Literature Search Biorxiv

Utility Scripts

All tools enforce a cross-process rate limits and retry with backoff on failure. To ensure you respect terms-of-service, do NOT write custom curl queries.

Pagination: The bioRxiv API returns results in pages of up to 100 papers. The search_by_dates.py script automatically fetches all pages and reports pagination progress to stderr (e.g., [Page 2] Fetched 200/543 papers...). The JSON output to stdout contains the complete filtered result set across all pages — no manual pagination is needed.

1. Search by Dates (search_by_dates.py)

Search for preprints within an explicit date range, optionally filtering by category, keywords, or author.

# Broad category search over a 2-week period
uv run scripts/search_by_dates.py --server biorxiv \
  --start_date 2024-01-01 --end_date 2024-01-14 \
  --category neuroscience > results.json

# Deep keyword filtering using OR logic and including abstracts
uv run scripts/search_by_dates.py --server medrxiv \
  --start_date 2023-11-01 --end_date 2023-11-30 \
  --category infectious_diseases \
  --keywords "covid" "sars-cov-2" --match_logic OR \
  --include_abstracts > covid_papers.json

# Finding papers by a specific author in a narrow window
uv run scripts/search_by_dates.py \
  --start_date 2024-05-01 --end_date 2024-05-14 \
  --author "Smith" > smith_papers.json

Required Arguments:

• --start_date: YYYY-MM-DD
• --end_date: YYYY-MM-DD

Optional Arguments:

• --server: biorxiv (default) or medrxiv
• --category: A valid subject category (see below). Highly recommended — dramatically reduces the data the script must download and filter.
• --keywords: List of strings to search in the title/abstract.
• --match_logic: AND (default) or OR for keywords.
• --author: Author name (case-insensitive string match).
• --include_abstracts: Flag to include full abstracts in the JSON output.

2. Fetch Metadata by DOI (search_by_doi.py)

Retrieve the detailed JSON metadata for a single paper if you already know its DOI. This is the most reliable entry point.

uv run scripts/search_by_doi.py --server biorxiv \
  --doi "10.1101/2023.08.15.551388" \
  --include_abstracts > paper_info.json

Downloading Full-Text PDFs

This skill does NOT support PDF downloads. To download the full-text PDF of a bioRxiv or medRxiv preprint, use the literature-search-europepmc skill. First, use the paper's DOI to look up its PMCID via EuropePMC, then use EuropePMC's PDF retrieval to download the document.

Valid Subject Categories

You can pass these to the --category flag in search_by_dates.py. The script will strictly validate them.

bioRxiv Categories:

animal_behavior_and_cognition, biochemistry, bioengineering, bioinformatics, biophysics, cancer_biology, cell_biology, clinical_trials, developmental_biology, ecology, epidemiology, evolutionary_biology, genetics, genomics, immunology, microbiology, molecular_biology, neuroscience, paleontology, pathology, pharmacology_and_toxicology, physiology, plant_biology, scientific_communication_and_education, synthetic_biology, systems_biology, zoology

medRxiv Categories:

addiction_medicine, allergy_and_immunology, anesthesia, cardiovascular_medicine, dentistry_and_oral_medicine, dermatology, emergency_medicine, endocrinology, epidemiology, forensic_medicine, gastroenterology, genetic_and_genomic_medicine, health_informatics, health_economics_and_outcomes_research, health_policy, health_systems_and_quality_improvement, hematology, hiv_aids, infectious_diseases, intensive_care_and_critical_care_medicine, medical_education, medical_ethics, nephrology, neurology, nursing, nutrition, obstetrics_and_gynecology, occupational_and_environmental_health, oncology, ophthalmology, orthopedics, otolaryngology, pain_medicine, palliative_care, pathology, pediatrics, pharmacology_and_therapeutics, primary_care_research, psychiatry_and_clinical_psychology, public_and_global_health, radiology_and_imaging, rehabilitation_medicine_and_physical_therapy, respiratory_medicine, rheumatology, sexual_and_reproductive_health, sports_medicine, surgery, toxicology, transplantation, urology