emerging-topic-scout（新兴话题侦察）

Emerging Topic Scout

A real-time monitoring system for identifying "incubation period" research hotspots in biological and medical sciences before they are defined by mainstream journals.

Overview

This skill continuously monitors:

• bioRxiv: Biology preprints via RSS/API ⚠️ *Currently blocked by Cloudflare*
• medRxiv: Medicine preprints via RSS/API ⚠️ *Currently blocked by Cloudflare*
• arXiv: Quantitative Biology preprints via RSS ✅ *Recommended alternative*
• Academic discussions: Social media and forum mentions

It uses trend analysis algorithms to detect sudden spikes in topic frequency, cross-platform mentions, and emerging keyword clusters.

⚠️ Network Access Notice

bioRxiv and medRxiv are currently protected by Cloudflare JavaScript Challenge, which prevents programmatic RSS access. As a workaround, this skill now supports arXiv q-bio (Quantitative Biology) as an alternative data source.

Recommended usage:

# Use arXiv for reliable data fetching
python scripts/main.py --sources arxiv --days 30

# bioRxiv/medRxiv may return 0 results due to Cloudflare protection
python scripts/main.py --sources biorxiv medrxiv --days 30  # May not work

Installation

cd /Users/z04030865/.openclaw/workspace/skills/emerging-topic-scout
pip install -r scripts/requirements.txt

Usage

Basic Scan (Recommended: Use arXiv)

python scripts/main.py --sources arxiv --days 7 --output json

Legacy bioRxiv/medRxiv (May not work due to Cloudflare)

python scripts/main.py --sources biorxiv medrxiv --days 7 --output json

Advanced Configuration (arXiv Recommended)

python scripts/main.py \
  --sources arxiv \
  --keywords "CRISPR,gene editing,machine learning" \
  --days 14 \
  --min-score 0.7 \
  --output markdown \
  --notify

Legacy Configuration (bioRxiv/medRxiv - May not work)

python scripts/main.py \
  --sources biorxiv medrxiv \
  --keywords "CRISPR,gene editing,long COVID" \
  --days 14 \
  --min-score 0.7 \
  --output markdown \
  --notify
# Note: bioRxiv/medRxiv may return 0 results due to Cloudflare protection

## Parameters

| Parameter | Type | Default | Description |
|-----------|------|---------|-------------|
| `--sources` | list | `arxiv` | Data sources to monitor (arxiv recommended due to Cloudflare issues with biorxiv/medrxiv) |
| `--keywords` | string | (auto-detect) | Comma-separated keywords to track |
| `--days` | int | `7` | Lookback period in days |
| `--min-score` | float | `0.6` | Minimum trending score (0-1) |
| `--max-topics` | int | `20` | Maximum topics to return |
| `--output` | string | `markdown` | Output format: `json`, `markdown`, `csv` |
| `--notify` | flag | `false` | Send notification for high-priority topics |
| `--config` | path | `config.yaml` | Path to configuration file |

## Output Format

### JSON Output

{ "scan_date": "2026-02-06T05:57:00Z", "sources": ["biorxiv", "medrxiv"], "hot_topics": [ { "topic": "gene editing therapy", "keywords": ["CRISPR", "base editing", "prime editing"], "trending_score": 0.89, "velocity": "rapid", "preprint_count": 34, "cross_platform_mentions": 127, "related_papers": [ { "title": "New CRISPR variant shows promise", "authors": ["Smith J.", "Lee K."], "doi": "10.1101/2026.01.15.xxxxx", "source": "biorxiv", "published": "2026-01-15", "abstract_summary": "..." } ], "emerging_since": "2026-01-20" } ], "summary": { "total_papers_analyzed": 1247, "new_topics_detected": 8, "high_priority_alerts": 2 } }

### Markdown Output

Emerging Topics Report - 2026-02-06

🔥 High Priority Topics

1. Gene Editing Therapy (Score: 0.89)

• Keywords: CRISPR, base editing, prime editing
• Growth Rate: Rapid (+145% vs last week)
• Preprints: 34 papers
• Cross-platform mentions: 127

Key Papers

1. "New CRISPR variant shows promise" - Smith J. et al.

- DOI: 10.1101/2026.01.15.xxxxx - Source: bioRxiv

## Configuration File

Create `config.yaml` for persistent settings:

sources: arxiv: enabled: true rss_url: "https://export.arxiv.org/rss/q-bio" description: "arXiv Quantitative Biology - Recommended (no Cloudflare)" biorxiv: enabled: false # Disabled due to Cloudflare protection rss_url: "https://www.biorxiv.org/rss/recent.rss" api_endpoint: "https://api.biorxiv.org/details/" note: "Currently blocked by Cloudflare JavaScript Challenge" medrxiv: enabled: false # Disabled due to Cloudflare protection rss_url: "https://www.medrxiv.org/rss/recent.rss" api_endpoint: "https://api.medrxiv.org/details/" note: "Currently blocked by Cloudflare JavaScript Challenge"

trending: min_papers_threshold: 5 velocity_window_days: 3 novelty_weight: 0.4 momentum_weight: 0.6

keywords: auto_detect: true custom_trackers: - "artificial intelligence" - "machine learning" - "single cell" - "spatial transcriptomics"

output: default_format: markdown save_history: true history_path: "./data/history.json"

notifications: enabled: false high_score_threshold: 0.8

## Trending Score Algorithm

The trending score (0-1) is calculated using:

