title	BioMed Scholar API
emoji	🔬
colorFrom	indigo
colorTo	blue
sdk	docker
app_port	7860

🔬 BioMed Scholar - Biomedical Search Engine

An intelligent, Google Scholar-style semantic search engine for biomedical literature and clinical trials powered by BioBERT and AI.

📊 What's Inside

• 1,800+ Documents: PubMed articles + clinical trials indexed
• 20+ Medical Topics: COVID-19, cancer, diabetes, Alzheimer's, HIV, cardiovascular, and more
• Smart Search: Hybrid keyword + semantic search with BioBERT embeddings
• Question Answering: Ask medical questions and get evidence-based answers
• Trending Topics: Explore what's popular in biomedical research

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✨ Features

🔍 Search Capabilities

Feature	Description
Semantic Search	AI-powered search understands medical context and synonyms
Hybrid Search	Combines keyword matching with semantic understanding
Search History	Quick access to your recent searches
Autocomplete	Smart suggestions as you type
Advanced Search	Boolean operators, exact phrases, author/journal filters
Search Highlighting	Matching terms highlighted in results

📚 Results & Export

Feature	Description
Save/Bookmark	Save articles to your reading list
Export Results	Download as CSV or BibTeX
Citation Generator	One-click citations in APA, MLA, Chicago, BibTeX
Share Search	Copy shareable link for your search
Pagination	Navigate through results with keyboard arrows
View Modes	List view or compact view

🎛️ Filters

Filter	Options
Source Type	All Sources, PubMed, Clinical Trials
Date Range	Any time, Since 2024/2023/2020, Custom range
Article Type	Research, Review, Meta-analysis, Case Study, Clinical Trial
Language	English, Spanish, German, French, Chinese, Japanese
Sort By	Relevance, Date (newest/oldest), Most Cited

📈 Analytics

• Trending Topics: See what's popular in biomedical research
• Publication Trends: Visualize research trends over time
• Related Searches: Discover related search terms

⌨️ Keyboard Shortcuts

Shortcut	Action
Ctrl + K	Focus search bar
Ctrl + Shift + F	Open advanced search
1 / 2 / 3	Switch to Articles / Q&A / Trends tab
B	Toggle reading list
D	Toggle dark mode
← / →	Navigate pages
?	Show keyboard shortcuts
Escape	Close modals

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🚀 Quick Start

1. Start Docker Services

cd docker
docker-compose up -d

This starts:

• Elasticsearch (port 9201)
• Redis (port 6380)
• PostgreSQL (port 5433)

2. Install Dependencies

pip install -r requirements.txt

3. Start Backend API

Open a new terminal:

uvicorn src.api.app:app --host 0.0.0.0 --port 8000 --reload

Wait for: ✅ API ready to accept requests

4. Start Frontend

Open another new terminal:

cd frontend
python -m http.server 8080

5. Open in Browser

Go to: http://localhost:8080

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🎯 How to Use

📖 Search Tab

1. Type your query (e.g., "COVID-19 treatment")
2. Use filters on the left sidebar:
   • Select source: PubMed, Clinical Trials, or Both
   • Choose date range
   • Adjust search mode slider (keyword ↔ semantic)
3. View results with:
   • Article details, authors, publication date
   • Save to reading list
   • Generate citations
   • View on PubMed/ClinicalTrials.gov

❓ Ask Questions Tab

1. Type a medical question (e.g., "What are the symptoms of diabetes?")
2. Select source and number of answers (1, 3, or 5)
3. Get evidence-based answers with:
   • Confidence scores
   • Source citations
   • Supporting evidence passages

📈 Trends Tab

• Explore trending research topics
• See growth percentages
• Click topics to search
• View publication trend charts

📚 Reading List

• Click bookmark icon on any article to save
• Access from the 🔖 icon in header
• Export as CSV or BibTeX
• Generate citations for saved articles

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🛑 How to Stop

# Stop Docker services
cd docker
docker-compose down

# Stop API & Frontend: Press Ctrl+C in their terminals

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🔧 Troubleshooting

Port already in use?

# Kill process on port 8000
Stop-Process -Id (Get-NetTCPConnection -LocalPort 8000).OwningProcess -Force

# Kill process on port 8080
Stop-Process -Id (Get-NetTCPConnection -LocalPort 8080).OwningProcess -Force

Elasticsearch not connecting?

# Check if Docker is running
docker ps

# Restart Docker services
cd docker
docker-compose restart

Need to reindex data?

python scripts/ingest_full_dataset.py

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📁 Project Structure

kash_proj/
├── src/                    # Source code
│   ├── api/               # FastAPI backend
│   ├── search_engine/     # Hybrid search
│   ├── qa_module/         # Question answering
│   └── nlp_engine/        # BioBERT models
├── frontend/              # Web interface
│   ├── index.html         # Main HTML with all components
│   ├── app.js             # JavaScript (search, bookmarks, citations)
│   └── styles.css         # Google Scholar-style CSS
├── docker/                # Docker services
│   └── docker-compose.yml
├── scripts/               # Utility scripts
│   ├── ingest_full_dataset.py
│   └── check_index_status.py
├── data/                  # Cached data
└── tests/                 # Integration tests

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🧪 Run Tests

pytest tests/test_integration.py -v

All tests should pass ✅

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📊 Check System Status

# Check indexed documents
python scripts/check_index_status.py

# Check API health
curl http://localhost:8000/api/v1/health

# Check statistics
curl http://localhost:8000/api/v1/statistics

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🛠️ Tech Stack

Layer	Technology
Backend	Python 3.9+, FastAPI, Uvicorn
NLP/AI	PyTorch, Transformers, BioBERT
Search	Elasticsearch 8.11.0
Cache	Redis 7
Database	PostgreSQL
Frontend	HTML5, CSS3, JavaScript (ES6+)
Deployment	Docker, Docker Compose

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📝 Sample Queries to Try

Search Queries

• COVID-19 vaccine efficacy
• cancer immunotherapy
• diabetes treatment 2024
• CRISPR gene editing
• mRNA vaccine technology

Questions

• What are the symptoms of COVID-19?
• How is diabetes treated?
• What causes Alzheimer's disease?
• What are the side effects of chemotherapy?
• How does HIV affect the immune system?

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🌙 Theme Support

BioMed Scholar supports both Light and Dark themes:

• Toggle with the sun/moon icon in the header
• Or press D key
• Preference is saved automatically

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📱 Responsive Design

The UI is fully responsive and works on:

• 🖥️ Desktop (full sidebar, all features)
• 💻 Laptop (adaptive layout)
• 📱 Mobile (collapsed sidebar, touch-friendly)

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🔒 Privacy

• No account required - works without login
• Local storage only - reading list and preferences saved in your browser
• No tracking - your searches stay private

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🤝 Contributing

1. Fork the repository
2. Create a feature branch: git checkout -b feature/amazing-feature
3. Commit your changes: git commit -m 'Add amazing feature'
4. Push to the branch: git push origin feature/amazing-feature
5. Open a Pull Request

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📄 License

This project is licensed under the MIT License.

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👨‍💻 Author

Sasidhara Kashyap Ch

Made with ❤️ using BioBERT, Elasticsearch, and FastAPI

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🙏 Acknowledgments

• BioBERT - Biomedical language model
• PubMed - Biomedical literature database
• ClinicalTrials.gov - Clinical trials registry
• Elasticsearch - Search engine
• FastAPI - Modern Python web framework