Bio-medical Ontologies Maintenance and Change Management

160 A. Shaban-Nejad and V. Haarslev
Fig. 5 demonstrates a portion of the FungalWeb application in categorical representation.
Fig. 5. A category model of portion of the FungalWeb application
Most common operations during ontology evolution, such as adding or deleting
a class/property/relationship, combining two classes into one, or adding a generalization/association
relationship, can be represented using category theory (Shaban-Nejad
and Haarslev 2007(b)). Based on our application, we designed our class
diagrams following Whitmire (1997) to track different states of our ontological
structure (Fig. 6). The Op i arrows in this figure represent the operations, which
cause an ontological state to change to another state. For instance, in Fig. 11,
the operation Op 1 causes the transition of an object from state St 1 to state St 2 . The
Op r (reverse operation) returns the system to its initial state (St 1 ). For more details
see (Shaban-Nejad and Haarslev 2007, 2008)
Fig. 6. A class diagram to track different operations and states in an evolving structure
Summary
Biology is known as a field with continuous evolution. As the knowledge about
biology rapidly grows and new methods become available, one can anticipate a