Skill: aquaskyline/biorxiv-openclaw-skill (version 1.0.0)

--- name: biorxiv version: 1.1.0 description: Access bioRxiv preprint repository for biology preprints. Use for: (1) Fetching recent preprints from specific categories like bioinformatics, genomics, molecular-biology, etc., (2) Getting papers by date range, (3) Listing available subject collections, (4) Retrieving paper metadata including titles, authors, DOIs, dates, and categories. No authentication required. --- # bioRxiv Skill This skill provides access to the bioRxiv preprint repository using the official bioRxiv API. ## When to Use - User asks for recent biology preprints - User wants papers from specific bioRxiv categories (bioinformatics, genomics, etc.) - User needs paper metadata (title, authors, DOI, date, category) - User asks for preprints from a specific date range ## Quick Start ### List Available Collections ```bash python scripts/biorxiv.py --list ``` ### Fetch Recent Papers ```bash # Default: bioinformatics papers python scripts/biorxiv.py --collection bioinformatics # Other collections python scripts/biorxiv.py --collection genomics python scripts/biorxiv.py --collection neuroscience python scripts/biorxiv.py --collection microbiology # Specific date range python scripts/biorxiv.py --collection bioinformatics --start 2026-03-01 --end 2026-03-09 # Limit results python scripts/biorxiv.py --collection bioinformatics --limit 10 ``` ### Output as JSON ```bash python scripts/biorxiv.py --collection bioinformatics --json ``` ## Available Collections - bioinformatics - genomics - molecular-biology - cell-biology - genetics - evolutionary-biology - ecology - neuroscience - plant-biology - microbiology - immunology - cancer-biology - biochemistry - biophysics - structural-biology - systems-biology - synthetic-biology - developmental-biology - computational-biology ## API Notes ### Official bioRxiv API - **Base URL:** `https://api.biorxiv.org/details/biorxiv/{start_date}/{end_date}/{cursor}` - **No authentication required** - Returns up to 100 papers per call - Supports category filtering via query parameter ### API Endpoints - `/details/biorxiv/[start]/[end]/[cursor]` — Paper metadata - `/pub/[start]/[end]/[cursor]` — Published articles only ## Usage Patterns ### Summarize Recent Papers 1. Fetch papers from desired collection 2. Parse titles and abstracts 3. Group by theme if multiple 4. Provide concise summary ### Find Papers by Topic 1. Search across multiple relevant collections 2. Filter by keywords in titles 3. Return most relevant results

path: references/api.md
content: # bioRxiv API Documentation

BioRxiv API base URL: `https://api.biorxiv.org`

## Endpoints

### Get Collection Details
- `GET /details/bioinformatics/<interval>/<cursor>`
- `<interval>`: Date range like "2026-03-01/2026-03-09"
- `<cursor>`: Starting position (0-indexed), default 0
- Returns: JSON with collection of papers

### Response Format
```json
{
  "collection": [
    {
      "doi": "10.1101/2026.03.01.123456",
      "title": "Paper Title",
      "authors": ["Author1", "Author2"],
      "author_corresponding": "Author1",
      "author_corresponding_institution": "University",
      "date": "2026-03-01",
      "version": "1",
      "type": "new"
    }
  ],
  "messages": [],
  "total": 100
}
```

## Available Collections
- bioinformatics
- genomics
- molecular-biology
- cell-biology
- genetics
- evolutionary-biology
- ecology
- neuroscience
- plant-biology
- microbiology
- immunology
- cancer-biology
- biochemistry
- biophysics
- structural-biology
- systems-biology
- synthetic-biology
- developmental-biology
- computational-biology

## Python Script Usage

```python
import requests

def get_papers(collection="bioinformatics", start_date="2026-03-01", end_date="2026-03-09", cursor=0):
    url = f"https://api.biorxiv.org/details/{collection}/{start_date}/{end_date}/{cursor}"
    resp = requests.get(url)
    return resp.json()
```


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