Collaborative Development of Ontologies using
BioPortal and WebProtégé
Patricia L. Whetzel, Natasha Noy, Tania Tudorache, Csongor Nyulas, and Mark A. Musen
Stanford University, Stanford, CA, USA
Introduction
Development of ontologies requires an integrated platform that not only
allows for ontology developers to collaboratively edit the ontology, but also
allows for the collection of comments from subject matter experts. The
integration of WebProtégé and BioPortal provides such an environment.
Web Protégé is a lightweight Web-based ontology browser and editor,
which provides a collaborative environment for editing. These features
include the ability to simultaneously browse and edit the ontology, to
discuss entities in the ontology (e.g. class, property, or individual), and to
track all changes to the ontology. Once the cycle of edits is complete and
a new version of the ontology is generated, many ontology developers
choose to release their ontology by placing it on the Web for others to
access the ontology and to collect comments from the community.
BioPortal provides such a mechanism to publish ontologies and collect
community feedback, in addition to a range of other functionality. Using the
BioPortal Web services, the ontology and it’s metadata can be published
directly to BioPortal. Subject matter experts can login to BioPortal, browse
the ontology and add comments to entities and propose changes. The
notes are stored in a common representation and therefore, the ontology
editors can see the note in the context of editing the ontology and make the
needed changes. Notes can be “archived” once the editing task is
complete, which will then hide the note from view in BioPortal.
Requirements for the implementation of an integrated editing platform for
ontology development and publishing have been collected from review of
existing tools and workflows of large collaborative ontology development
projects. One of the main drivers and users of this collaborative platform is
the World Health Organization in development of ICD-11.
Notes Core API
•The Notes Core API provides storage, and access
mechanism for creating Notes linked to ontology elements
•Notes are stored as an ontology of notes, including different
types of proposals:
- Term requests
- Property value changes
- Hierarchy changes
- Retirement of concepts
BioPortal Notes
Develop new ontology version
based on community feedback
Acknowledgements
BioPortal is developed by the National Center for Biomedical Ontology (NCBO), a National
Center for Biomedical Computing under the NIH Roadmap. BioPortal is developed in
conjunction with partners at the University of Victoria and the Mayo Clinic. For more
information on NCBO see http://www.bioontology.org.
Contact
BioPortal Support: support@bioontology.org
Protégé/WebProtege: protege-discussion@lists.stanford.edu
BioPortal Ontology Library
•Open ontology repository for publishing biomedical
ontologies
•Features
- Search across and within all ontologies
- Browse ontologies
- Provide feedback – Notes and Reviews
•Statistics
- Total number of ontologies: 216
- Number of classes/types: 1,438,792
•Supports many ontology formats: OWL, OBO format, Rich
Release Format, Protégé frames
WebProtégé
•Allows multiple users to:
- Edit an ontology simultaneously
- Discuss design decisions
- Make proposals
- Analyze changes
WebProtégé
Term
Details
Notes on
Term
Notes
on
Branch
THE NATIONAL CENTER FOR
BIOMEDICAL ONTOLOGY
Ontology Development Lifecycle
•Involves both Subject Matter Experts (SMEs) and Ontology
Developers
•Consists of:
- Discussion between SMEs and Ontology Developers
- Ontology Editing
- Publishing Ontology to the Web
- Collect Feedback on Published Ontology
Collect information from
Subject Matter Experts
Draft prototype ontology
Get feedback from Subject
Matter Experts
Refine Ontology based on
Publish Ontology feedback
Collect feedback from
community
BioPortal