Ontology Development Kit Guide

This guide is intended for editors of all OBO ontologies.

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

The guide weaves together day to day editing with Protege as well as use of ROBOT and other parts of the ODK

Contents:

• Initial Setup
  • 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
• Creating Regulation Terms
• 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 GO Subset (Slim)
• Adding a new GO Subset (Slim)
• Adding taxon restrictions
• Adding Terms to the Import Files