Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

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...

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Bibliographic Details
Published in:Nucleic acids research 2011-07, Vol.39 (suppl_2), p.W533-W540
Main Authors: Kobayashi, Norio, Ishii, Manabu, Takahashi, Satoshi, Mochizuki, Yoshiki, Matsushima, Akihiro, Toyoda, Tetsuro
Format: Article
Language:English
Subjects:
Animals
Databases, Genetic
Internet
Mice
Semantics
Software
Systems Integration
User-Computer Interface
Web Services
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkr353