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).
New photocatalyst speeds up the conversion of carbon dioxide into chemical resources
29.05.2017 | DGIST (Daegu Gyeongbuk Institute of Science and Technology)
Copper hydroxide nanoparticles provide protection against toxic oxygen radicals in cigarette smoke
29.05.2017 | Johannes Gutenberg-Universität Mainz
The world's highest gain high power laser amplifier - by many orders of magnitude - has been developed in research led at the University of Strathclyde.
The researchers demonstrated the feasibility of using plasma to amplify short laser pulses of picojoule-level energy up to 100 millijoules, which is a 'gain'...
Staphylococcus aureus is a feared pathogen (MRSA, multi-resistant S. aureus) due to frequent resistances against many antibiotics, especially in hospital infections. Researchers at the Paul-Ehrlich-Institut have identified immunological processes that prevent a successful immune response directed against the pathogenic agent. The delivery of bacterial proteins with RNA adjuvant or messenger RNA (mRNA) into immune cells allows the re-direction of the immune response towards an active defense against S. aureus. This could be of significant importance for the development of an effective vaccine. PLOS Pathogens has published these research results online on 25 May 2017.
Staphylococcus aureus (S. aureus) is a bacterium that colonizes by far more than half of the skin and the mucosa of adults, usually without causing infections....
Physicists from the University of Würzburg are capable of generating identical looking single light particles at the push of a button. Two new studies now demonstrate the potential this method holds.
The quantum computer has fuelled the imagination of scientists for decades: It is based on fundamentally different phenomena than a conventional computer....
An international team of physicists has monitored the scattering behaviour of electrons in a non-conducting material in real-time. Their insights could be beneficial for radiotherapy.
We can refer to electrons in non-conducting materials as ‘sluggish’. Typically, they remain fixed in a location, deep inside an atomic composite. It is hence...
Two-dimensional magnetic structures are regarded as a promising material for new types of data storage, since the magnetic properties of individual molecular building blocks can be investigated and modified. For the first time, researchers have now produced a wafer-thin ferrimagnet, in which molecules with different magnetic centers arrange themselves on a gold surface to form a checkerboard pattern. Scientists at the Swiss Nanoscience Institute at the University of Basel and the Paul Scherrer Institute published their findings in the journal Nature Communications.
Ferrimagnets are composed of two centers which are magnetized at different strengths and point in opposing directions. Two-dimensional, quasi-flat ferrimagnets...
24.05.2017 | Event News
23.05.2017 | Event News
22.05.2017 | Event News
29.05.2017 | Earth Sciences
29.05.2017 | Life Sciences
29.05.2017 | Physics and Astronomy