/biorxiv-database

id: biorxiv-database
name: biorxiv-database
version: 1.0.0
description: |-
  Efficient database search tool for bioRxiv preprint server.
stages: ["survey", "ideation", "experiment"]
tools: ["read_file", "search_project", "write_file", "run_terminal"]
summary: |-
  Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature r...
primaryIntent: research
intents: ["research", "data"]
capabilities: ["search-retrieval", "data-processing"]
domains: ["bioinformatics"]
keywords: ["biorxiv-database", "resource prep", "search-retrieval", "data-processing", "bioinformatics", "biorxiv", "database", "efficient", "search", "tool", "preprint", "server"]
source: builtin
status: verified
upstream:
  repo: dr-claw
  path: skills/biorxiv-database
  revision: 8322dc4ef575affaa374aa7922c0a0971c6db7d7
resourceFlags:
  hasReferences: true
  hasScripts: true
  hasTemplates: false
  hasAssets: false
  referenceCount: 1
  scriptCount: 1
  templateCount: 0
  assetCount: 0
  optionalScripts: true

biorxiv-database

Canonical Summary

Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature r...

Trigger Rules

Use this skill when the user request matches its research workflow scope. Prefer the bundled resources instead of recreating templates or reference material. Keep outputs traceable to project files, citations, scripts, or upstream evidence.

Resource Use Rules

• Read from `references/` only when the current task needs the extra detail.
• Treat `scripts/` as optional helpers. Run them only when their dependencies are available, keep outputs in the project workspace, and explain a manual fallback if execution is blocked.

Execution Contract

• Resolve every relative path from this skill directory first.
• Prefer inspection before mutation when invoking bundled scripts.
• If a required runtime, CLI, credential, or API is unavailable, explain the blocker and continue with the best manual fallback instead of silently skipping the step.
• Do not write generated artifacts back into the skill directory; save them inside the active project workspace.

Upstream Instructions

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 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 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 scripts/biorxiv_search.py \
  --keywords "AlphaFold" \
  --search-fields title \
  --days-back 365

2. Author Search

Find all papers by a specific author within a date range.

**Basic Usage:**

python scripts/biorxiv_search.py \
  --author "Smith" \
  --start-date 2023-01-01 \
  --end-date 2024-12-31 \
  --output smith_papers.json

**Recent Publications:**

# Last year by default if no dates specified
python scripts/biorxiv_search.py \
  --author "Johnson" \
  --output johnson_recent.json

3. Date Range Search

Retrieve all preprints posted within a specific date range.

**Basic Usage:**

python scripts/biorxiv_search.py \
  --start-date 2024-01-01 \
  --end-date 2024-01-31 \
  --output january_2024.json

**With Category Filter:**

python scripts/biorxiv_search.py \
  --start-date 2024-06-01 \
  --end-date 2024-06-30 \
  --category genomics \
  --output genomics_june.json

**Days Back Shortcut:**

# Last 30 days
python scripts/biorxiv_search.py \
  --days-back 30 \
  --output last_month.json

4. Paper Details by DOI

Retrieve detailed metadata for a specific preprint.

**Basic Usage:**

python scripts/biorxiv_search.py \
  --doi "10.1101/2024.01.15.123456" \
  --output paper_details.json

**Full DOI URLs Accepted:**

python scripts/biorxiv_search.py \
  --doi "https://doi.org/10.1101/2024.01.15.123456"

5. PDF Downloads

Download the full-text PDF of any preprint.

**Basic Usage:**

python scripts/biorxiv_search.py \
  --doi "10.1101/2024.01.15.123456" \
  --download-pdf paper.pdf

**Batch Processing:** For multiple PDFs, extract DOIs from a search result JSON and download each paper:

import json
from biorxiv_search import BioRxivSearcher

# Load search results
with open('results.json') as f:
    data = json.load(f)

searcher = BioRxivSearcher(verbose=True)

# Download each paper
for i, paper in enumerate(data['results'][:10]):  # First 10 papers
    doi = paper['doi']
    searcher.download_pdf(doi, f"papers/paper_{i+1}.pdf