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User Documentation

This section provides user-focused documentation for PBPKO, including how to use the ontology, browse terms, and integrate with PBPK modeling tools.

Getting Started

What is PBPKO?

The PBPK Ontology (PBPKO) is a standardized vocabulary for physiologically-based pharmacokinetic modeling. It provides:

  • Consistent terminology across PBPK modeling tools
  • Semantic annotation capabilities for models
  • Interoperability between different platforms
  • Reproducible research through standardized concepts

Quick Start

  1. Browse the ontology using online tools
  2. Download the ontology files
  3. Integrate with your modeling tools
  4. Annotate your models using PBPKO terms

Browsing PBPKO

Online Browsers

OLS (Ontology Lookup Service): - PBPKO on OLS - Search and browse terms - View relationships and definitions - Export term information

Ontobee: - PBPKO on Ontobee - Alternative browsing interface - Additional visualization options - Community annotations

BioPortal: - PBPKO on BioPortal - Comprehensive ontology browser - Additional metadata and annotations - Integration with other ontologies

Key Terms to Explore

Core Model Classes: - PBPKO:00003 - Physiologically Based Pharmacokinetic Modeling - PBPKO:00004 - Whole Body PBPK Model - PBPKO:00005 - Perfusion Limited Model

Parameter Types: - PBPKO:00006 - Physiological Parameters - PBPKO:00126 - Physicochemical Parameters - PBPKO:00139 - Biochemical Parameters

Biological Processes: - PBPKO:00140 - Absorption - PBPKO:00146 - Distribution - PBPKO:00188 - Metabolism - PBPKO:00322 - Elimination

Using PBPKO

Model Annotation

Basic Annotation: 

# Example: Annotating a PBPK model
:my_pbpk_model a pbpko:PBPKO_00003 ;
    rdfs:label "My PBPK Model" ;
    pbpko:PBPKO_10001 :absorption_process ;
    pbpko:PBPKO_10001 :distribution_process ;
    pbpko:PBPKO_10001 :metabolism_process ;
    pbpko:PBPKO_10001 :elimination_process .

Parameter Annotation: 

# Example: Annotating parameters
:liver_volume a pbpko:PBPKO_00066 ;
    rdfs:label "Liver Volume" ;
    rdfs:comment "Volume of liver compartment" ;
    pbpko:PBPKO_10005 :my_pbpk_model .

Tool Integration

ROBOT Integration: 

# Extract specific terms
robot extract --input pbpko.owl \
              --term-file terms.txt \
              --output extracted.owl

SPARQL Queries: 

# Find all parameter classes
PREFIX pbpko: <http://purl.obolibrary.org/obo/pbpko#>
SELECT ?term ?label WHERE {
    ?term rdfs:subClassOf pbpko:PBPKO_00002 .
    ?term rdfs:label ?label .
}

Common Use Cases

1. Model Documentation

Use PBPKO to: - Document model components - Standardize terminology - Enable model comparison - Support reproducibility

Example: 

:my_model a pbpko:PBPKO_00003 ;
    pbpko:PBPKO_10002 :central_compartment ;
    pbpko:PBPKO_10002 :liver_compartment ;
    pbpko:PBPKO_10002 :kidney_compartment ;
    pbpko:PBPKO_10005 :cardiac_output ;
    pbpko:PBPKO_10005 :liver_volume .

2. Parameter Standardization

Use PBPKO to: - Standardize parameter names - Define parameter relationships - Enable parameter sharing - Support validation

Example: 

:cardiac_output a pbpko:PBPKO_00013 ;
    rdfs:label "Cardiac Output" ;
    rdfs:comment "Volume of blood pumped by heart per unit time" ;
    pbpko:PBPKO_10005 :my_model .

3. Process Annotation

Use PBPKO to: - Annotate biological processes - Define process relationships - Enable process comparison - Support mechanistic modeling

Example: 

:hepatic_metabolism a pbpko:PBPKO_00188 ;
    rdfs:label "Hepatic Metabolism" ;
    rdfs:comment "Drug metabolism in liver" ;
    pbpko:PBPKO_10001 :my_model .

Best Practices

Annotation Guidelines

Consistent Labeling: - Use descriptive labels - Follow naming conventions - Include units when appropriate - Provide clear definitions

Relationship Usage: - Use appropriate property types - Maintain logical consistency - Document relationships clearly - Validate relationships

Quality Assurance

Validation Steps: - Check term definitions - Verify relationships - Validate logical consistency - Test with reasoners

Common Issues: - Inconsistent naming - Missing definitions - Incorrect relationships - Logical inconsistencies

Troubleshooting

Common Questions

Q: How do I find the right term? A: Use the online browsers to search for terms, or browse the hierarchy to find related concepts.

Q: Can I add new terms? A: Yes, see the Contributing Guide for information on adding new terms.

Q: How do I validate my annotations? A: Use ROBOT or other OWL tools to validate your annotations for consistency.

Getting Help

Resources: - Documentation - Comprehensive guides - GitHub Issues - Bug reports and questions - Community Discussions - User discussions

Contact: - Email: saurav.kumar@iispv.cat - GitHub: Open an issue - Community: Join discussions

Examples and Tutorials

Tutorial Series

  1. Introduction to PBPKO - Basic concepts and usage
  2. Browsing and Searching - Finding terms and relationships
  3. Model Annotation - Annotating PBPK models
  4. Tool Integration - Using PBPKO with modeling tools
  5. Advanced Usage - Complex annotation scenarios

Example Models

Simple Two-Compartment Model: - Central compartment - Peripheral compartment - Basic parameters - Simple processes

Complex Multi-Organ Model: - Multiple organ compartments - Detailed parameters - Complex processes - Advanced relationships

Resources

Documentation

Tools

Community