Originally, ontology is the philosophical study of the nature of existence as well as the basic categories of being and their relations. Ontology deals with questions concerning what entities exist or can be said to exist and how such entities can be grouped, related within a hierarchy, and subdivided according to similarities and differences.
The most successful application of ontology concept in systems biology is the gene ontology, which is a controlled vocabulary, a set of standard terms – words and phrases – used for indexing and describing the function of gene or other biomolecules. Specifically, all the defining terms are organized by defining their relationships, as a structured vocabulary ( Ontology Structure). For example, if we know one gene involves in the biological process such as hexose biosynthetic process, we can use the GO term hexose biosynthetic process to annotate the function of this gene. At the same time, this GO term has...