A comprehensive web dashboard for monitoring and analyzing the AOP-Wiki RDF knowledge base evolution over time. Built for the VHP4Safety project to provide insights into Adverse Outcome Pathways (AOPs) data trends, quality metrics, and structural analysis.
- Latest Data Overview: Current state snapshots of the AOP-Wiki database
- Historical Trends: Time-series analysis of database evolution
- Network Analysis: AOP connectivity and structural relationships
- Data Quality Metrics: Annotation completeness and ontology usage patterns
- Entity counts (AOPs, Key Events, Key Event Relationships, Stressors)
- Key Event component distribution and annotation depth
- Biological process and object ontology usage patterns
- AOP completeness analysis using configurable property types
- Network density and connectivity analysis
- Author contribution tracking over time
- CSV Download: Export underlying data from any plot for further analysis
- 10+ Download Options: Entity counts, components, usage patterns, trends, and more
- Multiple Formats: Absolute values and delta (change) datasets available
- Rich Metadata: All exports include version info and contextual data
- Parallel Processing: Concurrent plot generation for fast loading
- Health Monitoring: Real-time SPARQL endpoint status tracking
- Error Handling: Graceful degradation with fallback visualizations
- Responsive Design: Works seamlessly on desktop and mobile devices
- Flask Web Framework: Lightweight and fast web server
- SPARQL Integration: Direct queries to AOP-Wiki RDF endpoint
- Plotly Visualizations: Interactive, publication-quality charts
- Pandas Data Processing: Efficient data manipulation and caching
- Concurrent Execution: Multi-threaded plot generation
- Primary: AOP-Wiki SPARQL endpoint (
http://localhost:8890/sparql) - Configuration: Property metadata from
property_labels.csv - Ontology Sources: GO, CHEBI, PR, CL, UBERON, HP, MP, and others
- Time-series line plots for trends
- Bar charts for entity counts and metrics
- Pie charts for distributions and proportions
- Interactive hover details and responsive layouts
# Python 3.8+ required
python3 --version
# Install dependencies
pip install -r requirements.txt- SPARQL Endpoint: Ensure AOP-Wiki RDF endpoint is accessible
- Property Labels: Update
property_labels.csvwith desired AOP properties - Environment: Configure settings in
config.py
# Start the application
python app.py
# Access the dashboard
open http://localhost:5000# Verify system status
curl http://localhost:5000/health
# Monitor real-time status
open http://localhost:5000/status- Latest Data: Current database snapshots and quality metrics
- Historical Trends: Time-series analysis and evolution patterns
- Toggle Views: Switch between absolute values and deltas
- CSV Downloads: Export data from any plot using download buttons
- Responsive Charts: Hover for details, zoom, and pan capabilities
- Navigate to any plot with a "Download CSV" button
- Click to download the underlying dataset
- For historical trends: choose "CSV (Abs)" or "CSV (Δ)"
- Files include version metadata and contextual information
├── app.py # Main Flask application
├── plots.py # Plot generation and data processing
├── config.py # Configuration settings
├── property_labels.csv # AOP property metadata
├── templates/ # HTML templates
│ ├── index.html # Main dashboard layout
│ ├── trends.html # Historical trends section
│ └── status.html # System monitoring page
├── static/
│ └── css/main.css # Styling and responsive design
├── docs/ # Comprehensive Sphinx documentation
│ ├── source/ # Documentation source files
│ │ ├── conf.py # Sphinx configuration
│ │ ├── index.rst # Main documentation page
│ │ ├── modules.rst # API reference
│ │ ├── quickstart.rst # Quick start guide
│ │ ├── configuration.rst # Configuration guide
│ │ └── api.rst # Detailed API documentation
│ └── build/ # Generated documentation
└── requirements.txt # Python dependencies
- Create plot function in
plots.pywith data caching - Add Flask route for CSV download in
app.py - Include plot variable in template rendering
- Add download button to appropriate HTML template
- Colors: Modify
BRAND_COLORSinplots.py - Properties: Update
property_labels.csvwith new AOP properties - Endpoints: Configure SPARQL endpoint in
config.py - Layout: Customize templates and CSS for different layouts
SPARQL_ENDPOINT=http://localhost:8890/sparql
FLASK_HOST=0.0.0.0
FLASK_PORT=5000
LOG_LEVEL=INFO
PARALLEL_WORKERS=5
PLOT_TIMEOUT=60Edit property_labels.csv to customize AOP completeness analysis:
uri,label,type
http://aopkb.org/aop_ontology#has_key_event,Has Key Event,Content
http://purl.org/dc/elements/1.1/title,Title,Essential- Plots not loading: Check SPARQL endpoint connectivity
- Slow performance: Adjust
PARALLEL_WORKERSandPLOT_TIMEOUT - CSV downloads failing: Verify data caching is working correctly
- Memory issues: Reduce concurrent workers or increase system resources
Monitor application logs for detailed error information:
tail -f app_new.logUse the built-in monitoring endpoints:
/health- System health check/status- Real-time monitoring dashboard
- Fork the repository
- Create a feature branch
- Implement changes with tests
- Update documentation
- Submit a pull request
- Follow PEP 8 for Python code
- Include comprehensive Google/Sphinx style docstrings
- Use type hints for all functions and methods
- Test all SPARQL queries and visualizations
- Ensure responsive design for new UI elements
The project includes comprehensive Google/Sphinx format documentation:
# Install Sphinx dependencies
pip install sphinx sphinx-rtd-theme
# Build HTML documentation
cd docs && make html
# View documentation
open docs/build/html/index.html- Professional Sphinx Documentation: Complete API reference with VHP4Safety branding
- Google-Style Docstrings: All functions documented with comprehensive examples
- Interactive API Reference: Auto-generated from docstrings with cross-references
- Configuration Guides: Detailed environment variable and deployment documentation
- Quick Start Guides: Step-by-step setup and usage instructions
Todo
For questions, issues, or feature requests:
- Check the troubleshooting section above
- Review existing issues in the project repository
- Contact the VHP4Safety development team
- VHP4Safety: Virtual Human Platform for safety assessment
- AOP-Wiki: Adverse Outcome Pathways knowledge base