An easy-to-use bioinformatics interface has been developed by a research group led by Tetsuro Toyoda called the RIKEN Bioinformatics And Systems Engineering division (BASE), Yokohama. The web-service-based tool, called Semantic-JSON, and the portal, BioLOD, integrate access to information contained within genomics, proteomics, and other ‘omics’-based data repositories.
“Advances in life sciences increasingly depend upon cross-analysis and integration of diverse information from multiple large databases maintained on remote computer servers,” explains Toyoda. “The challenge is to facilitate data retrieval, integration and collaboration while maintaining database security.”
As a first step, various research organizations worldwide, including RIKEN, recently published 192 public and 190 private mammalian, plant and protein databases. The data are integrated by SciNetS.org, the Scientists’ Networking System. These databases contain more than 8.2 million individual data records.
Pioneering a new global trend, BASE provides ‘structured linked open data’ and private data via the newly developed BioLOD.org portal connecting with the World Wide Web Consortium (W3C) Linking Open Data initiative. These self-described data are interlinked using standard web technologies allowing automatic reading by computers, thereby making them more useful to researchers. The system facilitates information sharing and collaboration between researchers, but brings new challenges.
“The sheer amount of data contained in our biological data cloud outstripped the capacity of existing bioinformatics interfaces to cope with the complexity of researcher queries, motivating us to develop Semantic-JSON,” explains Toyoda.
Semantic-JSON has two major components. The secured, unified data repository integrates data meaningfully—or ‘semantically’ in computer parlance— from numerous sources. The web-based interface allows researchers to retrieve linked data seamlessly and securely using established bioinformatics programming languages and processing. Bioinformatics researchers can then use their specialized computational tools to analyze raw biological data (Fig. 1).
Databases already available through Semantic-JSON and BioLOD.org include the RIKEN Integrated Database of Mammals with 79 human and mouse omics databases, the RIKEN Integrated Database of Plants incorporating 30 similar databases for the plant species Arabidopsis thaliana, and the RIKEN Integrated Protein Database containing 18 databases.
Since December 2009, international researchers have successfully used the system to identify 28 million data relationships, generating some 4.5 terabytes of associated files. Around 134,000 programs from non-RIKEN researchers have accessed the server as of March 2011. Biological applications include genome design, DNA sequence processing, and the inference of phenotype biological characteristics from genomic information.
“Our next goal is to develop and improve the system to increase its functionality and the usefulness of its linked open data to the worldwide biological community,” says Toyoda.
Kobayashi, N., Ishii, M., Takahashi, S., Mochizuki, Y., Matsushima, A. & Toyoda, T. Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. Nucleic Acids Research published online 1 June, 2011 (doi: 10.1093/nar/gkr353).
Not of Divided Mind
19.01.2017 | Hertie-Institut für klinische Hirnforschung (HIH)
CRISPR meets single-cell sequencing in new screening method
19.01.2017 | CeMM Forschungszentrum für Molekulare Medizin der Österreichischen Akademie der Wissenschaften
An important step towards a completely new experimental access to quantum physics has been made at University of Konstanz. The team of scientists headed by...
Yersiniae cause severe intestinal infections. Studies using Yersinia pseudotuberculosis as a model organism aim to elucidate the infection mechanisms of these...
Researchers from the University of Hamburg in Germany, in collaboration with colleagues from the University of Aarhus in Denmark, have synthesized a new superconducting material by growing a few layers of an antiferromagnetic transition-metal chalcogenide on a bismuth-based topological insulator, both being non-superconducting materials.
While superconductivity and magnetism are generally believed to be mutually exclusive, surprisingly, in this new material, superconducting correlations...
Laser-driving of semimetals allows creating novel quasiparticle states within condensed matter systems and switching between different states on ultrafast time scales
Studying properties of fundamental particles in condensed matter systems is a promising approach to quantum field theory. Quasiparticles offer the opportunity...
Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.
As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...
19.01.2017 | Event News
10.01.2017 | Event News
09.01.2017 | Event News
19.01.2017 | Earth Sciences
19.01.2017 | Life Sciences
19.01.2017 | Physics and Astronomy