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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

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Collaborative Development of Ontologies using BioPortal and WebProtégé

  • 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 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