History¶
Development Timeline¶
2024¶
December 2024 - Initial Release (v1.0.0) - Initial ontology framework established - Core classes and properties defined - Basic ROBOT template structure created - First documentation published
Key Milestones: - Repository created on GitHub - Initial team assembled - First ontology terms added - Basic build process established
2025¶
January 2025 - Stable Release (v1.0.1) - First stable release - Core ontology structure completed - Basic parameter definitions added - Documentation improvements
February 2025 - Enhanced Release (v1.0.2) - Parameter additions and improvements - Template system enhancements - Documentation updates - Community feedback integration
February 2025 - Current Release (v1.0.3) - Updated parameter definitions - Improved ontology structure - Enhanced documentation - Bug fixes and improvements
Project Origins¶
Background¶
The PBPKO project was initiated in response to the growing need for standardized terminology in physiologically-based pharmacokinetic modeling. The lack of consistent vocabulary across different PBPK modeling tools and research groups was identified as a barrier to:
- Model interoperability
- Reproducible research
- Knowledge sharing
- Regulatory submissions
Initial Development¶
Project Initiation: - Started by IISPV team in collaboration with WUR and JSI - Focus on creating comprehensive PBPK ontology - Integration with existing biomedical ontologies - Community-driven development approach
Early Challenges: - Defining scope and boundaries - Establishing naming conventions - Creating consistent definitions - Building community support
Key Developments¶
Technical Milestones¶
Ontology Structure: - Hierarchical class organization - Property relationship definitions - Import management system - Validation framework
Development Tools: - ROBOT template system - Automated build process - Continuous integration - Quality assurance procedures
Documentation: - Comprehensive user guides - Developer documentation - API documentation - Tutorial materials
Community Milestones¶
Adoption: - First external users - Community feedback integration - User group formation - Conference presentations
Collaboration: - Academic partnerships - Industry collaborations - Regulatory engagement - International cooperation
Evolution of Scope¶
Initial Scope (v1.0.0)¶
- Basic PBPK model classes
- Core parameter types
- Essential biological processes
- Simple compartment structure
Expanded Scope (v1.0.1-1.0.2)¶
- Comprehensive parameter definitions
- Detailed compartment specifications
- Enhanced biological processes
- Improved property relationships
Current Scope (v1.0.3)¶
- Full parameter coverage
- Complete compartment system
- Comprehensive process definitions
- Advanced property relationships
Future Directions¶
Planned Developments¶
Short-term (2025): - Additional parameter types - Enhanced validation rules - Improved documentation - Community tools
Medium-term (2026): - Advanced modeling features - Tool integration - Regulatory applications - International expansion
Long-term (2027+): - AI/ML integration - Automated model generation - Real-time collaboration - Global standardization
Lessons Learned¶
Technical Lessons¶
Ontology Design: - Importance of clear definitions - Need for consistent naming - Value of hierarchical organization - Benefits of modular design
Development Process: - Value of automated testing - Importance of documentation - Need for community input - Benefits of iterative development
Community Lessons¶
Engagement: - Early community involvement crucial - Regular communication important - Feedback integration essential - Recognition motivates contributors
Adoption: - Clear benefits must be demonstrated - Easy adoption process needed - Training materials essential - Support systems required
Acknowledgments¶
Historical Contributors¶
Founding Team: - Saurav Kumar (IISPV) - Project lead - Shubh Sharma (IISPV) - Technical development - Deepika Deepika (IISPV) - Content curation - Vikas Kumar (IISPV) - Ontology design - Johannes Kruisselbrink (WUR) - Domain expertise - Panče Panov (JSI) - Validation and testing
Early Adopters: - Research groups who provided feedback - Conference attendees who asked questions - GitHub users who reported issues - Community members who suggested improvements
Institutional Support¶
IISPV - Primary development institution WUR - Collaboration and validation JSI - Technical expertise and testing Community - Feedback and adoption
Historical Resources¶
Archived Materials¶
Early Documentation: - Initial project proposals - Early design documents - Community feedback summaries - Development meeting notes
Version History: - Complete release history - Change logs - Migration guides - Deprecation notices
Community Archives: - Discussion forum archives - Conference presentation materials - Workshop recordings - User group meeting notes
For more detailed historical information, see the GitHub repository history and release notes.