Using WebProtege and NCBO BioPortal

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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


[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.