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DICP-Tool Prototype for Integrated Database Analysis

Details of the project adopted in FY2013(8 projects)

Subject Fast feature selection method for large-scale analysis of local sequence/structure/function relationships in proteins
Research Director Teppei Ebina
Title and affiliation Researcher, Brain Science Institute, RIKEN
Outline  Detecting amino acid sequence features of protein local structures and functional sites allows us to discover the relationships between protein sequence/structure/function. Interest in the fast search of the features has increased recently with rapid growth of protein databases as feature selection from very large data sets requires enormous computational costs. Here, we will develop a fast method of the feature selection by clustering amino acid sequence fragments using recently developed BOOL (Binary cOding Oriented cLustering) algorithm and will examine whether our method can identify "optimal" sequence features of protein local structures with faster computational time than other methods.
Presentation documents
(japanese ver. only)
Progress Report Meeting(PDF:456KB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:1.80MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:450KB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.1MB) クリエイティブ・コモンズ・ライセンス
Link to tools RVSB (Representative Vector Selection using BOOL)
Subject Network analysis system for genome-scale metabolic models with multi-omics data
Research Director Kozo Nishida
Title and affiliation Technical Staff, Quantitative Biology Center, RIKEN
Outline  In recent years, several genome-scale metabolic models have been reconstructed and published. For the purpose of navigating drug targets predicted from these models, KEGG PATHWAY, and user-specific omics-data, I develop a network analysis system. This system supports "E-coli metabolic model and KEGG PATHWAY integration", "Multi-omics pathway visualization", and "Drug targets navigation with KEGG MEDICUS".
Presentation documents
(japanese ver. only)
Progress Report Meeting (PDF:2.20MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:886KB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:906KB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.1MB) クリエイティブ・コモンズ・ライセンス
Link to tools KEGGscape
Subject Integration of KNApSAcK and the other chemical databases to understand efficacy of plants on human at the molecular level
Research Director Yosuke Nishimura
Title and affiliation Postgraduate Student, Bioinformatics Center, Institute for Chemical Research, Kyoto University
Outline  KNApSAcK is a database describing relationships between species and their metabolites. Its family databases (KNApSAcK family) include information about efficacy of plants on human at the phenotypic level. The aim of this project is to integrate the information at the phenotypic level from KNApSAcK with the information at the molecular level from the other chemical databases (e.g. ChEMBL) for understanding the relationships between these two levels that should be helpful to predict efficacy of plants by using metabolomics data.
Presentation documents
(japanese ver. only)
Progress Report Meeting(PDF:1.75MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:4.52MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:3.00MB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.1MB) クリエイティブ・コモンズ・ライセンス
Link to tools PCIDB(PhytoChemical Interactions DB)
Subject Development of a pipeline for generating ligand - protein binding site prediction tools using machine learning
Research Director Masaki Banno
Title and affiliation Postgraduate Student, Department of biotechnology, The University of Tokyo
Outline  We have developed a pipeline for generating tools that predict which residue binds a user-selected ligand in a protein sequence. We calculated all pairwise interactomic distances of protein ligand binding of atomic level in PDB database, and constructed ligand binding sites database. By integrating this database and other current biological databases, this pipeline generates high accuracy prediction tools based on machine learning method. These tools are able to predict the binding sites of a protein whose structural information is unknown at low calculation cost. Hence, this tool can be applied to genome wide prediction.
Presentation documents
(japanese ver. only)
Progress Report Meeting (PDF:5.10MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:4.66MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:3.3MB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.1MB) クリエイティブ・コモンズ・ライセンス
Link to tools ・UTProt Galaxy
(http://utprot.net/ > UTProt Galaxy > Shared Data > Published Workflows)
  Predict Ligand Binding Residue
  Get Non Redundant Ligand Binding Protein With Ligand Binding Residue
  Get Non Redundant Ligand Binding Protein
  Create Ligand Binding Residue Predictor
・PLBSPResidue(http://utprot.net/ > PLBSPResidue)
・Ligand Binding Residue Predictor Generator in UTProt Galaxy
・UTProt CKAN(http://utprot.net/ > UTProt CKAN)
Subject AtMetExpress: a database for mass spectrometry-based metabolite profiling data in Arabidopsis and development of related tools to facilitate omics-data integration
Research Director Atsushi Fukushima
Title and affiliation Research Scientist, Metabolome Informatics Research Team, Metabolomics Research Group, Center for Sustainable Resource Science, RIKEN
Outline  The project develops AtMetExpress system, consisting of a database for mass spectrometry-based metabolite profiling data in the model plant Arabidopsis (Arabidopsis thaliana) and related tools facilitating omics-data integration. The purpose of this study is to integrate publicly available metabolome datasets with other resources at National Bioscience Database Center (NBDC) to efficiently realize knowledge discovery in plant metabolomics.
Presentation documents
(japanese ver. only)
Progress Report Meeting(PDF:1.08MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:1.10MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:853KB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.1MB) クリエイティブ・コモンズ・ライセンス
Link to tools AtMetExpress
Subject Development of a method for detecting functional modules by analyzing co-occurrences of metadata in protein
Research Director Satoshi Fujii
Title and affiliation Assistant Professor, Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
Outline  The many kind of databases were published and open-accessed. It becomes important problem how we integrate the information from the databases and extract truly useful information. In this study, in order to detect the functional modules, I analyze an accumulation of co-occurrences between each of the metadata, which is annotated information in protein. In this time, I analyze the co-occurrences only on functional domains and motifs of proteins. The co-occurrences are detected by three definitions: 1) a pair of metadata (domains or motifs) that exist in the neighborhood in 3D protein structure, 2) a pair of metadata that present in a high frequency in all proteins and 3) a pair of metadata that match both 1) and 2). The results are summarized in a database and are published as a web-based tool.
Presentation documents
(japanese ver. only)
Progress Report Meeting(PDF:833KB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:1.57MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:680KB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.1MB) クリエイティブ・コモンズ・ライセンス
Link to tools PDBnet - Cooccurrence Search Tool
Subject Development of a web tool for the elucidation of glycan binding patterns of protein-glycan interaction
Research Director Masae Hosoda
Title and affiliation Postgraduate Student, Division of Bioinformatics, Graduate School of Engineering, Soka University
Outline  Glycomics research has focused attention on glycan function occurring within living organisms, and glycoinfomatics techniques are needed to be able to analyze many experimental data which are being accumulated, such as mass spectrometry data, microarray data, etc. In this work, we aim for the elucidation of the interaction mechanism between proteins and glycans from experimental data in the Integrated Database Project using our software tool to align multiple glycan structures.
Presentation documents
(japanese ver. only)
Progress Report Meeting (PDF:1.84MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:2.25MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:3.6MB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.1MB) クリエイティブ・コモンズ・ライセンス
Link to tools MCAW (Multiple Carbohydrate Alignment with Weights)
Subject Development of a metagenomic analysis pipeline that utilizes the MicrobeDB.jp data
Research Director Hiroshi Mori
Title and affiliation Assistant Professor , Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
Outline  The aim of this study is to develop a web application that can analyze user-uploaded metagenomic sequence data by applying the metagenomic analysis pipeline used in the MicrobeDB.jp. This web application will provide the basic information on the microbial community (e.g., the taxonomic and functional composition). In addition, users can compare this information with other metagenomic samples exist in the MicrobeDB.jp.
Presentation documents
(japanese ver. only)
Progress Report Meeting (PDF:1.38MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:1.79MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:1.2MB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.1MB) クリエイティブ・コモンズ・ライセンス
Link to tools MeGAP(MetaGenome Annotation Pipeline)

