Biomedical Engineering Reference
In-Depth Information
BioPortal is an open library of biomedical ontologies [20] created by the
NCBO. BioPortal adopts the philosophy of Web 2.0 applications to bring
structure and order to the collection and dissemination of biomedical ontolo-
gies. The system enables users to provide and discuss a wide array of knowl-
edge components, from submitting the ontologies themselves, to commenting
on and discussing classes in the ontologies uploaded by other users, to review-
ing ontologies in the context of their own ontology-based projects, to creating
mappings between overlapping ontologies and discussing and critiquing the
mappings.
BioPortal hosts more than 200 biomedical ontologies in OWL, Open
Biomedical Ontologies (OBO), RDFS, and Protégé frame formats and con-
tains more than 2.5 million ontology terms and over 4 million term-to-term
mappings. All the information available in BioPortal is accessible via RESTful
Web services, which encourages the mashing up of biomedical applications in
a straightforward way.
BioPortal and WebProtégé provide complementary services to support col-
laborative ontology development and dissemination: WebProtégé supports the
collaborative editing process, whereas BioPortal provides repository services
that are crucial in later stages of the collaborative process, such as reviewing,
versioning, creating mappings, and determining structural differences.
Once an author publishes an ontology in BioPortal, the larger community
is able to browse and search for terms in the ontology, to review its content,
and to add comments and proposals to classes in the ontology. Besides adding
notes and proposals through the BioPortal Web interface, the system also sup-
ports the posting of notes via Web services. In this way, other applications can
access the ontologies in BioPortal and can take advantage of all the services
provided by the system programmatically.
BioPortal also supports
peer review
of ontologies. This is a very important
feature that aids users who are looking for ontologies that they can reuse in
their own projects and who want to know what other users think about alter-
native resources and problems they may have encountered. A key piece of
information is the list of other projects that have used each ontology in
BioPortal, and the suitability of the ontology for the tasks of each project. Thus,
in addition to submitting ontologies to BioPortal, users may also submit
descriptions of their ontology-based projects and link those descriptions to
BioPortal ontologies. Registered users can provide comments on BioPortal
ontologies along several different dimensions, such as degree of formality,
documentation and support, usability, domain coverage, and quality of content.
BioPortal also supports
versioning
of ontologies. The development of large-
scale biomedical ontologies usually takes place in iterative steps with several
versions of the ontologies being published during the process. Users may store
multiple versions of an ontology in BioPortal and can access their content
through both the user interface and the Web services. Each version of the
ontology has an associated
version identifi er
that can be used in the
Web Services for retrieving the content of the ontology. Besides the version
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