Poster presentation for the caBIG 2010 Annual meeting.

1. 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
Develop new ontology
version based on
community feedback
Collect feedback from
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.
BioPortal WebProtégé
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
BioPortal Notes
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 feedback
Publish Ontology
community
BioPortal
LexEVS Protégé
Protégé
Notes Core
API