282 12 Building Bioinformatics Ontologies
veloped is a high quality one. An ontology is a precise formulation of the
concepts that form the basis for communication. Accordingly, the main parts
of an ontology are the concepts and the relationships between them. The next
two sections consider each of these in turn. Section 12.6 discusses the con-
cept hierarchy and explains how to ensure that it is properly designed, and
the design of the relationships is discussed in section 12.7. Once an ontology
has been designed, it should then be validated to ensure that it satisfies its
purpose. If flaws are discovered during validation, then the ontology must
be modified. Ontologies are also modified after they have been published,
as the field evolves. Techniques for ontology validation and modification are
presented in section 12.8. Finally, the chapter ends with some exercises.12.1 Purpose of Ontology Development
Before embarking on a project to develop an ontology it is important to have
a firm understanding of the purpose of your ontology and the community
that it is intended to serve. It is commonplace for ontology development
projects to have no explicitly stated purpose beyond the acquisition of the
domain knowledge. The assumption seems to be that the ontology should
not be dependent on any particular purpose. This situation is unfortunate
because it has been known at least since the middle of the nineteenth cen-
tury that the design of an ontology depends on its purpose and viewpoint
(Whewell 1847). This important fact has been forgotten and painfully redis-
covered frequently since then. The purpose of the ontology should include
the following:- Whythe ontology is being developed. One of the most common reasons
for building a formal ontology is to make shared information more usable.
However, there are other reasons why one would build a formal ontology.
It can be very useful for managing information used by small groups of
people or even by a single individual. This book, for example, was writ-
ten in XML, using an ontology that was built specifically for the needs of
this project. Yet another reason why one might build a formal ontology
is to analyze a domain, making explicit the assumptions being made by
the community. In this case, the very act of formalizing the domain can
be valuable irrespective of any other uses of the ontology. Finally, ontolo-
gies are often needed as part of a larger project, as in the example at the
beginning of the chapter.