Exploring Gene Ontology Annotations with OWL

Ontologies such as the Gene Ontology (GO) and their use in annotations make cross species comparisons of genes possible, along with a wide range of other activities. Tools, such as AmiGO, allow exploration of genes based on their GO annotations. This human driven exploration and querying of GO is obviously useful, but by taking advantage of the ontological representation we can use these annotations to create a rich polyhierarchy of gene products for enhanced querying. This also opens up possibilities for exploring GO annotations (GOA) for redundancies and defects in annotations. To do this we have created a set of OWL classes for mouse genes and their GOA. Each gene is represented as a class, with appropriate relationships to the GO aspects with which it has been annotated. We then use defined classes to query these gene product classes and to build a complex hierarchy. This standard use of OWL affords a rich interaction with GO annotations to give a fine partitioning of the gene products in the ontology.