Defining ontologies. Ontologies represent a specification of a domain of knowledge expressed in the structure of mathematical graphs (a tree being a special form of a graph). Connecting lines represent the relationship between the nodes, specifically IS-A relationships. Known protein functions are assigned to nodes (represented by circles) within the ontology graph. A child node always inherits the properties of all parent nodes, such that a complete description of the biochemical function of a protein involves retracing the path from the leaf to the root of the tree.