ### 1. Keyword Search Search for preprints containing specific keywords in titles, abstracts, or author lists. **Basic Usage:** ```python python scripts/biorxiv_search.py \ --keywords "CRISPR" "gene editing" \ --start-date 2024-01-01 \ --end-date 2024-12-31 \ --output results.json ``` **With Category Filter:** ```python python scripts/biorxiv_search.py \ --keywords "neural networks" "deep learning" \ --days-back 180 \ --category neuroscience \ --output recent_neuroscience.json ``` **Search Fields:** By default, keywords are searched in both title and abstract. Customize with `--search-fields`: ```python python scripts/biorxiv_search.py \ --keywords "AlphaFold" \ ...