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Database Integration Coordination Program(DICP)

Details of the project adopted in FY2018(2 project)

Subject Platform of metabolome informatics considering the material cycle
Research Director Masanori Arita
Title and affiliation Professor, National Institute of Genetics, Research Organization of Information and Systems
Outline Through compiling the spectral libraries of major metabolomics centers in Japan and abroad, we renovate the MassBank database as an international resource providing not only measured data (primary data) collected but also standardized spectral libraries (secondary data). Thereby we provide a basis for standards of compound identification. We also start a public repository for metabolome of biological samples, and work together with existing repositories in Europe and the United States to coordinate metadata. Furthermore, in order to link the metabolomics resources with other omics research, we also create the metabolic map visualizing 'meta' metabolism of material circulation. In summary, we establish metabolomics as an interdisciplinary field that also contributes to nutrition and environmental studies.
Subject Development of functional and interactive database for proteomics
Research Director Yasushi Ishihama
Title and affiliation Professor, Graduate School of Pharmaceutical Sciences, Kyoto University
Outline We will develop an integrated proteome database jPOST (Japan Proteame STandard Repository / Database) containing standardized, integrated and unified proteomic information from a wide variety of biological species with posttranslational modifications at various absolute expression levels. Based on the international standard repositories and the ability to re-analyze the raw data to produce higher-precision data, we will further develop more functions for jPOST to receive wider ranges of proteomic data. In addition, by linking with other omics data, we can map the biomolecules to signal transduction network and metabolic network to elucidate their cellular functions. The jPOST also accepts the proteogenomics data as well as metaproteomics data from gut microbiota, metabolomics data and glycomics data.

Details of the project adopted in FY2017(7 project)

Subject Development of an integrative epigenome database
Research Director Shinya Oki
Title and affiliation Assistant Professor, Graduate School of Medical Sciences, Kyushu University
Outline Based on an integrative ChIP-seq database (ChIP-Atlas), this research plans to add bisulfite-seq data, to expand the organisms for the collection, to establish systematic curation of the sample metadata, and to promote public relations. These activities are focused to raise ChIP-Atlas into an integrative epigenome database used by worldwide researchers to make novel insights and predictions for life sciences.
Presentation documents
(japanese ver. only)
Kickoff Meeting (18/Jul/2017)(2.9MB) クリエイティブ・コモンズ・ライセンス
Subject Network database integrating genomes, diseases and drugs
Research Director Minoru Kanehisa
Title and affiliation Professor, Institute for Chemical Research, Kyoto University
Outline We develop a new reference knowledge base named KEGG NETWORK for perturbed molecular networks involving human diseases and drugs. KEGG NETWORK is a collection of network variants, such as variants of signaling pathways, caused by gene variants and other factors. We also develop a network mapping tool for interpretation of personal genome sequences.
Presentation documents
(japanese ver. only)
Kickoff Meeting (18/Jul/2017)(4.0MB) クリエイティブ・コモンズ・ライセンス
Subject Construction of a Glycoscience Portal
Research Director Kiyoko F. Aoki-Kinoshita
Title and affiliation Professor, Faculty of Science and Engineering, Soka University
Outline In this project, we will develop GlyCosmos Portal, which will serve as the foundation for systems glycobiology. Both the existing glycan structure repository GlyTouCan as well as a new repository for glycoconjugates called GlyComb will be placed within this portal. Moreover, the development of GlyCosmos Database, which stores two integrated datasets (molecular structures of glycans and pathway information pertaining to glycogenes), will be developed and integrated with databases of genomes, proteomes, metabolomes, etc.
We aim to utilize glycan information across a wide range of life science fields by making it possible to browse and analyze signaling and metabolic pathways that incorporate glycan information.
Presentation documents
(japanese ver. only)
Kickoff Meeting (18/Aug/2017)(3.0MB) クリエイティブ・コモンズ・ライセンス
Subject Upgrading data validation and integration for Protein Data Bank
Research Director Genji Kurisu
Title and affiliation Professor, Institute for Protein Research, Osaka University
Outline Under the world-wide Protein Data Bank (PDB) partnership, Protein Data Bank Japan (PDBj) accepts and processes the regional PDB data, including newly expanded hybrid analysis, and forms a single global repository of PDB coordinates and NMR chemical shifts (BMRB). The PDBj is upgrading the validation report with semantic indexing, integrating the chemical structure database (CSD) and developing ASH viewer for the structure-based analysis of protein functions. The PDBj also holds annual workshops or seminars for users in order to facilitate usage of PDB and BMRB data.
Presentation documents
(japanese ver. only)
Kickoff Meeting (18/Aug/2017)(5.0MB) クリエイティブ・コモンズ・ライセンス
Subject Advanced practical development of the integrated database for microbes “MicrobeDB.jp”
Research Director Ken Kurokawa
Title and affiliation Professor, National Institute of Genetics, Research Organization of Information and Systems
Outline We have been developing an integrated database for microbes “MicrobeDB.jp” based on Semantic Web technologies. Now we are facing essential and serious problems, “How to utilize the integrated DB, and how to get new research ideas from the DB?” In the program, we tackle these subjects from data science perspectives, and work toward practical uses of the MicrobeDB.jp.
Presentation documents
(japanese ver. only)
Kickoff Meeting (7/Jul/2017)(4.5MB) クリエイティブ・コモンズ・ライセンス
Subject DBKERO; a database to integrate multi-omics data for interpretation and functional annotations of human genome variations in diseases
Research Director Sumio Sugano
Title and affiliation Professor, Graduate School of Frontier Sciences, University of Tokyo
Outline In this project, we will develop a database where human genomic variance (somatic or germ line single nucleotide substitutions) are associated with epigenome and transcriptome information. This integration should give an important clue when biological interpretations of the variation found in the genomes of patients having diseases are conducted. We will put a primary focus on cancer genomes, but, eventually will expand the database to cover diverse diseases. Unique features of this database lies that it will include the multi-omics information from model systems, such as culture cells and mice models. This part should be particularly important as it is not always easy to collect the similar data directly from human clinical samples. Also this database will serve as a local database server for the CREST data collected for IHEC (International Human Epigenome Consortium).
Presentation documents
(japanese ver. only)
Kickoff Meeting (18/Jul/2017)(4.5MB) クリエイティブ・コモンズ・ライセンス
Subject Development of a new platform for plant genome information analyses toward an era of individual genomes
Research Director Satoshi Tabata
Title and affiliation Director, Kazusa DNA Research Institute
Outline We aim to expand and improve present Plant Genome DataBase Japan (PGDBj) by implementing new function that enables users to compare and utilize various genome-related information such as genomic sequences, transcripts and DNA markers among multiple plant species. Furthermore, a web-based tool for SNP typing and haplotype analysis with the NGS data submitted by the users will be developed for the upcoming era of individual genome sequencing in plant species.
Presentation documents
(japanese ver. only)
Kickoff Meeting (7/Jul/2017)(5.4MB) クリエイティブ・コモンズ・ライセンス