Using Protégé to develop biomedical ontologies collaboratively

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About the tutorial

This tutorial will introduce attendees to the basics of editing ontologies in Protégé. We will introduce the basics of editing OWL ontologies and using reasoning to verify consistency and infer the structure of the users' ontology [1]. We will discuss how to set up Protégé to work in a distributed collaborative environment with multiple users contributing to the content and carrying out discussions to reach consensus [2]. We will also give a brief overview of the various Protégé tools and plug-ins for ontology visualization that facilitate ontology comprehension [3].

Tutorial topics

Protégé basics for OWL ontologies

  • Defining classes and the class hierarchy in Protégé; inheritance
  • Basic OWL features:
    • domains and ranges of properties;
    • restrictions;
    • disjoint classes

Defining individuals

  • Individuals basics
  • Custom-tailoring the forms to acquire information about individuals

Using Protégé for collaborative ontology development

  • Setting up the Protégé server
  • Using the Web client and the desktop client
  • Adding comments and discussions
  • Setting up user roles and privileges

Reasoning with OWL ontologies

  • Setting up a classifier
  • Using a description logic classifier with a Protégé ontology
  • Using explanation and debugging facilities

Ontology visualization facilities in Protégé (time permitting)


Natasha Noy is a senior research scientist at the Stanford Center for Biomedical Informatics Research and is a member of the Protégé group and of the National Center for Biomedical Ontology.


[1] M. Horridge, H. Knublauch, A. Rector, R. Stevens. C.Wroe A Practical Guide To Building OWL Ontologies Using The Protege-OWL Plugin and CO-ODE Tools

[2] T. Tudorache, N. F. Noy, S. W. Tu, M. A. Musen. Supporting collaborative ontology development in Protege Seventh International Semantic Web Conference, Karlsruhe, Germany, Springer. Published in 2008.

[3] Visualization plug-ins for Protégé