Technology and Development Unit for Knowledge Base of Mouse Phenotype

Technology and Development Unit for Knowledge Base of Mouse Phenotype aims the extension of accesses to bioresources by the informational technologies to analyze and represent biological properties which bioresources have.
Each bioresource reveals unique biological characteristics or properties, which convey essential information for researches, developments and innovations using bioresources. The integration, analysis and visualization of the connections between these various biological properties and utilities in human social activities (e.g. researches in biological sciences, medical treatment, drug discoveries, health caring and environmental issues) reveal a new challenge in the bioinformatics.
We address technological development of the integration, analysis, representation and dissemination of biological property and measurement data of bioresources using technologies of ontology, semantic web, statistical analyses. We also work for issues of the standardization of biological information in the cyber space by the international corroborations such as the participation of the International Mouse Phenotyping Consortium.

Research Subjects

• Development of data integration technologies with ontologies.
• Development of integrated database of biological properties of bio-resources.
• Development of databases for automatic suggestion of phenotype-disease association.
• Development of statistical methodology and workflow for comprehensive multi-paremeter phenotype data.

Publications

1. Masuya H.:
   "Roles and applications of biomedical ontologies in Experimental Animal Science"
   Experimental Animals, 61(4):365-373 (2012)
2. Furuichi T, Masuya H, Murakami T, Nishida K, Nishimura G, Suzuki T, Imaizumi K, Kudo T, Ohkawa K, Wakana S, Ikegawa S.:
   "ENU-induced missense mutation in the C-propeptide coding region of Col2a1 creates a mouse model of platyspondylic lethal skeletal dysplasia, Torrance type."
   Mamm Genome. 2011 22: 318-28. (2011)
3. Masuya H., Makita Y., Kobayashi N., Nishikata K., Yoshida Y., Mochizuki Y., Doi K., Takatsuki T., Waki K., Tanaka N., Ishii M., Matsushima A., Takahashi S., Hijikata A., Kozaki K., Furuichi T., Kawaji H., Wakana S., Nakamura Y., Yoshiki A., Murata T., Fukami-Kobayashi K., Mohan S., Ohara O., Hayashizaki Y., Mizoguchi R., Obata Y., Toyoda T.:
   "The RIKEN integrated database of mammals"
   Nucleic Acids Research, 39: D861-D870 (2010)
4. Furuse T., Wada Y., Hattori K., Yamada I., Kushida T., Shibukawa Y., Masuya H., Kaneda H., Miura I., Seno N., Kanda T., Hirose R., Toki S., Nakanishi K., Kobayashi K., Sezutsu H., Gondo Y., Noda T., Yuasa S., Wakana S.:
   "Phenotypic characterization of a new Grin1 mutant mouse generated by ENU mutagenesis"
   European Journal of Neuroscience, 31:1281-1291 (2010)
5. Tanaka N., Waki K., Kaneda H., Suzuki T., Yamada I., Furuse T., Kobayashi K., Motegi H., Toki H., Inoue M., Minowa O., Noda T., Takao K., Miyakawa T., Takahashi A.,Koide T., Wakana S., Masuya H.:
   "SDOP-DB: A comparative standardised-protocol database for mouse phenotypic analyses"
   Bioinformatics, 26(8):1133-1134 (2010)
6. Schofield P.N. et al.:
   "Post-publication sharing of data and tools"
   Nature, 461(7261):171-173 (2009)
7. Yoshida Y., Makita Y., Hieda N., Asano(Matsusita) S., Matsushima A., Ishii M., Mochizuki Y., Masuya H., Wakana S., Kobayashi N., Toyoda T.:
   "PosMed(Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional"
   Nucleic Acids Research, 37(2): W147-W152 (2009)
8. Wakana S., Suzuki T., Furuse T., Kobayashi K., Miura I., Kaneda H., Yamada I., Motegi H., Toki H., Inoue M., Minowa O., Noda T., Waki K., Tanaka N., Masuya H. Obata Y.:
   "Introduction to the Japan Mouse Clinic at the RIKEN BioResource Center"
   Experimental Animals, 58(5):443-450 (2009)
9. Kaminuma E., Masuya H., Miura I., Motegi H., Takahashi K., Nakazawa M., Matsui M., Gondo Y., Noda T., Shiroishi T., Wakana S., Toyoda T.:
   "Objective evaluation measures of marker selection in large-scale SNP genotyping"
   Journal of Bioinformatics and Computational Biology, 6: 905-917 (2008)
10. Taylor C. F. et al.:
    "Promoting Coherent Minimum Reporting Requirements for Biological and Biomedical Investigations: The MIBBI Project"
    Nature Biotechnology, 26: 889-896 (2008)