About PBPKO¶

Overview¶

The Physiologically-Based Pharmacokinetic Ontology (PBPKO) is a comprehensive ontology designed to support the modeling and understanding of pharmacokinetics in biological systems. PBPKO provides a standardized vocabulary and conceptual framework for describing physiologically-based pharmacokinetic (PBPK) models, their components, and the biological processes they represent.

Purpose and Scope¶

PBPKO aims to:

Standardize terminology used in PBPK modeling across different research groups and software platforms
Enable interoperability between different PBPK modeling tools and databases
Support model annotation with semantic metadata for better reproducibility
Facilitate knowledge discovery through structured representation of PBPK concepts
Enable automated reasoning about PBPK model components and relationships

Key Features¶

Comprehensive Coverage¶

PBPKO covers the essential components of PBPK modeling:

Core Model Classes: PBPK models, compartments, transporters, and enzymes
Biological Processes: Absorption, distribution, metabolism, and elimination (ADME)
Parameter Types: Physiological, physicochemical, and biochemical parameters
Output Metrics: Concentration profiles, pharmacokinetic parameters, and evaluation metrics

Ontological Foundation¶

PBPKO is built on solid ontological foundations by importing:

Basic Formal Ontology (BFO) for upper-level categories
Relation Ontology (RO) for standard relationships
Gene Ontology (GO) for biological processes
Ontology for Biomedical Investigations (OBI) for investigation-related terms
Systems Biology Ontology (SBO) for biochemical parameters

ROBOT-Based Development¶

The ontology is developed using ROBOT (ROBOT is an OBO Tool) framework, which provides:

Template-based term generation
Automated reasoning and validation
Consistent annotation patterns
Integration with OBO Foundry standards

Target Users¶

PBPKO is designed for:

PBPK Modelers: Researchers developing and using PBPK models
Software Developers: Building PBPK modeling tools and platforms
Database Curators: Managing PBPK model repositories
Regulatory Scientists: Evaluating PBPK models for regulatory submissions
Ontologists: Extending and maintaining the ontology

Applications¶

PBPKO can be used for:

Model Annotation: Adding semantic metadata to PBPK models
Tool Integration: Enabling interoperability between modeling platforms
Knowledge Discovery: Finding related models and parameters
Quality Assurance: Validating model completeness and consistency
Education: Teaching PBPK concepts through structured vocabulary

Development Status¶

PBPKO is actively developed and maintained by a collaborative team from:

IISPV (Institut d'Investigació Sanitària Pere Virgili)
WUR (Wageningen University & Research)
JSI (Jožef Stefan Institute)

The ontology follows OBO Foundry principles and is designed for long-term sustainability and community adoption.