ABSTRACT
Formal ontology deals with the interconnections of things, with objects and properties, parts and wholes, relations and collectives [234]. Computational ontological analysis depends implicitly or explicitly on the way the ontologies being used have implemented formal ontological principles. In this chapter we discuss two upper level ontologies that have been by far the most influential in the field of bio-ontologies, and then demonstrate how they are critical to understanding the structure of GO and of GO annotations.
