Editors Workflow

This guide describes the standard workflow for editing the Mouse Muscle Atlas ontology.

Prerequisites

• Protégé installed
• Git configured
• Docker installed (for ODK commands)

Editing Workflow

1. Get the Latest Version

git pull origin main

2. Create a Branch

git checkout -b your-feature-branch

3. Edit in Protégé

1. Open src/ontology/mma-edit.owl in Protégé
2. Make your changes
3. Save the file

4. Run Quality Checks

cd src/ontology
sh run.sh make test

5. Commit and Push

git add src/ontology/mma-edit.owl
git commit -m "Add new terms for X"
git push origin your-feature-branch

6. Create Pull Request

Create a pull request on GitHub and wait for automated checks to pass.

Adding New Terms

When adding new terms, ensure you include:

• Label: Human-readable name
• Definition: Clear description with source citation
• Parent class: Appropriate superclass
• Synonyms: Alternative names (if applicable)

ID Ranges

Each editor should use their assigned ID range. Check src/ontology/mma-idranges.owl for your range.