 

Details of the project adopted in FY2014(4 projects)

Subject Development of pdbBAM, comprehensive mapping of PDBj protein sequences on human genome
Research Director Matsuyuki Shirota
Title and affiliation Assistant Professor, Graduate School of Medicine, Tohoku University
Outline  In this trial, I will convert the amino acid sequences of the protein structures in PDBj to the sponding mRNA sequences, map them onto human reference genome and generate pdbBAM, which integrates the genomic positions and mutations of all of the PDBj structures in BAM format. This tool aims to enable the scientists to grasp the availability of 3D-structural information in each genomic position by browsing high-throughput sequencing results. pdbBAM will bridge the gap between personal genomics and structural biology and help to accelerate the study of personalized medicine and drug discovery.
Presentation documents
(japanese ver. only)
Kickoff Meeting(PDF:599KB) クリエイティブ・コモンズ・ライセンス
Progress Report Meeting (PDF:6.7MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:1.28MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:1.01MB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.2MB) クリエイティブ・コモンズ・ライセンス
Link to tools pdbBAM
Subject A general framework for interlinking data between RDF stores and its application to ortholog analysis
Research Director Hirokazu Chiba
Title and affiliation Research Staff, National Institute for Basic Biology
Outline  Recently, several biological databases have been reconstructed as RDF stores that are accessible via SPARQL, and they now appear to form distributed databases over the Web. To discover biological knowledge using these databases, it is crucial to develop a technology to interlink the data between them. Herein, I will propose a general framework for interlinking the data between RDF stores with easy operation. On the basis of this framework, I will integrate various types of gene information using the ortholog database as a hub of links, thus aiming at the discovery of biological knowledge.
Presentation documents
(japanese ver. only)
Kickoff Meeting(PDF:916KB) クリエイティブ・コモンズ・ライセンス
Progress Report Meeting (PDF:313KB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:2.16MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:388KB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.2MB) クリエイティブ・コモンズ・ライセンス
Link to tools SPANG
Subject An extension of biochemical reaction network analysis environment
Research Director Kozo Nishida
Title and affiliation Technical staff, Quantitative Biology Center, RIKEN
Outline  In last fiscal year, we have developed a software environment of a biochemical reaction network analysis, integrating multi-omics, pathway and drug target. E. coli. has been only supported in the software platform. In this fiscal year, we reorganize the workflow of the software environment, and add new framework of a Cyberinfrastructure proposed by Cytoscape. We then extend our target organism to Arabidopsis thaliana, demonstrating the versatility of our analysis environment.
Presentation documents
(japanese ver. only)
Kickoff Meeting(PDF:532KB) クリエイティブ・コモンズ・ライセンス
Progress Report Meeting (PDF:385KB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:947KB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:735KB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.2MB) クリエイティブ・コモンズ・ライセンス
Link to tools keggutil
togotrial2014
Subject Pipeline of phase-defined complete sequencing for the HLA genes
Research Director Kazuyoshi Hosomichi
Title and affiliation Visiting Researcher, Division of Human Genetics, National Institute of Genetics
Outline  The human leukocyte antigen (HLA) has been associated with more than 100 different diseases, mostly autoimmune diseases. In addition specific alleles of HLA genes are strongly associated with drug hypersensitivity induced by specific drugs. Therefore, the HLA typing is one of the important tools as clinical application, medical research, and population genetics. I would like to start the project to establish phase-defined sequencing pipeline which was optimized for HLA gene sequences using NGS data, and has been available as web-based analysis tool. The pipeline will be greatly advantageous for clinical (diagnostic) application that requires a user-friendly protocol, with high throughput and accuracy.
Presentation documents
(japanese ver. only)
Kickoff Meeting(PDF:2.4MB) クリエイティブ・コモンズ・ライセンス
Progress Report Meeting (PDF:25MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:2.86MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(PDF:1.59MB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(PDF:0.2MB) クリエイティブ・コモンズ・ライセンス
Link to tools p-galaxy
p-galaxy help, HLA ANALYSIS TOOLS

