Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Protégé Ontology Editor

  • Mark A. Musen
  • The Protégé Team
Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_1104

Definition

Protégé is a widely used software system that helps developers to create and edit  ontologies. Available through the Stanford University Center for Biomedical Informatics Research for more than 2 decades, Protégé provides a mechanism for model builders to define the entities, relationships among entities, and properties of entities in given application areas. As of this writing, there are more than 200,000 registered users of the system, who have developed thousands of ontologies and knowledge-based applications. Thousands of Protégé users communicate with one another and the Protégé development team on e-mail distribution lists, where they report problems they may encounter using the software, announce the availability of new third-party Protégé plug-ins, seek help building and extending ontologies, and obtain general modeling advice. Protégé is available through an open-source license and is downloadable from a Stanford Web site (http://protege.Stanford.EDU).

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References

  1. Day-Richter J, Harris MA, Haendel M et al (2007) OBO-Edit – an ontology editor for biologists. Bioinformatics 23(16):2198–2200PubMedGoogle Scholar
  2. Ernst NA, Storey M-A, Allen P (2005) Cogitive support for ontology modeling. Int J Hum Comput Stud 62(5):553–577Google Scholar
  3. Gennari JH, Musen MA, Fergerson RW, Grosso WE, Crubézy M, Eriksson H, Noy NF, Tu SW (2003) The evolution of Protégé: an environment for knowledge-based systems development. Int J Hum Comput Stud 58(1):89–123Google Scholar
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  5. Moreira DA, Musen MA (2007) OBO to OWL: a Protégé OWL tab to read/save OBO ontologies. Bioinformatics 23(14):1868–1870PubMedGoogle Scholar
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  8. Musen MA, Fergerson RW, Grosso WE, Noy NF, Crubézy M, Gennari JH (2000) Component-based support for building knowledge-acquisition systems. In: Proceedings of the conference on intelligent information processing (IIP 2000) of the international federation for information processing sixteenth world computer congress (WCC 2000), Beijing, Aug 2000. pp 18–22Google Scholar
  9. Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Storey M-A, Smith B, the NCBO team (2012) The national center for biomedical ontology. J Am Med Inform Assoc 19(2):190–195PubMedGoogle Scholar
  10. Noy NF, Tudorache T, de Coronado S, Musen MA (2008) Developing biomedical ontologies collaboratively. In: Proceedings of the AMIA annual symposium. American Medical Informatics Association, Washington, DC, Nov 2008, pp 520–524Google Scholar
  11. Noy NF, Tudorache T, Nyulas CI, Musen MA (2010) The ontology life cycle: integrated tools for editing, publishing, peer review, and evolution of ontologies. In: Proceedings of the AMIA annual symposium, Nov 2010, pp 552–556Google Scholar
  12. O’Connor MJ, Knublauch H, Tu SW, Grossof B, Dean M, Grosso WE, Musen MA (2005) Supporting rule system interoperability on the Semantic Web with SWRL. In: Proceedings of the fourth international semantic web conference, Galway. pp 974–986Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Stanford Center for Biomedical Informatics ResearchStanford UniversityStanfordUSA