Asada Yukuhiko, Sugahara Michihiro, Mizutani Hisashi, Naitow Hisashi, Tanaka Tomoyuki, Matsuura Yoshinori, Agari Yoshihiro, Ebihara Akio, Shinkai Akeo, Kuramitsu Seiki, Yokoyama Shigeyuki, Kaminuma Eri, Kobayashi Norio, Nishikata Koro, Shimoyama Sayoko, Toyoda Tetsuro, Ishikawa Tetsuya, Kunishima Naoki
Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):914-9. doi: 10.1107/S0907444913001728. Epub 2013 Apr 19.
Information from structural genomics experiments at the RIKEN SPring-8 Center, Japan has been compiled and published as an integrated database. The contents of the database are (i) experimental data from nine species of bacteria that cover a large variety of protein molecules in terms of both evolution and properties (http://database.riken.jp/db/bacpedia), (ii) experimental data from mutant proteins that were designed systematically to study the influence of mutations on the diffraction quality of protein crystals (http://database.riken.jp/db/bacpedia) and (iii) experimental data from heavy-atom-labelled proteins from the heavy-atom database HATODAS (http://database.riken.jp/db/hatodas). The database integration adopts the semantic web, which is suitable for data reuse and automatic processing, thereby allowing batch downloads of full data and data reconstruction to produce new databases. In addition, to enhance the use of data (i) and (ii) by general researchers in biosciences, a comprehensible user interface, Bacpedia (http://bacpedia.harima.riken.jp), has been developed.
日本理化学研究所SPring-8中心的结构基因组学实验信息已被汇编并作为一个综合数据库发布。该数据库的内容包括：(i) 来自9种细菌的实验数据，这些数据在进化和特性方面涵盖了各种各样的蛋白质分子 (http://database.riken.jp/db/bacpedia)；(ii) 来自经过系统设计的突变蛋白的实验数据，用于研究突变对蛋白质晶体衍射质量的影响 (http://database.riken.jp/db/bacpedia)；以及(iii) 来自重原子数据库HATODAS中重原子标记蛋白质的实验数据 (http://database.riken.jp/db/hatodas)。该数据库整合采用了语义网，适用于数据重用和自动处理，从而允许批量下载完整数据并进行数据重建以生成新的数据库。此外，为了提高生物科学领域普通研究人员对数据(i)和(ii)的使用，还开发了一个易于理解的用户界面Bacpedia (http://bacpedia.harima.riken.jp)。
