Biomedical Engineering Reference
In-Depth Information
communicable diseases. Each TAG will support several international working
groups and an additional corps of fi eld testers who will use online tools to
evaluate the evolving ontology and to generate proposals for revisions and
enhancements. Third, ICD-11 will include direct linkages to terms in other
standardized terminologies, such as SNOMED-CT. The WHO plans to open
the development of ICD-11 to the broader community in a social process
similar to that supported by Wikipedia.
The NCI Thesaurus is a biomedical reference ontology that covers areas of
basic cancer biology, translational science, and clinical oncology developed at
the NCI Center for Bioinformatics and Information Technology [9, 10]. The
content of the NCI Thesaurus is contributed by internal editors who work
separately. Every month or so, a curator goes over the editors' proposed
changes and approves or rejects them. Once the curation process is completed,
a new version of the NCI Thesaurus is published, and the entire development
process starts again.
Each of these projects relies on both a well-defi ned social process as well
as a set of specialized interactive tools to support collaborative ontology
engineering—each in a very different way. At the U.S. National Center for
Biomedical Ontology (NCBO), we have been working to engineer both pro-
cesses and tools to enable alternative forms of collaborative ontology
engineering.
In this chapter, we will present methods and tools to support the community-
driven authoring of large biomedical ontologies. In Section 12.2, we present
Collaborative Protégé—a tool that supports collaboration as an integral part
of the ontology editing process, and that has features for tracking provenance
and changes, as well as discussions in the context of the ontology. In Section
12.3 , we describe WebProt é g é — a Web - based client for Collaborative Prot é g é
that we built as a highly customizable platform which can be adapted as a
knowledge acquisition tool for domain experts. Section 12.4 presents the archi-
tecture of the collaboration framework that both Collaborative Protégé and
WebProtégé are using. In Section 12.5, we give an overview of BioPortal—a
repository of biomedical terminologies and ontologies on the Web. BioPortal
provides Web services for publishing, storing, and retrieving ontologies from
the repository, supports a proposal and discussion mechanism, and has facili-
ties for versioning and mapping between ontologies. Work on Collaborative
Protégé and WebProtégé is becoming tightly linked, as the NCBO explores
coordinated methods of community-based ontology authoring, dissemination,
and peer review. We discuss our experience with these technologies and talk
about future plans in Section 12.6.
12.2
COLLABORATIVE PROT É G É
Our laboratory has developed Protégé—probably the most widely used open-
source ontology and knowledge base editor [11]. At the time of this writing,
Protégé has more than 150,000 registered users. Users can build ontologies in
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