GOing from functional genomics to biological significance.

The chicken genome is sequenced and this, together with microarray and other functional genomics technologies, makes post-genomic research possible in the chicken. At this time, however, such research is hindered by a lack of genomic structural and functional annotations. Bio-ontologies have been developed for different annotation requirements, as well as to facilitate data sharing and computational analysis, but these are not yet optimally utilized in the chicken. Here we discuss genomic annotation and bio-ontologies. We focus specifically on the Gene Ontology (GO), chicken GO annotations and how these can facilitate functional genomics in the chicken. The GO is the most developed and widely used bio-ontology. It is the de facto standard for functional annotation. Despite its critical importance in analyzing microarray and other functional genomics data, relatively few chicken gene products have any GO annotation. When these are available, the average quality of chicken gene products annotations (defined using evidence code weight and annotation depth) is much less than in mouse. Moreover, tools allowing chicken researchers to easily and rapidly use the GO are either lacking or hard to use. To address all of these problems we developed ChickGO and AgBase. Chicken GO annotations are provided by complementary work at MSU-AgBase and EBI-GOA. The GO tools pipeline at AgBase uses GO to derive functional and biological significance from microarray and other functional genomics data. Not only will improved genomic annotation and tools to use these annotations benefit the chicken research community but they will also facilitate research in other avian species and comparative genomics.