VaProS: a database-integration approach for protein/genome information retrieval

Handle URI:
http://hdl.handle.net/10754/622076
Title:
VaProS: a database-integration approach for protein/genome information retrieval
Authors:
Gojobori, Takashi ( 0000-0001-7850-1743 ) ; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R.; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei
Abstract:
Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)
Citation:
Gojobori T, Ikeo K, Katayama Y, Kawabata T, Kinjo AR, et al. (2016) VaProS: a database-integration approach for protein/genome information retrieval. Journal of Structural and Functional Genomics. Available: http://dx.doi.org/10.1007/s10969-016-9211-3.
Publisher:
Springer Nature
Journal:
Journal of Structural and Functional Genomics
Issue Date:
24-Dec-2016
DOI:
10.1007/s10969-016-9211-3
Type:
Article
ISSN:
1345-711X; 1570-0267
Sponsors:
This research is supported by the Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science) from Japan Agency for Medical Research and Development (AMED).
Additional Links:
http://link.springer.com/article/10.1007%2Fs10969-016-9211-3
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorGojobori, Takashien
dc.contributor.authorIkeo, Kazuhoen
dc.contributor.authorKatayama, Yukieen
dc.contributor.authorKawabata, Takeshien
dc.contributor.authorKinjo, Akira R.en
dc.contributor.authorKinoshita, Kengoen
dc.contributor.authorKwon, Yeondaeen
dc.contributor.authorMigita, Ohsukeen
dc.contributor.authorMizutani, Hisashien
dc.contributor.authorMuraoka, Masafumien
dc.contributor.authorNagata, Kojien
dc.contributor.authorOmori, Satoshien
dc.contributor.authorSugawara, Hideakien
dc.contributor.authorYamada, Daichien
dc.contributor.authorYura, Keien
dc.date.accessioned2016-12-26T13:42:26Z-
dc.date.available2016-12-26T13:42:26Z-
dc.date.issued2016-12-24en
dc.identifier.citationGojobori T, Ikeo K, Katayama Y, Kawabata T, Kinjo AR, et al. (2016) VaProS: a database-integration approach for protein/genome information retrieval. Journal of Structural and Functional Genomics. Available: http://dx.doi.org/10.1007/s10969-016-9211-3.en
dc.identifier.issn1345-711Xen
dc.identifier.issn1570-0267en
dc.identifier.doi10.1007/s10969-016-9211-3en
dc.identifier.urihttp://hdl.handle.net/10754/622076-
dc.description.abstractLife science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.en
dc.description.sponsorshipThis research is supported by the Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science) from Japan Agency for Medical Research and Development (AMED).en
dc.publisherSpringer Natureen
dc.relation.urlhttp://link.springer.com/article/10.1007%2Fs10969-016-9211-3en
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectBig data analysisen
dc.subjectDatabase integrationen
dc.subjectLysosomal storage diseaseen
dc.subjectProtein 3D structureen
dc.titleVaProS: a database-integration approach for protein/genome information retrievalen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalJournal of Structural and Functional Genomicsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionNational Institute of Genetics, Mishima, Japanen
dc.contributor.institutionGraduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japanen
dc.contributor.institutionInstitute for Protein Research, Osaka University, Osaka, Japanen
dc.contributor.institutionGraduate School of Information Sciences, Tohoku University, Sendai, Japanen
dc.contributor.institutionTohoku Medical Megabank Organization, Tohoku University, Sendai, Japanen
dc.contributor.institutionDepartment of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japanen
dc.contributor.institutionDepartment of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japanen
dc.contributor.institutionCenter for Informational Biology, Ochanomizu University, Tokyo, Japanen
kaust.authorGojobori, Takashien
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