Biomedical Engineering Reference
In-Depth Information
(see Section 12.2.1). The Metaproject ontology is used to confi gure the ontol-
ogy repository and the user access policies (see Section 12.2.4). The Workfl ow
ontology (not discussed in this chapter) is used to confi gure the steps for a
collaboration workfl ow [17, 18].
We developed a set of Java application programming interfaces (APIs) that
provide independent pieces of functionality. Most of the Java APIs are used
for accessing and modifying the information stored in one of the meta-
ontologies used in the collaboration process. Several of these Java APIs have
been generated automatically from the meta-ontology using a Java code gen-
erator. In this sense, we can say that the collaboration framework is an
ontology-driven architecture. Some of the main Java APIs are shown in Figure
12.9. The Change tracking API and the Notes API retrieve the information
stored as instances in the ChAO. The APIs provide convenient methods for
the developers and hide the fact that the change and notes information is
backed by an ontology. For example, a developer may call a method cls.
getChanges() to retrieve all changes associated with a class; it is not important
to know that the change information is stored as instances of the ChAO. The
Ontology access API provides services to access the ontology content stored
in the Protégé ontology repository. The Policy Manager library has services
for accessing and modifying the user policies in a programmatic way.
The Protégé ontology repository stores all the ontologies that are available
to the collaboration framework and hence also to the Collaborative Protégé
and WebProtégé clients. Besides storing the domain ontologies, such as ICD-
11 and the NCI Thesaurus, the repository also stores the associated ChAO
instances for each of the domain ontologies. This association is stored in the
Metaproject ontology (see Section 12.2.4). The collaboration framework is an
essential part of the Protégé server (see Section 12.2). Because all clients
(Collaborative Prot é g é , WebProt é g é , and other applications) connect to a
common collaboration framework, their users will see one another's changes
to an ontology as they happen. For instance, if a user adds a class in a
Collaborative Protégé-rich client, other users connected to the same server
with WebProtégé will see the change in their clients right away. This feature
allows users to edit a shared ontology in a collaborative environment with the
tool of their choice.
12.5
PUBLISHING ONTOLOGIES WITH BIOPORTAL
Ontology authors and domain experts use Collaborative Protégé and
WebProtégé to edit a shared ontology in a collaborative setting. It is a common
scenario that once the ontology has reached a mature state, it will be published
on the Web to allow the authors to get feedback from a broader user com-
munity [19, 20]. We present in this section a solution for publishing ontologies
on the Web using BioPortal (http://bioportal.bioontology.org), and we describe
how BioPortal services support collaboration and reuse.
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