Biomedical ontologies provide a representational system to support the integration and retrieval of biological knowledge. The Gene Ontology (GO) is widely used to annotate molecular attributes of genes and provides a common paradigm for comparative functional analysis research. One way to expand the view of the function of any one gene product is to compare annotations of genes that share close evolutionary relationships and are likely to function in similar ways, such as orthologous genes. We are exploring the power of the GO and orthology sets to provide a comprehensive view of annotations coordinated across species by presenting annotations visualized within the ontology relationship structure. This work describes the application of our ontology visualization approach to a set of model organism genes that are orthologous to human disease genes.