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

Abstract

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.

VarioML framework for comprehensive variation data representation and exchange

“…The JSON tooling provided with VarioML makes it possible for implementers to develop dynamic user interfaces with substantially less effort and cost [67], expanding on the possibilities demonstrated by the ‘Web Analysis of the Variome’ project [68,69]. A logical next step to contribute to the end-to-end variome pipeline would be to build a variant annotator widget, usable with different database implementations.…”

Ontologies as integrative tools for plant science

“…Although these applications represent relatively simple uses of ontologies, they give some indication of the potential for data reuse. More sophisticated applications such as Semantic J-SON ( Kobayashi et al, 2011 ) can be used for biological applications including genome design, sequence processing, inference over phenotype databases, and full-text search indexing. The PO project has also developed an application to make PO data available over the web, in real time, making it more accessible to developers wanting to incorporate it into their own applications (http://plantontology.org/docs/otherdocs/web_services_ guide.html).…”

“…All data items, including semantic relations, must be specifi ed with a Uniform Resource Identifi er (URI). A relationship between two data items is written as "triple" of three URIs: subject, predicate, and object ( Kobayashi et al, 2011 ). An example of a triple from the PO is: ABCG11 expressed_in epidermal cell , where the URI for the subject ABCG11 is its TAIR (The Arabidopsis Information Resource) locus ID, the URI for the predicate expressed_in is its Relation Ontology ID, and the URI for the object epidermal cell is its PO ID.…”

ExpressWeb: A Web application for clustering and visualization of expression data

“…Several languages have been used to develop ExpressWeb: HTML5 and CSS3 for the web interface, javascript for the dynamic tools (Highchart library to create dynamic Heatmap and the vis.js library to create network from the data), JSON (Kobayashi, et al, 2011) and JQuery for the use of DOM and Ajax in order to manage the data in dynamic manner. The language of the main script is PHP.…”