title: Data integration using scanners with SQL output--the bioscanners project at sourceforge.
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.
authors.affiliation: Max Planck Insitute of Molecular PlantPhysiology, University of Potsdam, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany.
authors.forename: Detlef
authors.initials: D
authors.lastname: Groth
authors.forename: Stefanie
authors.initials: S
authors.lastname: Hartmann
authors.forename: Martin
authors.initials: M
authors.lastname: Friemel
authors.forename: Natascha
authors.initials: N
authors.lastname: Hill
authors.forename: Stefan
authors.initials: S
authors.lastname: Müller
authors.forename: Albert J
authors.initials: AJ
authors.lastname: Poustka
authors.forename: Georgia
authors.initials: G
authors.lastname: Panopoulou
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D020407:Internet; D011381:Programming Languages; D013223:Statistics as Topic; D013997:Time Factors