Biomedical Engineering Reference
In-Depth Information
implementation of hospital information systems to the organization of experi-
mental data for bioinformatics research, developers now identify the key issue
to be the manner in which salient concepts are labeled and defi ned and ulti-
mately used computationally. In the past decade, the notion of ontology has
become a well-recognized substrate for research in informatics and computer
science. Ontologies are formal descriptions of the entities that exist in an
application area, the properties of those entities, and the relationships among
those entities that can be referenced by both humans and computers.
In biology and medicine, ontologies have become central to the construc-
tion of intelligent decision support systems, simulation systems, information
retrieval systems, and natural language systems [1, 2]. The World Wide Web
Consortium (W3C) has developed the resource description framework (RDF)
[3] and Web Ontology Language (OWL) [4], standard languages for represent-
ing ontologies on the Semantic Web. The introduction of these W3C standards
has become an impetus to an even wider use of ontologies and knowledge-
based resources. W3C has an extremely active Semantic Web for Health Care
and Life Sciences Interest Group [5]. A fast growing collection of well-known
biomedical ontologies and terminologies [e.g., BioPAX, the National Cancer
Institute (NCI) Thesaurus, the Ontology of Biomedical Investigations] now
embraces W3C's OWL standard.
With this adoption of ontologies by the broad biomedical community,
however, comes a new challenge: Ontologies and terminologies can become
so large, diverse, and specialized that it is often impossible for any single cen-
tralized group to develop them effectively. Indeed, several prominent ontology
engineering projects are promoting community participation as a key element
in their development work. Below, we describe briefl y three of the most visible
collaborative ontology projects now ongoing: The Gene Ontology (GO), The
11th revision of the International Classifi cation of Diseases (ICD), and the NCI
Thesaurus . GO is one of the more prominent examples of an ontology that is
a product of a collaborative process [6]. GO provides terminology for consis-
tent description of gene products in different model-organism databases in
terms of their associated biological processes, cellular components, and molec-
ular functions in a species-independent manner. Members of the GO com-
munity constantly suggest new terms for this ontology. Three full-time curators
examine the suggestions and incorporate them into GO as appropriate on a
continual basis.
The ICD (http://www.who.int/classifi cations/icd/en/) is a public global stan-
dard to organize and classify information about diseases and related health
problems. The World Health Organization (WHO) plans three major shifts for
the upcoming 11th revision of ICD (ICD-11) [7, 8]: First, the ICD will repre-
sent clinical knowledge explicitly in machine-processable form using OWL.
The WHO plans to use an ontological approach, formalizing the defi nitions of
each clinical entity and organizing the terms in a semantically meaningful way.
Second, the WHO will open the process of ICD revision to a wide community
of experts. Topic advisory groups (TAGs) will serve as planning and coordinat-
ing bodies for specifi c areas of medicine, such as oncology, mental health, and
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