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

Takashi Gojobori,Hideaki Sugawara,Akira R Kinjo,Koji Nagata,Masafumi Muraoka,Kei Yura,Kazuho Ikeo,Daichi Yamada,Kengo Kinoshita,Yeondae Kwon,Yukie Katayama,Ohsuke Migita,Takeshi Kawabata,Satoshi Omori,Hisashi Mizutani

doi:10.1007/s10969-016-9211-3

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/.

Highlights

The advance of the molecular biology has yielded a huge amount of biological data including DNA/RNA/protein sequences [1,2,3], their expression levels [4], difference in the sequences of individuals [5], three-dimensional (3D) structures of the biomolecules [6], phenotypes of the organisms [7] and so forth
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
These data have been stored in independent databases located on the Internet and researchers exploit these databases for new knowledge of the target of their study

Summary

Introduction

The advance of the molecular biology has yielded a huge amount of biological data including DNA/RNA/protein sequences [1,2,3], their expression levels [4], difference in the sequences of individuals [5], three-dimensional (3D) structures of the biomolecules [6], phenotypes of the organisms [7] and so forth These data have been stored in independent databases located on the Internet and researchers exploit these databases for new knowledge of the target of their study. Some efforts have been dedicated to solve these difficulties (e.g., http://identifiers.org), it will take time for the research community to agree on a unified convention To overcome these difficulties in a search of multiple databases in the information of life science, we started developing a new type of application that searches databases in different locations simultaneously by a simple search query and displays the result in a simple interface at http://p4d-info.nig.ac.jp/vapros/. The detail of VaProS and the example of the usage are presented

Materials and methods

Method of access Original location

Results and discussion

Findings

Conclusion