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Editors Documentation

This section provides documentation for PBPKO editors and contributors, including development workflows, quality standards, and maintenance procedures.

Editor Responsibilities

Core Duties

Term Development: - Create new terms following PBPKO standards - Maintain existing term definitions - Ensure logical consistency - Validate term relationships

Quality Assurance: - Review term definitions for clarity - Validate ontological relationships - Check for logical consistency - Ensure compliance with standards

Community Engagement: - Respond to user questions - Review pull requests - Provide feedback to contributors - Maintain community standards

Development Workflow

Term Creation Process

1. Identify Need: - Check if term already exists - Verify necessity and scope - Define clear requirements - Plan term relationships

2. Create Term: - Use ROBOT templates - Follow naming conventions - Provide clear definitions - Include appropriate relationships

3. Review Process: - Self-review for completeness - Peer review by team members - Community feedback integration - Final validation

4. Integration: - Merge into main ontology - Update documentation - Announce changes - Monitor usage

Template Usage

Vocabulary Template (vocab.tsv): 

ID  Label   Definition  Parent  Type    Editor  Reviewer1   Reviewer2
pbpko:PBPKO_00099   New Term    Definition of new term  Parent Class    Class   0000-0001-8345-1349 0000-0002-9795-5967

Properties Template (properties.tsv): 

ID  Label   Type    Super Property  Domain  Range
pbpko:PBPKO_10099   has_new_property    owl:ObjectProperty  pbpko:has_parameter PBPK Model  Parameter

Quality Standards

Term Quality

Definition Requirements: - Clear and unambiguous - Scientifically accurate - Consistent with ontology style - Include context when helpful

Naming Conventions: - Use title case for labels - Avoid abbreviations in labels - Use consistent terminology - Follow established patterns

Relationship Standards: - Use appropriate property types - Maintain logical consistency - Document relationships clearly - Validate with reasoners

Documentation Standards

Term Documentation: - Complete definitions - Appropriate synonyms - Clear examples - Relevant references

Process Documentation: - Document development decisions - Record change rationale - Maintain change logs - Update user documentation

Review Process

Review Criteria

Technical Review: - Ontological soundness - Logical consistency - Relationship validity - Definition clarity

Content Review: - Scientific accuracy - Domain relevance - Completeness - Usability

Process Review: - Template compliance - Documentation completeness - Review process adherence - Quality standards compliance

Review Workflow

1. Initial Review: - Check template compliance - Validate basic requirements - Identify major issues - Provide initial feedback

2. Detailed Review: - Thorough content analysis - Relationship validation - Consistency checking - Quality assessment

3. Final Review: - Comprehensive validation - Final approval decision - Integration planning - Documentation updates

Maintenance Procedures

Regular Maintenance

Monthly Tasks: - Review pending terms - Update documentation - Check for inconsistencies - Monitor community feedback

Quarterly Tasks: - Comprehensive ontology review - Update import ontologies - Review and update standards - Plan future development

Annual Tasks: - Complete ontology audit - Major documentation update - Community survey - Strategic planning

Issue Resolution

Bug Reports: - Acknowledge receipt - Investigate issue - Develop solution - Implement fix - Verify resolution

Feature Requests: - Evaluate feasibility - Assess impact - Plan implementation - Develop feature - Test and deploy

Community Issues: - Respond promptly - Provide clear guidance - Escalate when needed - Follow up on resolution

Tools and Resources

Development Tools

ROBOT: - Template processing - Ontology validation - Import management - Release generation

Protégé: - Manual ontology editing - Visualization - Reasoning - Validation

Git/GitHub: - Version control - Collaboration - Issue tracking - Documentation

Quality Assurance Tools

Validation Tools: - ROBOT validation - HermiT reasoner - Pellet reasoner - Fact++ reasoner

Testing Tools: - Automated testing - Regression testing - Performance testing - Integration testing

Training and Development

Editor Training

Initial Training: - Ontology basics - PBPKO structure - Development tools - Quality standards

Ongoing Development: - Advanced techniques - New tool training - Best practices - Community engagement

Knowledge Sharing

Documentation: - Maintain comprehensive guides - Update procedures - Share best practices - Document lessons learned

Community Engagement: - Regular meetings - Knowledge sharing sessions - Training workshops - Conference presentations

Collaboration Guidelines

Team Communication

Regular Meetings: - Weekly team meetings - Monthly planning sessions - Quarterly reviews - Annual planning

Communication Channels: - GitHub issues and discussions - Email for formal communication - Slack for quick questions - Video calls for complex discussions

External Collaboration

Community Engagement: - Respond to user questions - Participate in discussions - Share knowledge and expertise - Build relationships

Academic Collaboration: - Research partnerships - Publication collaboration - Conference presentations - Workshop organization

Performance Metrics

Quality Metrics

Term Quality: - Definition completeness - Relationship accuracy - Consistency scores - User satisfaction

Process Quality: - Review completion time - Issue resolution time - Documentation quality - Community engagement

Impact Metrics

Usage Metrics: - Download statistics - Citation counts - User adoption - Community growth

Development Metrics: - Term creation rate - Issue resolution rate - Documentation updates - Community contributions

Resources

Documentation

Tools

  • ROBOT - Ontology development
  • Protégé - Ontology editor
  • GitHub - Version control and collaboration
  • OLS - Ontology browser

Community