WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.
WebProtégé is an open-source Web application for editing OWL 2 ontologies. It contains several features to aid collaboration, including support for the discussion of issues, change notification and revision-based change tracking. WebProtégé also features a simple user interface, which is geared towards editing the kinds of class descriptions and annotations that are prevalent throughout biomedical ontologies. Moreover, it is possible to configure the user interface using views that are optimized for editing Open Biomedical Ontology (OBO) class descriptions and metadata. Some of these views are shown in the Supplementary Material and can be seen in WebProtégé itself by configuring the project as an OBO project.


METHODS
WebProtégé is freely available for use on the Web at http://webprotege.stanford.edu. It is implemented in Java and JavaScript using the OWL API and the Google Web Toolkit. All major browsers are supported. For users who do not wish to host their ontologies on the Stanford servers, WebProtégé is available as a Web app that can be run locally using a Servlet container such as Tomcat. Binaries, source code and documentation are available under an open-source license at http://protegewiki.stanford.edu/wiki/WebProtege.
Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305, USA.
Matthew
M
Horridge
Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305, USA.
Tania
T
Tudorache
Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305, USA.
Csongor
C
Nuylas
Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305, USA.
Jennifer
J
Vendetti
Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305, USA.
Natalya F
NF
Noy
Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305, USA.
Mark A
MA
Musen
D064229:Biological Ontologies; D003299:Cooperative Behavior; D020407:Internet; D012984:Software