This thesis describes the implementation of an interface for querying established correspondences between anatomical structures across species. I was the main developer of this query engine, called the Comparative Anatomy Information System. My work involved developing methods to query the knowledge base, perform the specified comparison, display the anatomical hierarchies and results, and implement features to make the application user-friendly. The comparisons are based on the Structural Difference Method (SDM) for finding similarities and differences, developed in previous work. Since the CAIS knowledge base is sparsely populated, it has thus far been difficult to conduct extensive user testing, but I include two usage scenarios proposed by one of my mentors that outline some proposed uses of the application. These scenarios reflect the need for a system like CAIS that communicates anatomical correspondences to researchers who work on animal modeling of disease with a background other than traditional comparative anatomy.