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How to contribute to PBPKO

We welcome contributions to the PBPK Ontology (PBPKO)! This guide will help you get started with contributing to the ontology development.

Getting Started

Prerequisites

Before contributing to PBPKO, you should have:

  • Basic understanding of ontologies and OWL
  • Familiarity with PBPK modeling concepts
  • Git and GitHub knowledge
  • ROBOT tool experience (recommended)

Repository Setup

  1. Fork the repository 

    # Fork https://github.com/InSilicoVida-Research-Lab/pbpko on GitHub

  2. Clone your fork 

    git clone https://github.com/YOUR_USERNAME/pbpko.git
cd pbpko

  3. Add upstream remote 

    git remote add upstream https://github.com/InSilicoVida-Research-Lab/pbpko.git

Types of Contributions

1. Adding New Terms

To add new terms to PBPKO:

  1. Identify the need - Check if the term already exists
  2. Use ROBOT templates - Add terms using the TSV templates in Robot/templates/
  3. Follow naming conventions - Use consistent naming patterns
  4. Provide definitions - Include clear, concise definitions
  5. Add references - Cite relevant literature

2. Improving Existing Terms

You can improve existing terms by:

  • Adding better definitions
  • Including synonyms
  • Adding references
  • Improving relationships
  • Adding examples

3. Documentation Improvements

Help improve the documentation by:

  • Fixing typos and errors
  • Adding examples
  • Improving clarity
  • Adding missing information

4. Bug Reports

Report issues by:

  • Creating GitHub issues
  • Providing detailed descriptions
  • Including examples when possible
  • Suggesting solutions if you have them

Contribution Workflow

1. Create a Branch

git checkout -b feature/your-feature-name

2. Make Changes

  • Edit the appropriate files
  • Follow the coding standards
  • Test your changes

3. Commit Changes

git add .
git commit -m "Add: brief description of changes"

4. Push and Create Pull Request

git push origin feature/your-feature-name

Then create a pull request on GitHub.

ROBOT Templates

PBPKO uses ROBOT templates for term management. See ROBOT Templates for detailed information.

Template Files

  • vocab.tsv - Main vocabulary terms
  • properties.tsv - Object and data properties
  • input.tsv - Additional input data

Coding Standards

Term IDs

  • Use format: PBPKO:XXXXX
  • Sequential numbering
  • No gaps in numbering

Labels

  • Use title case
  • Be descriptive and concise
  • Avoid abbreviations when possible

Definitions

  • Start with capital letter
  • End with period
  • Be clear and unambiguous
  • Include context when helpful

Synonyms

  • Include common abbreviations
  • Include alternative spellings
  • Use pipe (|) to separate multiple synonyms

Review Process

All contributions go through a review process:

  1. Automated checks - ROBOT validation
  2. Peer review - Team members review changes
  3. Testing - Verify changes work correctly
  4. Approval - Maintainer approval required

Getting Help

If you need help:

  • Check existing documentation
  • Open a GitHub issue
  • Contact the maintainers
  • Join our discussions

Recognition

Contributors are recognized in:

  • GitHub contributors list
  • Ontology acknowledgements
  • Publication acknowledgements (when appropriate)

Code of Conduct

We follow a code of conduct that promotes:

  • Respectful communication
  • Inclusive environment
  • Constructive feedback
  • Professional behavior

Next Steps

After reading this guide:

  1. Check out ROBOT Templates
  2. Look at Build Process
  3. Review Managing Documentation
  4. Start contributing!

Thank you for your interest in contributing to PBPKO!