Difference between revisions of "Using Protégé to develop biomedical ontologies collaboratively"
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== About the tutorial == | == 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 == | == Tutorial topics == | ||
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== Faculty == | == 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. | 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. [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. | ||
| + | |||
| + | [3] [http://protegewiki.stanford.edu/index.php/Visualization Visualization plug-ins for Protégé] | ||
Revision as of 15:35, 18 November 2008
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)
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. Supporting collaborative ontology development in Protege Seventh International Semantic Web Conference, Karlsruhe, Germany, Springer. Published in 2008.