The most successful application of ontology concept in systems biology is the gene ontology, which is a set of standard terms – words and phrases – used for indexing and describing the function of the gene. Specifically, all the defining terms are organized by a structured vocabulary, which is called ontology structure.
The structure of GO can be described in terms of a graph, where each GO term is a node, and the relationships among the terms are arcs between the nodes. The relationships used in GO are directed – for example, a mitochondrion is an organelle, but an organelle is not a mitochondrion – and the graph is acyclic, meaning that cycles are not allowed in the graph. The ontologies resemble a hierarchy, as child terms are more specialized and parent terms are less specialized, but unlike a hierarchy, a term may have more than one parent term. For example, the biological process term hexose biosynthetic process has two parents, hexose metabolic...