The advent of genome science promotes world-wide large-scale mouse mutagenesis projects. In parallel, development of comprehensive and standardized phenotyping platforms (mouse clinics) for evaluations of various biological traits such as morphology, sensory, behavior, pathology and so on, are underway as well. These projects will provide advanced mutant resources associated with "high-quality" functional information. This represents a new challenge to bioinformatics, integration, standardization and sharing of phenotype information broadly and deeply. In PhenoSITE, we propose several technologies to contribute advanced integration of mouse phenotype related information, including databases and ontologies.