Difference between revisions of "Using WebProtege and NCBO BioPortal"

Latest revision as of 14:35, 14 April 2009

About the tutorial

Many biomedical ontologies and ontologies in other domains are products of collaborative work by a community of users. In this tutorial, we will discuss two tools that support various stages of collaborative ontology development. WebProtege is a version of the popular Protege ontology development tool that runs in a web browser. WebProtege is designed with collaborative development in mind and provides a simple view of the ontology structure, enables different users to edit an ontology simultaneously, to discuss the ontology content and to document these discussions in the context of the ontology. Users are also able to start change proposals, to vote, to browse and to discuss the change history of an ontology component.

While WebProtege enables the editing of ontologies, the NCBO BioPortal provides a community-based repository of ontologies where developers can publish their ontologies, solicit feedback from the community, define mappings between their ontologies and other ontologies.

This tutorial will introduce attendees to the basics of editing ontologies in WebProtege, present options for custom-tailoring the editing environment, and discuss how to use the collaboration facilities. We will provide the basics of setting up the WebProtege server. We will then introduce Bioportal, discuss how to publish an ontology in BioPortal and link it to other ontologies, and how to provide and collect feedback on your ontology. We will also give a brief overview of the ontology services that BioPortal provides for all ontologies in its repositories and discuss how these services can be used in other applications.

Tutorial topics

Basics of ontology editing in WebProtégé

Defining classes and the class hierarchy; inheritance
Basic OWL features:
- domains and ranges of properties;
- restrictions;
- disjoint classes
Customizing the view

Using WebProtégé for collaborative ontology development

Adding comments and discussions
Users and privileges
Hands-on exercise

Publishing ontology in BioPortal

Uploading ontology to BioPortal and defining ontology metadata
Uploading new versions
Creating mappings to other ontologies

BioPortal ontology services

Using BioPortal REST services to access ontologies and ontology metadata

References

[1] 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.

[2] WebProtege User's guide

[3] N. F. Noy, T. Tudorache, S. de Coronado, M. A. Musen Developing Biomedical Ontologies Collaboratively AMIA 2008 Annual Symposium, Washington, DC.

[4] Musen M, Shah N, Noy N, Dai B, Dorf M, Griffith N, Buntrock JD, Jonquet C, Montegut MJ, Rubin DL. BioPortal: Ontologies and Data Resources with the Click of a Mouse AMIA 2008 Annual Symposium, Washington, DC.

[5] N. F. Noy, N. B. Griffith, M. A. Musen. Collecting Community-Based Mappings in an Ontology 7th International Semantic Web Conference (ISWC 2008), Karlsruhe, Germany, Springer. Published in 2008.

@@ Line 29: / Line 29: @@
 === BioPortal ontology services ===
 * Using BioPortal REST services to access ontologies and ontology metadata
+== References ==
+[1] 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.
+[2] [http://protegewiki.stanford.edu/index.php/WebProtegeUsersGuide WebProtege User's guide]
+[3] N. F. Noy, T. Tudorache, S. de Coronado, M. A. Musen [https://bmir.stanford.edu/publications/view.php/developing_biomedical_ontologies_collaboratively Developing Biomedical Ontologies Collaboratively]  AMIA 2008 Annual Symposium, Washington, DC.
+[4] Musen M, Shah N, Noy N, Dai B, Dorf M, Griffith N, Buntrock JD, Jonquet C, Montegut MJ, Rubin DL. [http://www.ncbi.nlm.nih.gov/pubmed/18999306 BioPortal: Ontologies and Data Resources with the Click of a Mouse]  AMIA 2008 Annual Symposium, Washington, DC.
+[5] N. F. Noy, N. B. Griffith, M. A. Musen. [https://bmir.stanford.edu/publications/view.php/collecting_community_based_mappings_in_an_ontology Collecting Community-Based Mappings in an Ontology] 7th International Semantic Web Conference (ISWC 2008), Karlsruhe, Germany, Springer. Published in 2008.