Enzyme kinetics informatics: from instrument to browser

A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw experimental data from which the parameters were calculated. This is largely due to the lack of software o...

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Bibliographic Details
Published in:The FEBS journal 2010-09, Vol.277 (18), p.3769-3779
Main Authors: Swainston, Neil, Golebiewski, Martin, Messiha, Hanan L, Malys, Naglis, Kania, Renate, Kengne, Sylvestre, Krebs, Olga, Mir, Saqib, Sauer-Danzwith, Heidrun, Smallbone, Kieran, Weidemann, Andreas, Wittig, Ulrike, Kell, Douglas B, Mendes, Pedro, Müller, Wolfgang, Paton, Norman W, Rojas, Isabel
Format: Article
Language:English
Subjects:
Automatic Data Processing
Biochemistry
Bioinformatics
data analysis
Data Mining
Databases, Protein
enzyme
Enzymes
Enzymes - metabolism
Internet
Kinetics
metadata
Recombinant Proteins - metabolism
Software
Systems Biology - methods
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Summary:A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw experimental data from which the parameters were calculated. This is largely due to the lack of software or standards to support the capture, analysis, storage and dissemination of such experimental data. Introduced here is an integrative system to manage experimental enzyme kinetics data from instrument to browser. The approach is based on two interrelated databases: the existing SABIO-RK database, containing kinetic data and corresponding metadata, and the newly introduced experimental raw data repository, MeMo-RK. Both systems are publicly available by web browser and web service interfaces and are configurable to ensure privacy of unpublished data. Users of this system are provided with the ability to view both kinetic parameters and the experimental raw data from which they are calculated, providing increased confidence in the data. A data analysis and submission tool, the kineticswizard, has been developed to allow the experimentalist to perform data collection, analysis and submission to both data resources. The system is designed to be extensible, allowing integration with other manufacturer instruments covering a range of analytical techniques.
ISSN:1742-464X
1742-4658
DOI:10.1111/j.1742-4658.2010.07778.x