Japan’s RIKEN develops ‘virtual cloud center’ for life- science data

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WAKO, Japan—Aiming to create a new paradigm for life-science data sharing, RIKEN, Japan's multi-disciplinary research institute, is making multiple databases accessible through its Scientists' Networking System (SciNetS) using the new Semantic-JavaScript Object Notation (JSON) programming interface.

According to RIKEN, Semantic-JSON accesses SciNetS, a "virtual laboratory cloud center" developed at the institute's Bioinformatics and Systems Engineering (BASE) division.

The new, lightweight web service interface gives researchers access to massive amounts of life-science research data across multiple public and private domains. According to RIKEN, SciNetS provides a secure, flexible and lightweight interface to millions of data records and their network of semantic relationships, "ushering in a new era of collaboration, analysis and information-sharing for life-science research and applied innovation."

The research institute says the service also overcomes the "data deluge" often experienced in gene annotation, protein structure analysis, plant ontologies and transcriptomes. Adding to these challenges, much of the data handled at each step of the research process is private, making integration with public data more difficult and hindering collaboration. Overcoming these challenges requires systems for securely integrating data resources and making their information widely available through a flexible interface, RIKEN says.

The solution brings together a total of 192 public database projects, both internal and external to RIKEN. SciNetS creates common ground for sharing life-science data resources by linking these resources together in a network of semantic relationships based on standardized Semantic Web techniques, RIKEN explains.

Semantic-JSON provides a flexible interface to SciNetS on the web, enabling bioinformaticians to access specific data from across the SciNetS network using the programming languages and information tools they normally use in their research. The interface does so by defining a set of simple but relevant commands for accessing and searching SciNetS data and their semantic relationships, delivering results in the widely used JSON format.

RIKEN has already applied Semantic-JSON to a number of projects, including international data collaborations on mouse phenotypes, domestic integrated database projects and the GenoCon International Rational Genome Design Contest. Looking ahead, RIKEN plans to use the interface to distribute life-science data across its research centers and with international collaborators via the SciNetS project. This research result appeared in the online version of the British scientific journal Nucleic Acids Research on June 1.

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