COLLABORATIVE DEVELOPMENT OF LARGE - SCALE BIOMEDICAL ONTOLOGIES - Collaborative Computational Technologies for Biomedical Research - page 198

identifi er, each ontology also has an associated virtual identifi er that points to
the latest version of the ontology. The virtual identifi er allows other users and
applications to access the latest version of an ontology without needing to be
aware of previous versions.
BioPortal can also compute the structural difference (diffs) between two
versions of an ontology, and users can download the diff as an RDF fi le. The
structural diffs provide crucial information for the users of the ontology who
need to ensure that other ontologies or the software on which they rely for
their applications evolve in concert with the primary changes.

12.6 DISCUSSION AND FUTURE WORK

We have described Collaborative Prot é g é , WebProt é g é , and BioPortal — three
tools that provide essential support for the collaborative development of
large-scale biomedical ontologies. We have shown how Collaborative Protégé
and WebProtégé help users in the collaborative authoring of ontologies, while
BioPortal allows the publishing of ontologies and the gathering of feedback
from the larger user community.
We envision that these tools will work increasingly seamlessly in the near
future. For example, we are working to make it possible to upload an ontology
directly from WebProtégé into BioPortal. In a similar way, a user should be
able to start a WebProtégé editing session for an ontology in BioPortal with
a simple click. We envision a model in which BioPortal will host not only the
published versions of an ontology to which users may add comments and
proposals but also a working version that is not made public and to which the
ontology authors may apply the community's proposed changes using
WebProt é g é .
We are working to offer better support for managing the workfl ow required
for proposals for ontology changes. Any registered user of BioPortal currently
can create structured proposals for ontology changes. Ontology authors with
the appropriate privileges (e.g., a curator) should be able to open an ontology
in WebProtégé and to review the change proposals submitted through
BioPortal. For appropriate proposals, curators should be able to apply the
changes automatically. In the next step, the curator would set the status of the
proposal to Implemented or Rejected, which should be refl ected in the pro-
posal status when viewed in BioPortal. Once all the changes have been
addressed, the updated ontology should be published as a new version in
BioPortal. To support this workfl ow, we need to implement several new fea-
tures. First, we need to be able to browse the BioPortal proposals into
WebProtégé. Second, curators need to be able to set the status of a proposal
once a decision has been taken. For example, a new term proposal contains
fi elds such as identifi er, defi nition, synonym, and preferred name. We need to
implement automatic importers for each of the common proposal types that
would read the fi elds from the proposal and create the appropriate classes and