5 Survey of Ontologies in Bioinformatics
There are a large number of biomedical ontologies and databases that are cur-
rently available, and more continue to be developed. There is even a site that
tracks the publicly available sources. Ontologies have emerged because of
the need for a common language to develop effective human and computer
communication across scattered, personal sources of data and knowledge.
In this chapter, we provide a survey of ontologies and databases used in
the bioinformatics community. In the first section we focus on human com-
munication. The ontologies in this section are concerned with medical and
biological terminology and with ontologies for organizing other ontologies.
The rest of the chapter shifts the focus to computer communication. In sec-
tion 5.2 we survey the main XML-based ontologies for bioinformatics. The
remaining sections consider some of the many databases that have been de-
veloped for biomedical purposes. Each database has its own structure and
therefore can be regarded as defining an ontology. However, the focus is on
the data contained in the database rather than on the language used for rep-
resenting the data. These databases differ markedly from one another with
respect to how the data are specified and whether they are compatible with
the ontologies in the first two sections. Many of the databases are available
in several formats. Only databases that can be downloaded were included in
the survey.
5.1 Bio-Ontologies
We have seen that ontologies are a versatile mechanism for understanding
concepts and relationships. In this section the concern is with the human
communication of biomedical concepts as well as with understanding what
knowledge is available. We first consider ontologies dealing with terminol-
