6

1

Introduction

genes, proteins, and metabolites)—now called interactomics—and the inference of

regulatory networks from such data has also become a significant part of bioinfor-

matics.

1.3

An Ontology of Bioinformatics

The organization of concepts into a concept system is often called an ontology of

the field. The concept is represented by designations (the set of which constitutes

the terminology of the field) and described in definitions. Figure 1.1 shows such a

system for bioinformatics. Another view is shown in Fig. 1.2.

Problem. Give definitions of the concept designations placed in Fig. 1.1. Hint.

Objects, such as “genome”, are perceived or conceived. Their properties, which may

be common to a set of objects, are abstracted into essential or delimiting characteris-

tics (feature specifications), typically falling into different categories, and which are

combined as a set to form a concept.

Problem. Appraise Fig. 1.1 and discuss whether the organization of the designated

concepts is appropriate, and whether other concepts should be included.

Problem. Discuss Fig. 1.2 in terms of structures and functions.

Fig. 1.1 A (partial) ontology for bioinformatics