A Secure Data Repository Integrating Huge
 Volumes of Digital Contents as a Semantic Web

     Norio Kobayashi1 , Yuko Makita1 , Eli Kaminuma1 , Shuji Kawaguchi1 , Yuko
      Yoshida1 , Yoshiki Mochizuki1 , Akihiro Matsushima1 , Manabu Ishii1 , Ryo
       Umetsu1 , Satomi Asano1 , Naohiko Heida1 , Tetsuya Sakurai2 , Takashi
                 Kuromori2 , Kazuo Shinozaki2 , and Tetsuro Toyoda1
      1
          Bioinformatics And Systems Engineering division (BASE), RIKEN, JAPAN
                                  toyoda@base.riken.jp??
                      2
                        Plant Sciences Center (PSC), RIKEN, JAPAN



1         Abstract

Recent omics sciences are strongly supported by the advances in various detec-
tion technologies, such as the next generations high-throughput sequencers, high-
resolution imaging devices and remote-sensing technologies. The obtained data,
the processed data and knowledge extracted from the data are huge, heterolo-
gous, complex and interconnected, and preventing us from sharing or depositing
all of the data to the public databases. We have developed a semantic-web-based
data repository by using the Semantic Web Folders (SWF for short) technology
which is able to share large-scale omics data, experimental raw data, images,
sequences and analysed data within a closed community and to publish all or a
part of the data from the repository. SWF is designed not only for the data pub-
lishing infrastructure, but also as a collaboration tool that allows researchers to
generate a database. More concretely, SWF is designed to achieve the following
features: 1) implementing an ontology-based data structure including file folders
which enables users to write and store various kind of omics data, 2) supporting
various data input/output formats including standardized data formats, 3) im-
plementing a data viewer/editor including a meta search engine over SWF data,
and 4) providing a communication tool that allow users to collaborate with each
other to edit their data. In the current implementation of SWF, we employ a
30 TB Network Attached Strage system that stores a file folder associated with
a ontology term. Moreover, more than 100 database projects including public
ontology data and RIKEN’s original and public databases have been integrated
on SWF. SWF is available at http://database.riken.jp.




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