Score = (Novelty × 0.4) + (Momentum × 0.4) + (CrossRef × 0.2)

Where:

• Novelty: Inverse frequency of topic in historical data
• Momentum: Rate of increase in mentions over velocity window
• CrossRef: Mentions across multiple platforms

## API Endpoints

### bioRxiv API
- Base: `https://api.biorxiv.org/`
- Details: `/details/[server]/[DOI]/[format]`
- Publication: `/pub/[DOI]/[format]`

### medRxiv API
- Same structure as bioRxiv

## Data Storage

Historical data is stored in `data/history.json` for:
- Trend comparison
- Velocity calculation
- Duplicate detection

## Examples

### Example 1: Quick Daily Scan (arXiv - Recommended)

python scripts/main.py --sources arxiv --days 1 --output markdown

### Example 2: Daily Scan with bioRxiv (May not work)

python scripts/main.py --sources biorxiv --days 1 --output markdown

Note: May return 0 results due to Cloudflare protection

Example 2: Weekly Deep Analysis

python scripts/main.py \
  --days 7 \
  --min-score 0.7 \
  --max-topics 50 \
  --output json \
  > weekly_report.json

Example 3: Track Specific Research Area

python scripts/main.py \
  --keywords "Alzheimer,neurodegeneration,amyloid" \
  --days 30 \
  --min-score 0.5

Known Issues

bioRxiv/medRxiv Cloudflare Protection

Status: ❌ Blocked Issue: bioRxiv and medRxiv RSS feeds are protected by Cloudflare JavaScript Challenge, which prevents programmatic access. The site returns an HTML page requiring JavaScript execution and cookie validation.

Attempted Solutions:

1. ✅ Added browser User-Agent headers → Failed (Cloudflare detects bot)
2. ✅ Added complete browser headers (Accept, Accept-Language, etc.) → Failed
3. ❌ Browser automation (Selenium/Playwright) → Not implemented (complex, heavy dependency)

Workaround: ✅ Use arXiv instead

• arXiv q-bio (Quantitative Biology) RSS is accessible without protection
• Contains computational biology, bioinformatics, and quantitative biology papers
• Successfully tested: 35+ papers fetched in 30-day window

Usage:

# Recommended: Use arXiv
python scripts/main.py --sources arxiv --days 30

# Not working: bioRxiv/medRxiv
python scripts/main.py --sources biorxiv medrxiv --days 30  # Returns 0 papers

Troubleshooting

Rate Limiting

If you encounter rate limits, increase the --delay parameter (default: 1s between requests).

Missing Papers (0 results from bioRxiv/medRxiv)

This is expected due to Cloudflare protection. Use --sources arxiv instead.

RSS Feed Access Denied

Some institutional firewalls may block preprint servers. Ensure you can access:

• ✅ https://export.arxiv.org/rss/q-bio (should work)
• ❌ https://www.biorxiv.org/rss/recent.rss (Cloudflare blocked)

Low Trending Scores

For niche topics, lower --min-score threshold or increase --days for more data.

References

See references/README.md for:

• API documentation links
• Research papers on trend detection
• Related tools and resources

License

MIT License - Part of OpenClaw Skills Collection

Risk Assessment

Security Checklist

• [ ] No hardcoded credentials or API keys
• [ ] No unauthorized file system access (../)
• [ ] Output does not expose sensitive information
• [ ] Prompt injection protections in place
• [ ] API requests use HTTPS only
• [ ] Input validated against allowed patterns
• [ ] API timeout and retry mechanisms implemented
• [ ] Output directory restricted to workspace
• [ ] Script execution in sandboxed environment
• [ ] Error messages sanitized (no internal paths exposed)
• [ ] Dependencies audited
• [ ] No exposure of internal service architecture

Prerequisites

# Python dependencies
pip install -r requirements.txt

Evaluation Criteria

Success Metrics

• [ ] Successfully executes main functionality
• [ ] Output meets quality standards
• [ ] Handles edge cases gracefully
• [ ] Performance is acceptable

Test Cases

1. Basic Functionality: Standard input → Expected output
2. Edge Case: Invalid input → Graceful error handling
3. Performance: Large dataset → Acceptable processing time

Lifecycle Status

• Current Stage: Draft
• Next Review Date: 2026-03-06
• Known Issues:

- ⚠️ bioRxiv/medRxiv blocked by Cloudflare (use arXiv as workaround) - Network access limitations for some RSS feeds

• Planned Improvements:

- Investigate bioRxiv/medRxiv API alternatives - Consider browser automation for Cloudflare bypass - Add more arXiv categories (q-bio subcategories) - Performance optimization