bioRxiv / medRxiv Search

Goal

Search and retrieve preprint metadata (title, authors, abstract, DOI, category, etc.) from bioRxiv and medRxiv using the official REST API. Supports keyword filtering, subject category filtering, date-range search, and DOI lookup.

Instructions

1. Keyword Search (Recent Papers)

Search last 30 days for papers matching keywords in title/abstract.

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "protein folding" --max_results 5 --output protein_folding.json

2. Date Range Search

Retrieve preprints posted in a specific date range, with optional keyword/category filter.

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "CRISPR" --start 2025-01-01 --end 2025-06-01 --max_results 10 --output crispr_2025.json

3. Category Filter

Filter by subject category (use shortcuts or full names).

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --category neuroscience --days 14 --max_results 10

Supported Category Shortcuts:

• biochemistry, bioinformatics, biophysics
• cancer → cancer_biology
• cell-bio → cell_biology
• dev-bio → developmental_biology
• ecology, epidemiology, evolution
• genetics, genomics, immunology
• microbiology, molecular-bio → molecular_biology
• neuroscience, pharmacology, physiology
• plant-bio → plant_biology
• synthetic-bio → synthetic_biology
• systems-bio → systems_biology

4. Search medRxiv

Use --server medrxiv for medical preprints.

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "COVID vaccine efficacy" --server medrxiv --max_results 5 --output covid_vaccine.json

5. DOI Lookup

Retrieve metadata for a specific preprint by DOI.

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --doi 10.1101/2021.01.01.000000 --output paper.json

Examples

Recent Neuroscience Papers

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --category neuroscience --days 7 --max_results 5

Genomics Papers with Keyword Filter

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "single cell sequencing" --category genomics --start 2024-01-01 --end 2024-12-31 --max_results 10 --output scrna_2024.json

Constraints

• No official rate limit specified by bioRxiv API; script includes 0.5s delay per request as courtesy.
• Pagination: API returns 30 results per page; script paginates automatically up to --max_results.
• Keyword filtering: Done client-side (API lacks full-text search); date range must be broad enough to surface relevant papers.
• Environment: Requires base-agent conda environment.
• Dependencies: Uses requests.
• Metadata fields: DOI, URL, title, authors, abstract, date, category, server, version, license, published journal (if available).

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Author: mlederbauer Contact: GitHub @learningmatter-mit