Biomedical Engineering Reference
In-Depth Information
Protégé using different representation formalisms, ranging from frames to
RDF(S) and to OWL, and can store their ontologies in fi le or database back-
ends. Protégé is both robust and scalable and is being used in production
environments by many government and industrial groups. Prot é g é supports a
plugin architecture that allows other developers to implement their own
custom extensions that can be used either in the Protégé user interface or as
part of other applications that use Protégé services.
Protégé also offers a client-server mode, in which multiple users can
browse and edit a shared ontology at the same time. If a user makes a change
to an ontology, then other users will see that change right away. This immedi-
ate synchronization of changes minimizes the number of editing confl icts in
a collaborative setting, because each of the distributed users receive updates
from the other clients in a matter of seconds. The immediate updates make
editing confl icts (e.g., two users editing the same property value at the same
time) less likely. A different approach for synchronizing changes is found in
source-control repositories, such as SVN or CVS. In these settings, users check
out a copy of the shared ontology and perform changes in the local copy.
When the user is done making changes, he or she has to commit the local
changes back to the shared copy stored in the repository. In this setting, it is
much more likely that editing confl icts will occur, because other users may
already have changed the shared copy since the time that the user checked
out his or her own copy. The user has to solve the confl icting changes manu-
ally, and this is a very effort-intensive and error-prone task. Both synchroniza-
tion modes, the immediate mode available in Protégé and the check-out/
check-in approach used in SVN, are appropriate for different collaboration
scenarios. We have chosen to use the immediate synchronization mode
because it is preferred when distributed users may need to make changes
that may have ramifi cations that are dispersed within the edited content and
when the users cannot tolerate being locked out from making certain edits
for long periods of time.
Although enabling distributed users to browse and edit a shared copy
of an ontology brings a lot of advantages, there are still many features that
are needed to support real collaboration among ontology builders. Our group
has developed Collaborative Prot é g é ( http://protegewiki.stanford.edu/wiki/
Collaborative_Protege) as an extension of the client-server version of Protégé
to support collaboration as an integral part of the ontology development
process [12, 13]. Collaborative Protégé has features for adding comments and
notes and discussion threads to ontology classes, properties, and individuals.
All changes made by users are tracked and stored together with the related
provenance information. It is also possible to add different types of proposals
for changes to entities in the ontology and then later to ask users to vote on
these proposals. An access policy mechanism allows an administrator to set
different privileges for different user groups and hence to restrict access based
on particular accounts. A chat feature enables users who are connected at the
same time to a Protégé server to exchange text messages and to send refer-
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