Bioinformatics And Systems Engineering division, RIKEN. 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W533-40. doi: 10.1093/nar/gkr353. Epub 2011 Jun 1.
Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.
全球生物信息学研究数据库的云框架变得庞大而异构；解决方案面临着各种相互矛盾的挑战，包括跨集成、检索、安全性和开放性。为此，截至 2011 年 3 月，包括理研所在内的一些组织发布了 192 个哺乳动物、植物和蛋白质生命科学数据库，拥有 820 万条数据记录，这些数据通过科学家网络系统（SciNetS.org）集成到了链接开放数据（Linked Open Data，LOD）或私有数据（Private Data，LPD）中。该数据库集成框架涵盖的大量链接数据基于语义 Web，研究人员通过在安全的数据空间中管理公共和私有数据库中的元数据来进行协作。这超过了现有接口工具（如 SPARQL）的数据查询能力。实际研究还需要使用原始数据进行数据分析的专门工具。为了解决这些挑战，我们在 2009 年 12 月开发了轻量级语义 JSON 接口，以便在生物信息学家常用的编程语言（如 Perl 和 Ruby）的控制下安全地访问链接和原始生命科学数据的每个片段。研究人员成功地在 2800 万个语义关系上使用了该接口，用于包括基因组设计、序列处理、表型数据库推理、全文搜索索引以及本体和 LOD 树查看器等人类可读内容在内的生物应用。SciNetS.org 的语义 JSON 服务可在 http://semanticjson.org 获得。
