Ontology Development Kit Guide

This guide is intended for maintainers and editors of OBO ontologies.

The first part of the guide is how to set up a new ontology project. This requires some technical steps.

The second part of the guide is for day to day editing.

NOTE this guide is adapted from the GO editors guide. Some instructions may still be too GO-specific.

Contents:

• Creating a new Ontology using the ODK
  • 1. Install and Start Docker
  • 2. Download the wrapper script and pull latest ODK version
  • 3. Run the wrapper script
  • 4. Push to Git hosting website
• Initial Setup for Ontology Developers
  • Installing Protege
  • ID Ranges
  • Setting ID ranges in Protege
• Configuration
  • Configuring New Entities Metadata
  • Configuring User details
• Installing and Using git
  • Installing git
  • Cloning the go-ontology repository from GitHub
  • Editing the .profile (or .bashrc) file to indicate the branch you are working on
• Daily Workflow
  • Updating the local copy of the ontology with ‘git pull’
  • Creating a New Working Branch with ‘git checkout’
  • Continuing work on an existing Working Branch
  • Loading, navigating and saving the Ontology in Protégé
  • Committing, pushing and merging your changes to the repository
• Creating a New Ontology Term
• Synonyms
  • The scope of a synonym may fall into one of four categories:
  • Synonym types
  • Database cross references
• Deleting Asserted Subclasses
• Obsoleting an Existing Ontology Term
• Merging Ontology Terms
• Term Comments
  • Adding Comments to Terms
  • Do Not Annotate
  • Do Not Manually Annotate
• Adding a term to a Subset (Slim)
• Adding a new Subset (Slim)
• Adding taxon restrictions
• Adding Terms to the Import Files