Data integration using scanners with SQL output - The Bioscanners project at sourceforge

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doi doi:10.2390/biecoll-jib-2010-122
submission February 19, 2010
published March 25, 2010
NCBI PubMed PubMed ID 20375454

Detlef Groth, Stefanie Hartmann, Martin Friemel, Natascha Hill, Stefan Müller, Albert J Poustka and Georgia Panopoulou

Correspondence should be addressed to:
Detlef Groth
Bioinformatics Group, University of Potsdam, c/o Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm
ed.gpm.mlog-pmipm@nullhtorgd


Abstract

There is currently no standardized approach for parsing output that the numerous bioinformatical tools generate. Because the framework approach of the Bio-toolkits has some shortcomings, we searched for alternative approaches. To this end, we evaluated scanner generators for various programming languages with respect to their potential of standalone, small and fast applications that can easily delivered on any modern and many ancient operating system. We developed sample applications that generate standard SQL database code and thereby greatly simplify the parsing work of data integration and data analysis. At the sourceforge project page the source code and some binaries for a selection of our applications are freely available at http://bioscanners.sourceforge.net.

Reference

Detlef Groth, Stefanie Hartmann, Martin Friemel, Natascha Hill, Stefan Müller, Albert J Poustka and Georgia Panopoulou. Data integration using scanners with SQL output - The Bioscanners project at sourceforge. Journal of Integrative Bioinformatics, 7(3):122, 2010. Online Journal: http://journal.imbio.de/index.php?paper_id=122
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