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ROBOT Templates

PBPKO uses ROBOT templates for systematic ontology development and maintenance. This page explains how to use the template system effectively.

Overview

ROBOT templates provide a structured way to manage ontology terms using TSV (Tab-Separated Values) files. This approach ensures consistency and enables automated processing.

Template Files

1. vocab.tsv

Purpose: Main vocabulary terms and classes

Location: Robot/templates/vocab.tsv

Key Columns: - ID - Term identifier (e.g., pbpko:PBPKO_00001) - Label - Human-readable label - Definition - Textual definition - Parent - Parent class - Type - OWL class type - Editor - Contributor ORCID - Reviewer1 - First reviewer ORCID - Reviewer2 - Second reviewer ORCID

2. properties.tsv

Purpose: Object and data properties

Location: Robot/templates/properties.tsv

Key Columns: - ID - Property identifier - Label - Property label - Type - Property type (owl:ObjectProperty, owl:DataProperty) - Super Property - Parent property - Domain - Property domain - Range - Property range

3. input.tsv

Purpose: Additional input data and configurations

Location: Robot/templates/input.tsv

Template Usage

Adding New Terms

  1. Open vocab.tsv
  2. Add new row with:
  3. Unique ID (next sequential number)
  4. Descriptive label
  5. Clear definition
  6. Appropriate parent class
  7. Editor information

Example: 

pbpko:PBPKO_00099   New Parameter   Definition of new parameter Parameters  Class   0000-0001-8345-1349 0000-0002-9795-5967

Adding Properties

  1. Open properties.tsv
  2. Add new row with:
  3. Unique property ID
  4. Property label
  5. Property type
  6. Domain and range if applicable

Example: 

pbpko:PBPKO_10099   has_new_property    owl:ObjectProperty  pbpko:has_parameter PBPK Model  Parameter

Template Processing

ROBOT Commands

Generate ontology from templates: 

robot template --template Robot/templates/vocab.tsv \
               --template Robot/templates/properties.tsv \
               --output Robot/ontologies/edit.owl

Validate templates: 

robot template --template Robot/templates/vocab.tsv --check

Merge with imports: 

robot merge --input Robot/ontologies/edit.owl \
           --input Robot/ontologies/imported_modules.owl \
           --output Robot/ontologies/pbpko.owl

Best Practices

Term Creation

  1. Consistent Naming
  2. Use title case for labels
  3. Avoid abbreviations in labels

  4. Use consistent terminology

  5. Clear Definitions

  6. Start with capital letter
  7. End with period
  8. Be specific and unambiguous

  9. Include context when helpful

  10. Proper Classification

  11. Choose appropriate parent classes
  12. Follow ontological principles
  13. Maintain logical hierarchy

Property Creation

  1. Meaningful Names
  2. Use descriptive property names
  3. Follow naming conventions

  4. Avoid generic terms

  5. Proper Domains and Ranges

  6. Specify appropriate domains
  7. Define clear ranges
  8. Ensure logical consistency

Documentation

  1. Complete Information
  2. Fill all required columns
  3. Provide editor information

  4. Include reviewer assignments

  5. References

  6. Cite relevant literature
  7. Provide source URLs
  8. Include DOI when available

Template Validation

Automated Checks

ROBOT performs several validation checks:

  • Syntax validation - TSV format correctness
  • ID uniqueness - No duplicate IDs
  • Reference validation - Valid parent classes
  • Logical consistency - Ontological soundness

Manual Review

Before submitting:

  1. Check definitions - Ensure clarity and accuracy
  2. Verify relationships - Confirm logical connections
  3. Review naming - Check consistency
  4. Validate references - Ensure citations are correct

Common Issues

Template Errors

Missing required columns: - Ensure all mandatory columns are filled - Use empty cells for optional information

Invalid IDs: - Follow ID format: pbpko:PBPKO_XXXXX - Use sequential numbering - Avoid gaps in numbering

Circular references: - Check parent-child relationships - Ensure no circular dependencies

Processing Errors

ROBOT template errors: - Check TSV format - Verify column headers - Ensure proper escaping

Merge conflicts: - Resolve import conflicts - Check for duplicate terms - Validate logical consistency

Advanced Usage

Custom Templates

You can create custom templates for specific purposes:

  1. Specialized vocabularies
  2. Domain-specific terms
  3. Temporary term collections

Template Automation

Consider automating template processing:

  1. CI/CD integration
  2. Automated validation
  3. Scheduled processing

Getting Help

For template-related issues:

  1. Check ROBOT documentation
  2. Review existing templates
  3. Contact maintainers
  4. Open GitHub issues

Resources