title: VaProS: a database-integration approach for protein/genome information retrieval.
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/ .
authors.affiliation: Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.|National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.affiliation: National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan.
authors.forename: Kazuho
authors.initials: K
authors.lastname: Ikeo
authors.affiliation: Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan.
authors.forename: Yukie
authors.initials: Y
authors.lastname: Katayama
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kawabata
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
authors.forename: Akira R
authors.initials: AR
authors.lastname: Kinjo
authors.affiliation: Graduate School of Information Sciences, Tohoku University, Miyagi, Sendai, 980-8597, Japan.|Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Sendai, 980-8573, Japan.
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
authors.affiliation: Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan.
authors.forename: Yeondae
authors.initials: Y
authors.lastname: Kwon
authors.affiliation: Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, 157-8535, Japan.|Department of Pediatrics, St. Marianna University School of Medicine, Miyamae, Kawasaki, 216-8511, Japan.
authors.forename: Ohsuke
authors.initials: O
authors.lastname: Migita
authors.affiliation: National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan.
authors.forename: Hisashi
authors.initials: H
authors.lastname: Mizutani
authors.affiliation: National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan.
authors.forename: Masafumi
authors.initials: M
authors.lastname: Muraoka
authors.affiliation: Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Nagata
authors.affiliation: Graduate School of Information Sciences, Tohoku University, Miyagi, Sendai, 980-8597, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Omori
authors.affiliation: National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Sugawara
authors.affiliation: Center for Informational Biology, Ochanomizu University, 2-1-1, Otsuka, Bunkyo, Tokyo, 112-8610, Japan.
authors.forename: Daichi
authors.initials: D
authors.lastname: Yamada
authors.affiliation: National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan. yura.kei@ocha.ac.jp.|Center for Informational Biology, Ochanomizu University, 2-1-1, Otsuka, Bunkyo, Tokyo, 112-8610, Japan. yura.kei@ocha.ac.jp.
authors.forename: Kei
authors.identifier: http://orcid.org/0000-0003-0197-5478
authors.initials: K
authors.lastname: Yura
mesh_terms: D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D016678:Genome; D006801:Humans; D020407:Internet; D051379:Mice; D011487:Protein Conformation; D051381:Rats; D017422:Sequence Analysis, DNA; D012984:Software
keywords: Big data analysis; Database integration; Lysosomal storage disease; Protein 3D structure