“SABIO-RK” supports search for biochemical reactions and their kinetics – EML Research developed important tool for systems biology
Life means motion. In every cell, there are permanently many chemical reactions occurring. Modern systems biology aims at understanding the multiple reaction pathways in the cells of an organism by combining experimental data with simulation methods. Therefore, to carry out their studies systems biologists need reliable kinetic data for the reactions studied. However, the published kinetic data is not standardized and widely distributed among scientific journals. This raises the problem for researchers to overlook and access this information.
The Heidelberg research institute EML Research has developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) to facilitate the search and retrieval of kinetic data. “In Spanish, ´Sabio´ means a wise man”, says EML Research group leader Isabel Rojas. SABIO-RK is a web-accessible database designed to support researchers interested in information about biochemical reactions and their kinetics. It contains and merges information such as substrates, products and modifying compounds (i.e. inhibitors or activators) of reactions, information about the catalyzing enzymes, organism, tissue and cellular location where the reactions take place and the kinetic laws governing the reactions. SABIO-RK is the first database storing the formulas of kinetic laws. Kinetic laws are essential for executing computer simulations.
The user can search for reactions based on their reactants, characteristics or their involvement in reaction networks, as well as for the reaction's kinetics based
on the experimental conditions under which they were determined. The system supports the creation of a SBML (Systems Biology Mark-up Language) file
containing the information selected by the user. This file can then be used as the basis for the definition of a simulation model in SBML. Links to other databases
like Swissprot and Pubmed enable the user to gather further information about proteins corresponding to the enzymes, and to refer to the original publication, respectively.
The data is manually extracted from literature and verified by curators concerning standards, formats, vocabularies and units. The data extracted from literature is unified with complementing information collected from other resources.
Up to now, more than 1600 articles have been analyzed. The database contains about 7500 entries, referring to more than 1900 reactions and about 300 organisms. “In the long run”, says Isabel Rojas, “we want to make SABIO-RK the encyclopaedia of reaction kinetics.”
SABIO-RK is will be made freely available online for scientific purposes as of May 3, 2006.
http://sabiork.villa-bosch.de/
Scientific contact:
Dr. Isabel Rojas
Group Leader
EML Research gGmbH
Tel: +49-6221-533-231
Fax: +49-6221-533-298
[email protected]
Further information:
Dr. Peter Saueressig
EML Research gGmbH
Public Relations
Tel: +49-6221-533-245
Fax: +49-6221-533-198
[email protected]
The EML Research gGmbH (www.eml-research.de) is a non-profit institute conducting research in Information Technology and its applications. A strong focus is set on bioinformatics. Research is carried out in close collaboration with universities and other research institutes. EML Research projects are supported by the Klaus Tschira Foundation (KTS) (www.kts.villa-bosch.de), as well as by the European Union, the German Ministry of Research and Education (BMBF) and by the German Research Foundation (DFG). EML Research is a partner in the first German Center for Modeling and Simulation in the Biosciences (BIOMS, www.bioms.de). KTS and EML Research are housed in the Villa Bosch in Heidelberg, the former residence of Nobel Prize laureate Carl Bosch (1874 - 1940).
|
