Daily Literature Search Skill

Automated literature search system for academic researchers. Performs scheduled searches across multiple databases (PubMed, OpenAlex, Semantic Scholar), automatically deduplicates results, downloads open-access papers, and generates daily reports.

🎯 Use Cases

• - Daily literature monitoring for specific research topics
• Automated paper collection for literature reviews
• Stay updated on latest publications in your field
• Build personal paper library with automatic categorization

📦 Components

1. Core Search Script (daily_literature_search.py)

Main execution script with the following features:

• - Multi-source search: PubMed, OpenAlex, Semantic Scholar
• Automatic deduplication: By DOI (within batch + against local library)
• OA detection: Uses Unpaywall API to identify open-access papers
• Auto-download: Downloads OA papers from PubMed Central or publisher sites
• Smart categorization: Classifies papers by topic (configurable keywords)
• Daily reports: Generates Markdown reports with search statistics

2. Upload Analyzer (analyze_uploaded.py)

Analyzes and categorizes manually uploaded papers:

• - Filename-based classification: Uses keyword matching
• DOI extraction: From filenames and metadata
• Batch processing: Handles multiple files at once
• Report generation: Creates categorization summary

⚙️ Configuration

Directory Structure

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Search Keywords (Customizable)

Edit SEARCH_KEYWORDS in daily_literature_search.py:

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Classification Keywords

Edit B_ALL_KEYWORDS and MM_KEYWORDS in analyze_uploaded.py to match your research domains.

🚀 Usage

Manual Execution

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Scheduled Execution (Cron)

Add to crontab for automatic daily searches:

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Configuration Options

📊 Output

Daily Report Example

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File Organization

• - Reports: INLINECODE12
• Logs: INLINECODE13
• Papers: INLINECODE14

🔧 Advanced Features

1. Library Deduplication

Automatically checks new results against existing library:

• - Scans all category directories for existing DOIs
• Extracts DOIs from filenames and historical logs
• Skips papers already in library
• Reports duplicate statistics

2. Open Access Detection

Uses Unpaywall API to identify OA papers:

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3. PubMed Central Integration

Automatically tries PMC for biomedical papers:

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🛠️ Customization Guide

Change Research Topics

1. 1. Edit SEARCH_KEYWORDS in INLINECODE16
2. Update category names and keywords
3. Modify directory structure if needed

Add New Categories

1. 1. Create new directory: INLINECODE17
2. Add classification keywords in classify_paper() function
3. Update report generation to include new category

Integrate with Notification Systems

Add email/Slack/Discord notifications after search completion:

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📋 Requirements

Python Dependencies

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API Access (Optional but Recommended)

• - Semantic Scholar API Key: Higher rate limits
• OpenAlex API Key: Polite pool access
• Unpaywall: Free, no key needed (email required)

Set environment variables:

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⚠️ Important Notes

1. 1. Rate Limits: Respect API rate limits, especially without API keys
2. Storage: Monitor disk space for downloaded PDFs
3. Copyright: Only download open-access or legally available papers
4. Email: Set USER_EMAIL for polite API access

🔄 Version History

• - 1.0.0 (2026-03-18): Initial release

🤝 Contributing

To contribute improvements:

1. 1. Fork the skill repository
2. Test changes with your own literature search
3. Submit pull request with description of improvements

📄 License

This skill is provided as-is for academic research purposes. Users are responsible for compliance with publisher terms and copyright laws.