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| Project name | Standardization project of genotype and phenotype database format |
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| Area | Biotechnology・Medical technology |
| Purpose | The purpose of this project is to develop integrated use for the genotype and phenotype data base with a big meaning aiming at the achievement of the individual healthcare and the drug administering optimization, etc. by Japan initiation. By that the study results of Japan are promptly sent to the world. In addition, study results all over the world are promptly obtained. Japan Biological Information Consortium (JBIC) has already developed Polymorphism Markup Language (PML) as the OMG standard of genotype data description format under the bio-data standardization project of the Ministry of Economy, Trade and Industry. And also JBIC has developed the request for proposal of the standard description format of genotype-phenotype database. We develop the standard description format of genotype and phenotype database under PML and the request for proposal. We apply it to the Database constructed by the NEDO project, Genomic polymorphism analysis and evaluate the efficacy of it. |
| Introduction | We developed the DNA Variation and Phenotype Data model as the standard data description format of genotype and phenotype database. It was approved as the OMG standard. Moreover we published the PML which is the radical model of DNA Variation and Phenotype Data model at the International Conference. |
| Keyword | DNA Variation and Phenotype Database | standardization |
| Started fiscal year | 2005-2008 |
| Project head | Hideaki Sugawara |
| Institute of the head | National Institute of Genetics (NIG) |
| Budget (million yen) | 561(H17), 434(H18), 265(H19), 342(H20) |
| Representative Institute of the commission | New Energy and Industrial Technology Development Organization (NEDO) |
| Companies | Bergen Center for Computational Science (BCCS), Norway | Cold Spring Harbor Laboratory (CSHL), USA | European Bioinformatics Institute (EBI), UK | Helsinki University, Finland, F | National Center for Biotechnology Information (NCBI), USA | South African National Bioinformatics Institute(SANBI) | Stanford University | University College London | University of Leicester | Yale University | Institute of Genomic and Integrative Biology, India(IGIB) | International Rice Research Institute, Philippines | Japan Science and Technology Agency (JST), Japan | National Cancer Center Research Institute (NCCRI), Japan | National Institute of Genetics (NIG), Japan | Riken Genomic Science Center, Japan | Institute for Chemical Research, Kyoto University | School of Medicine and Faculty of Medicine, The University of Tokyo | Tokai University School of Medicine |
| Published papers (PubMed IDs) | Under investigation |
| Patent (Japan, overseas) | Under investigation |
Product (Database, Tool)
OpenPML
|
Summary | The study of correlations between genome variation and phenotype diversity is a key theme in the current biosciencefield. This has lead to a large number of different studies generating huge amounts of data, which typically must be shared amongst many collaborators and researchers. To store and use such data efficiently, it is paramount that biomedical researchers describe the data in a compatible and similar way. The Japan Biological Informatics Consortium has developed a data model(PaGE-OM:Phenotype and Genotype-Object Model), which have validated PaGE-OM by applying it to various existing phenotype and genotype databases, and will demonstrating how further databases can be expressed in the PaGE-OM. （cited from original site） |
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| Data type | DNA-polymol |