XML schemas for common bioinformatic data types and their application in workflow systems.
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.
Seibel
Philipp N
PN
Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany. philipp.seibel@biozentrum.uni-wuerzburg.de <philipp.seibel@biozentrum.uni-wuerzburg.de>
Krüger
Jan
J
Hartmeier
Sven
S
Schwarzer
Knut
K
Löwenthal
Kai
K
Mersch
Henning
H
Dandekar
Thomas
T
Giegerich
Robert
R
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