1.5 The Meaning of a Hierarchy 21
Figure 1.11 Chemical hierarchy (EcoCyc 2003).top-down or bottom-up technique, it is always presumed that one can define
every class using shared common characteristics of the members.
There are many algorithms for constructing hierarchical classifications, es-
pecially taxonomies, based on attributes of entities (Jain and Dubes 1988).
Such algorithms are usually referred to asdata-clusteringalgorithms. An ex-
ample of a hierarchy constructed by a data-clustering algorithm is shown in
figure 5.3. The entities being clustered in this case are a set of genes, and the
hierarchy appears on the left side of the figure. Such automated classifica-
tions have become so routine and common that many tools construct them
by default.
The notions of taxonomy and hierarchy have been an accepted part of
Western civilization since the time of Aristotle. They have been a part of
this culture for so long that they have the status of being completely obvious
and natural. Aristotle already emphasized that classifications must be “cor-
rect,” as if they had the status of a law of nature rather than being a means for
understanding the world. This attitude toward classification was not ques-