bioRxiv Database

A Python toolkit for programmatic access to bioRxiv preprints. Supports comprehensive metadata retrieval with structured JSON output for integration into research workflows.

Use Cases

• Query recent preprints by topic or research domain
• Monitor publications from specific researchers
• Perform systematic literature reviews
• Analyze publication trends across time periods
• Retrieve citation metadata and DOIs
• Download preprint PDFs for text analysis
• Filter results by subject category

Quick Start

# Install dependencies
pip install requests

# Search by keywords
python scripts/biorxiv_client.py --terms "protein folding" --recent 30 --out results.json

# Search by author
python scripts/biorxiv_client.py --author "Chen" --recent 180

# Get specific paper by DOI
python scripts/biorxiv_client.py --doi "10.1101/2024.05.22.594321"

# Download PDF
python scripts/biorxiv_client.py --doi "10.1101/2024.05.22.594321" --fetch-pdf paper.pdf

Command-Line Options

Option	Description
-t, --terms	Search keywords (multiple allowed)
-a, --author	Author name to search
--doi	Specific DOI to retrieve
--since	Start date (YYYY-MM-DD)
--until	End date (YYYY-MM-DD)
--recent	Search last N days
-s, --subject	Subject category filter
--fields	Fields to search: title, abstract, authors
-o, --out	Output file (default: stdout)
--max	Maximum results to return
--fetch-pdf	Download PDF (requires --doi)
-v, --verbose	Enable debug output

Programmatic API

from scripts.biorxiv_client import PreprintClient

client = PreprintClient(debug=True)

# Search by keywords
results = client.find_by_terms(
    terms=["enzyme engineering"],
    since="2024-01-01",
    until="2024-12-31",
    subject="biochemistry"
)

# Search by author
papers = client.find_by_author(name="Garcia", since="2023-01-01")

# Get paper by DOI
metadata = client.get_by_doi("10.1101/2024.05.22.594321")

# Download PDF
client.fetch_pdf(doi="10.1101/2024.05.22.594321", destination="paper.pdf")

# Normalize output
formatted = client.normalize(metadata, include_abstract=True)

Subject Categories

Category	Category
animal-behavior-and-cognition	molecular-biology
biochemistry	neuroscience
bioengineering	paleontology
bioinformatics	pathology
biophysics	pharmacology-and-toxicology
cancer-biology	physiology
cell-biology	plant-biology
clinical-trials	scientific-communication-and-education
developmental-biology	synthetic-biology
ecology	systems-biology
epidemiology	zoology
evolutionary-biology
genetics
genomics
immunology
microbiology

Response Structure

{
  "query": {
    "terms": ["protein folding"],
    "since": "2024-03-01",
    "until": "2024-09-30",
    "subject": "biophysics"
  },
  "count": 87,
  "papers": [
    {
      "doi": "10.1101/2024.05.22.594321",
      "title": "Example Preprint Title",
      "authors": "Chen L, Patel R, Kim S",
      "corresponding_author": "Chen L",
      "institution": "Research Institute",
      "posted": "2024-05-22",
      "revision": "1",
      "category": "biophysics",
      "license": "cc_by",
      "paper_type": "new results",
      "abstract": "Abstract content here...",
      "pdf_link": "https://www.biorxiv.org/content/10.1101/2024.05.22.594321v1.full.pdf",
      "web_link": "https://www.biorxiv.org/content/10.1101/2024.05.22.594321v1",
      "journal_ref": ""
    }
  ]
}

Best Practices

Recommendation	Details
Date ranges	Narrow ranges improve response time. Split large queries into chunks.
Category filters	Use --subject to reduce bandwidth and improve precision.
Rate limiting	Built-in 0.5s delay between requests. Add more for bulk operations.
Result caching	Save JSON outputs to avoid redundant API calls.
Version awareness	Preprints may have multiple versions. PDF URLs encode version numbers.
Error checking	Verify count in outputs. Zero results may indicate date or connectivity issues.
Debug mode	Use --verbose for detailed request/response logging.

Reference Files

File	Contents
api-reference.md	Complete bioRxiv REST API documentation
examples.md	Extended code examples and workflow patterns