View source for Using Protégé to develop biomedical ontologies collaboratively

== About the tutorial ==

This tutorial will introduce attendees to the basics of editing ontologies in [http://protege.stanford.edu 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) ===


== Faculty == 
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.

== References == 
[1] M. Horridge, H. Knublauch, A. Rector, R. Stevens. C.Wroe [http://www.co-ode.org/resources/tutorials/ProtegeOWLTutorial.pdf 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. [http://bmir.stanford.edu/publications/view.php/supporting_collaborative_ontology_development_in_protege Supporting collaborative ontology development in Protege] Seventh International Semantic Web Conference, Karlsruhe, Germany, Springer. Published in 2008. 

[3] [http://protegewiki.stanford.edu/index.php/Visualization Visualization plug-ins for Protégé]