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Journal Article

Data integration using scanners with SQL output--the bioscanners project at sourceforge

MPS-Authors

Friemel,  M.
Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons50470

Poustka,  A. J.
Evolution and Development (Albert Poustka), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons50458

Panopoulou,  G.
Evolution and Development (Albert Poustka), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Groth.pdf
(Any fulltext), 956KB

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Citation

Groth, D., Hartmann, S., Friemel, M., Hill, N., Muller, S., Poustka, A. J., et al. (2010). Data integration using scanners with SQL output--the bioscanners project at sourceforge. Journal of Integrative Bioinformatics, 7(3), e122-e122. doi:10.2390/biecoll-jib-2010-122.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0010-7C7C-9
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.