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Editing the AISM and AISM-based ontologies using Protégé

Here we outline the steps to be able to add, edit and annotate terms in an existing AISM-based ontology. Some instructions here are adopted from the Gene Ontology protocols.

In order to perform the steps in this section you will need to:

  1. Have Protégé installed
  2. Have a clone of your forked repository in your computer

Explore the ontology and its hierarchy

Open Protégé. Click on File, Open…, and find the abbreviation_for_your_ontology-edit.owl file (e.g., GitHub/abbreviation_for_your_ontology/src/ontology/abbreviation_for_your_ontology-edit.owl

In my computer, this is GitHub/aism/src/ontology/aism-edit.owl

Click on the entities tab in the top left area:

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This will show you the main features that you will be working with:

  • The classes window (left block, outlined in blue), where you can see the hierarchy
  • The annotations window (top box on the right, outlined in green)
  • Description window (bottom box on the right, outlined in pink)
  • Annotation properties tab (top left, red arrow)
  • Object properties tab (top left, yellow arrow)

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Next, set up Protégé to auto generate IRI-s. If you already have Protégé set up for auto-generating IRI's, you can either import existing terms from other ontologies, if needed, or you can add new terms to the current ontology, making sure to include all the necessary annotations.