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Automated, Quantitative Cognitive/Behavioral Screening of Mice: For Genetics, Pharmacology, Animal Cognition and Undergraduate Instruction
Published on: February 26, 2014
Phenosite: a web database integrating the mouse phenotyping platform and the experimental procedures in mice
Hiroshi Masuya1, Sumi Yoshikawa, Naohiko Heida
1Mouse Functional Genomics Research Group, RIKEN GSC, Tsukuba, Ibaraki, Japan. hmasuya@gsc.riken.jp
Journal of Bioinformatics and Computational Biology
|January 4, 2008
Summary
Large-scale mouse mutagenesis programs generate valuable data. PhenoSITE integrates this phenotypic data using an experimental-evidence-based approach for reliable, accessible mouse mutant information.
Area of Science:
- Genetics and Genomics
- Bioinformatics
- Developmental Biology
Background:
- Collaborative large-scale mouse mutagenesis programs aim to elucidate gene functions and biological systems.
- Integrating phenotypic data from diverse international facilities presents challenges due to varying terminologies and tacit understandings.
- A standardized, evidence-based approach is crucial for reliable data integration.
Purpose of the Study:
- To develop a robust system for integrating phenotypic data from large-scale mouse mutagenesis programs.
- To establish an experimental-evidence-based approach for defining and sharing phenotype information.
- To enhance the accessibility and reliability of mouse mutant resource information.
Main Methods:
- Development of PhenoSITE, a website integrating phenotype-related information using experimental evidence.
- Creation of a baseline database for the phenotyping platform.
- Implementation of an ontology to associate international phenotypic definitions with experimental terminologies.
- Establishment of databases for standardized operation procedures and mouse mutants.
- Development of integrated viewers for ontology-based classification, chromosomal location, and data integration.
Main Results:
- PhenoSITE successfully integrates phenotype information using an experimental-evidence-based approach.
- The developed ontology links international phenotypic definitions with platform-specific experimental terminologies.
- Databases for standardized protocols and mouse mutants enhance data management.
- Integrated viewers provide enhanced accessibility to mutant resource information through matrix and ontology-mediated views.
Conclusions:
- The experimental-evidence-based approach ensures the reliability of integrated phenotypic data from different platforms.
- PhenoSITE facilitates the sharing and utilization of valuable mouse mutant resources.
- This initiative supports a deeper understanding of gene function and biological systems through integrated data analysis.
