This work addresses ontology design problems by treating ontologies as theories and by defining a set of operations that map ontologies into ontologies, including their constraints. The work first summarizes the base knowledge needed to define the class of ontologies used and proposes four operations to manipulate them. It then shows how the operations work and how they may help design new ontologies. The core of this work is describing the implementation of the operations over a Protégé plug-in, detailing the architecture and including case-use examples.