title: XML schemas for common bioinformatic data types and their application in workflow systems.
abstract: BACKGROUND
  Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats.
  
  
  RESULTS
  Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net.
  
  
  CONCLUSIONS
  The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany. philipp.seibel@biozentrum.uni-wuerzburg.de <philipp.seibel@biozentrum.uni-wuerzburg.de>
authors.forename: Philipp N
authors.initials: PN
authors.lastname: Seibel
authors.forename: Jan
authors.initials: J
authors.lastname: Krüger
authors.forename: Sven
authors.initials: S
authors.lastname: Hartmeier
authors.forename: Knut
authors.initials: K
authors.lastname: Schwarzer
authors.forename: Kai
authors.initials: K
authors.lastname: Löwenthal
authors.forename: Henning
authors.initials: H
authors.lastname: Mersch
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003628:Database Management Systems; D016247:Information Storage and Retrieval; D011381:Programming Languages; D016415:Sequence Alignment; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface