The RIKEN integrated database of mammals

Hiroshi Masuya, Yuko Makita, Norio Kobayashi, Koro Nishikata, Yuko Yoshida, Yoshiki Mochizuki, Koji Doi, Terue Takatsuki, Kazunori Waki, Nobuhiko Tanaka, Manabu Ishii, Akihiro Matsushima, Satoshi Takahashi, Atsushi Hijikata, Kouji Kozaki, Teiichi Furuichi, Hideya Kawaji, Shigeharu Wakana, Yukio Nakamura, Atsushi YoshikiTakehide Murata, Kaoru Fukami-Kobayashi, Sujatha Mohan, Osamu Ohara, Yoshihide Hayashizaki, Riichiro Mizoguchi, Yuichi Obata, Tetsuro Toyoda

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

The RIKEN integrated database of mammals (http:// scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.

Original languageEnglish
Pages (from-to)D861-D870
JournalNucleic acids research
Volume39
Issue numberSUPPL. 1
DOIs
Publication statusPublished - 1 Jan 2011

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    Masuya, H., Makita, Y., Kobayashi, N., Nishikata, K., Yoshida, Y., Mochizuki, Y., Doi, K., Takatsuki, T., Waki, K., Tanaka, N., Ishii, M., Matsushima, A., Takahashi, S., Hijikata, A., Kozaki, K., Furuichi, T., Kawaji, H., Wakana, S., Nakamura, Y., ... Toyoda, T. (2011). The RIKEN integrated database of mammals. Nucleic acids research, 39(SUPPL. 1), D861-D870. https://doi.org/10.1093/nar/gkq1078