Abstract
BackgroundToday, 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.ResultsAcknowledging 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 , the BioDOM library can be obtained at .ConclusionThe 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.
Highlights
Today, there is a growing need in bioinformatics to combine available software tools into chains, building complex applications from existing single-task tools
We describe some of these XML schemas and show examples of their application
The BioDOM library contains one Java class for each natively supported XML format, which implements methods to create the corresponding data structure by adding the necessary parts to the new document or importing data from ordinary data formats to XML elements. Each of these classes is based on the abstract class AbstractBioDOM, which provides commonly required methods for all converters, e.g. for setting and getting the documents object model (DOM) content, validating the document against an XML schema or creating a string representation of the XML data contained in the object
Summary
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, 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
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