2
Recent technological advances have resulted in an onslaught of biological
information that is accessible online. In the postgenomic era, a major bottle-
neck is the coherent integration of all these public, online resources. Online
bioinformatics databases are especially difficult to integrate because they are
complex, highly heterogeneous, dispersed, and incessantly evolving. Scien-
tific discovery increasingly involves accessing multiple heterogeneous data
sources, integrating the results of complex queries, and applying further
analysis and visualization applications in order to acquire new knowledge.
However, online data are often described only in human-readable formats
(most commonly free text) that are difficult for computers to analyze due
to the lack of standardized structures. An ontology is a computer-readable
system for encoding knowledge which specifies not only the concepts in a
given field but also the relationships among those concepts. Ontologies pro-
vide insight into the nature of information produced by that field and are
an essential ingredient in any attempts to arrive at a shared understanding
of concepts in a field. Thus the development of ontologies for biological
information and the sharing of those ontologies within the bioinformatics
community are pivotal for biologists who rely heavily on online data.
The first part of the book introduces the basic concepts and semantics of
ontologies. It begins with the fundamental notions of hierarchies and rela-
tionships. The web is becoming the primary mechanism for the exchange
of information and data. Accordingly, the emphasis in this book is on the
eXtensible Markup Language (XML) and XML-based languages. The next
three chapters explain the semantics of XML, rules and the newly proposed
Semantic Web, a layer above the World Wide Web that adds meaning to hy-
pertext links. Finally, chapter 5 provides a survey of ontologies and data-
bases in Bioinformatics. This chapter covers the major bio-ontologies used
in computational biology, including the Gene Ontology and open biological
ontologies.
