Method for automated comparison of PANTHER and FlyBase assignments. The PANTHER/X ontology was designed as a more lightweight version of GO, and therefore the PANTHER–GO associations will not generally have the same degree of specificity as FlyBase–GO associations. To compare the FlyBase and PANTHER associations directly, it was often necessary to trace up the GO classification to match a given FlyBase association to a PANTHER association. For example, PANTHER may associate a protein with the term tyrosine kinase receptor (yellow), which corresponds to the GO category transmembrane receptor protein tyrosine kinase (GO:0004714; yellow area designates the term and its children). If this same protein is associated by FlyBase with one or more of the GO categories in yellow, we consider PANTHER and FlyBase assignments as a “match.” However, if the protein is associated by FlyBase with transmembrane receptor protein serine/threonine kinase (blue area, a sibling but not a child), we consider the PANTHER and FlyBase associations as “unmatched.”
