The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays, next-generation sequencing for gene expression and proteomics. However, for researchers to derive value from these functional genomics datasets, they must be able to model this data in biologically relevant ways, to do so requires that the equine genome be more fully annotated. There are two interrelated types of genomic annotation: structural and functional. Structural annotation is delineating and demarcating the genomic elements (such as genes, promoters, and regulatory elements). Functional annotation is assigning function to structural elements. The Gene Ontology (GO) is the de facto standard for functional annotation, and is routinely used as a basis for modelling and hypothesis testing, large functional genomics datasets.