GOODIES is the Gene Ontology (GO) based data mining program. The algorithm was announced in the well-known journal ‘Bioinformatics’. It efficiently derives the common biological meanings between biological individuals such as large amount of genes or proteins by using the systematic structure of GO and the annotation of GO. For instance, if the one group that consists of genes is given, the GOODIES considers the various biological functions of each genes and extracts the most appropriate biological meaning that represents the group partially or as a whole. GOODIES is able to perform the biological analysis of DNA chip data group analysis, prediction of combined gene’s function and functional grouping of the large amount of biological individuals.