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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. Conclusion: 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. Background Today, bioinformatic analyses are becoming more and more complex tasks. Large scale analyses usually integrate several independently calculated results. A good example for such a complex application is automated genome annotation, a process starting from detecting promotor regions and automatically predicting genes to complete functional annotation of novel genomes [1-3]. To accomPublished: 06 November 2006 BMC Bioinformatics 2006, 7:490 doi:10.1186/1471-2105-7-490 Received: 21 June 2006 Accepted: 06 November 2006 This article is available from: http://www.biomedcentral.com/1471-2105/7/490 © 2006 Seibel et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.