Phenosite: A Web Database Integrating the Mouse Phenotyping Platform and the Experimental Procedures in Mice

Abstract

Recently, a number of collaborative large-scale mouse mutagenesis programs have been launched. These programs aim for a better understanding of the roles of all individual coding genes and the biological systems in which these genes participate. In international efforts to share phenotypic data among facilities/institutes, it is desirable to integrate information obtained from different phenotypic platforms reliably. Since the definitions of specific phenotypes often depend on a tacit understanding of concepts that tends to vary among different facilities, it is necessary to define phenotypes based on the explicit evidence of assay results. We have developed a website termed PhenoSITE (Phenome Semantics Information with Terminology of Experiments: http://www.gsc.riken.jp/Mouse/), in which we are trying to integrate phenotype-related information using an experimental-evidence-based approach. The site's features include (1) a baseline database for our phenotyping platform; (2) an ontology associating international phenotypic definitions with experimental terminologies used in our phenotyping platform; (3) a database for standardized operation procedures of the phenotyping platform; and (4) a database for mouse mutants using data produced from the large-scale mutagenesis program at RIKEN GSC. We have developed two types of integrated viewers to enhance the accessibility to mutant resource information. One viewer depicts a matrix view of the ontology-based classification and chromosomal location of each gene; the other depicts ontology-mediated integration of experimental protocols, baseline data, and mutant information. These approaches rely entirely upon experiment-based evidence, ensuring the reliability of the integrated data from different phenotyping platforms.

ENU Mutagenesis Screening for Dominant Behavioral Mutations Based on Normal Control Data Obtained in Home-Cage Activity, Open-Field, and Passive Avoidance Tests

“…Table 7 indicates the behavioral phenotypes of the mutant lines identified in this study. Four mutants exhibiting hyperactivity in the OF test and one mutant exhibiting hyperactivity in the OF test and PA deficit were the same animals identified by Masuya et al [15] as mutants with hyper-locomotor activity in the Modified-SHIRPA method. We identified mutants exhibiting hyperactivity in the HA or OF tests, hypoactivity in the OF test, high value of max/total in the OF test, and PA deficits.…”

“…DBF 1 mice showed significantly higher values than D2 for activity (0-5 min) of both sexes, total activity, and activity (0-10 min) of females. DBF 1 and D2 mice showed no significant differences for center % of both sexes, for activity (0-5 min) of both sexes, for activity (0-10) of males, and for activity (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20) of both sexes. In summary, B6 mice were the most active, and DBF 1 mice showed values higher or similar to D2 in most of the activity parameters of both sexes, although male D2 mice exhibited a significantly higher value than DBF 1 for max for 1 min, and showed a significantly higher value than B6 or DBF 1 for max/total.…”

“…Among the 12 mutant lines detected by the HA and OF tests, 11 exhibited hyperactivity and only one exhibited hypoactivity. (a) These mice were identified as mutants with hyper locomotor activity by the Modified-SHIRPA method in a previous study [15].…”

“…The raw behavioral data of the normal control animals obtained in this study is accessible as comma delimited text files at Phenosite (http://www.brc.riken.jp/ lab/gsc/mouse/), a web database integrating the mouse phenotyping platform and experimental procedures in mice [15].…”

Introduction to the Japan Mouse Clinic at the RIKEN BioResource Center

“…The EMPReSS slim SOPs are annotated using high-level mouse phenotype ontology terms to give a general description of the purpose of the procedure and provide a global summary of all parameters within the SOPs [3]. We plan to frequently exchange information regarding standard operating procedures of mouse phenotyping with EUMODIC and other large-scale related projects [15].…”