Details of the project adopted in FY2015(3 projects)

Subject Integrative database for exploiting published ChIP-seq data
Research Director Shinya Oki
Title and affiliation Assistant Professor, Graduate School of Medical Sciences, Kyushu University
Outline In this project, all of the ChIP-seq raw data deposited in public databases (approx. 30,000 experimental data) will be processed to produce peak-call and coverage data. These data assembly will be visualized on a free genome browser (IGV), graphically showing binding evidence of proteins to any given loci in multiple cell types. Furhter analysises will be performed to predict genes regulated by given transcription factors (TFs) and novel TF-TF complexes colocalizing on multiple genomic loci.
Presentation documents
(japanese ver. only)
Kickoff Meeting(PDF:5.83MB) クリエイティブ・コモンズ・ライセンス
Togo Symposium 2015 Poster presentation(PDF:2.9MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:3.7MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(3.8MB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(0.4MB) クリエイティブ・コモンズ・ライセンス
Link to tools ChIP-Atlas
Subject Development of a mobile application for cross-search of various herbal medicines
Research Director Tetsuo Katsuragi
Title and affiliation Assistant Professor, Department of Computer Science and Engineering, Toyohashi University of Technology
Outline Recently, there are growing needs of applying traditional crude drug systems for medical treatment. Nevertheless, the information related to these crude systems is still spreading, it is still merely available in the digital format and is based on published literature. In this research, towards the future development of databases for these crude drug systems, we develop a mobile-phone application in the Android platform for various kinds of crude drug systems. A plug-in system is introduced for adding other traditional crude drug systems to help users modifying the existing crude drug database or updating the database with the new crude drug systems from other countries that are expected to be available in future. This application offers a cross-database search for crude drug recipes and their efficacies by symptoms or herbal medicine ingredients.
Presentation documents
(japanese ver. only)
Kickoff Meeting(PDF:444KB) クリエイティブ・コモンズ・ライセンス
Togo Symposium 2015 Poster presentation(PDF:1.1MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:1.3MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(0.5MB)クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(0.4MB) クリエイティブ・コモンズ・ライセンス
Link to tools Herbal Medicine Systems
Subject Interaction energy analysis between lectin and glycochain based on quantum mechanical calculation
Research Director Shogo Nakano
Title and affiliation Assistant Professor, School of Food and Nutritional Sciences, University of Shizuoka
Outline Interaction energy between lectin and glycochain will be estimated by quantum mechanical calculation (QM). In addition, we try to develop algorithm to predict structural flexibility and affinity of lectin and various glycochain. PyMOL plugin supporting analysis for results of QM calculation will be developed to expand database of lectin and glycochain toward researchers who major in structural biology and computational chemistry. The results will be connected to other database, such as disease, medicine and environmental compounds.
Presentation documents
(japanese ver. only)
Kickoff Meeting(PDF:1.36MB) クリエイティブ・コモンズ・ライセンス
Togo Symposium 2015 Poster presentation(PDF:1.5MB) クリエイティブ・コモンズ・ライセンス
Final Report Meeting(PDF:3.0MB) クリエイティブ・コモンズ・ライセンス
Reports
(japanese ver. only)
Final Report(3.0MB) クリエイティブ・コモンズ・ライセンス
Evaluation Ex-post(0.4MB) クリエイティブ・コモンズ・ライセンス
Link to tools PyPaics