Using Protégé to develop biomedical ontologies collaboratively - Revision history

Noy at 22:37, 18 November 2008

2008-11-18T22:37:27Z

Noy at 22:35, 18 November 2008

2008-11-18T22:35:55Z

Noy: Using the Protégé ontology editor to develop ontologies collaboratively moved to Using Protégé to develop biomedical ontologies collaboratively

2008-11-17T23:12:52Z

Using the Protégé ontology editor to develop ontologies collaboratively moved to Using Protégé to develop biomedical ontologies collaboratively

Noy at 23:09, 17 November 2008

2008-11-17T23:09:29Z

Noy: Protege moved to Using the Protégé ontology editor to develop ontologies collaboratively: typesetting

2008-11-17T23:09:08Z

Protege moved to Using the Protégé ontology editor to develop ontologies collaboratively: typesetting

Noy: New page: '''Using the Protégé ontology editor to develop ontologies collaboratively''' == About the tutorial == This tutorial will introduce attendees to the basics of editing ontologies in [h...

2008-11-17T23:07:41Z

New page: '''Using the Protégé ontology editor to develop ontologies collaboratively''' == About the tutorial == This tutorial will introduce attendees to the basics of editing ontologies in [h...

New page

'''Using the Protégé ontology editor to develop 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. 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. We will also give a brief overview of the various Protégé tools and plug-ins for ontology visualization that facilitate ontology comprehension.

== 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.

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 == 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
+[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. [https://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.
+[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]

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 == 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. 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. We will also give a brief overview of the various Protégé tools and plug-ins  for ontology visualization that facilitate ontology comprehension.
+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 ==
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 == 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.