XML schemas for common bioinformatic data types and their application in workflow systems
Seibel PN, Krüger J, Hartmeier S, Schwarzer K, Löwenthal K, Mersch H, Dandekar T, Giegerich R (2006)
BMC Bioinformatics 7(1): 490.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Seibel, Philipp N.;
Krüger, JanUniBi;
Hartmeier, SvenUniBi;
Schwarzer, Knut;
Löwenthal, Kai;
Mersch, Henning;
Dandekar, Thomas;
Giegerich, RobertUniBi
Einrichtung
Abstract / Bemerkung
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.
Erscheinungsjahr
2006
Zeitschriftentitel
BMC Bioinformatics
Band
7
Ausgabe
1
Art.-Nr.
490
ISSN
1471-2105
Page URI
https://pub.uni-bielefeld.de/record/1773871
Zitieren
Seibel PN, Krüger J, Hartmeier S, et al. XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics. 2006;7(1): 490.
Seibel, P. N., Krüger, J., Hartmeier, S., Schwarzer, K., Löwenthal, K., Mersch, H., Dandekar, T., et al. (2006). XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics, 7(1), 490. https://doi.org/10.1186/1471-2105-7-490
Seibel, Philipp N., Krüger, Jan, Hartmeier, Sven, Schwarzer, Knut, Löwenthal, Kai, Mersch, Henning, Dandekar, Thomas, and Giegerich, Robert. 2006. “XML schemas for common bioinformatic data types and their application in workflow systems”. BMC Bioinformatics 7 (1): 490.
Seibel, P. N., Krüger, J., Hartmeier, S., Schwarzer, K., Löwenthal, K., Mersch, H., Dandekar, T., and Giegerich, R. (2006). XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics 7:490.
Seibel, P.N., et al., 2006. XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics, 7(1): 490.
P.N. Seibel, et al., “XML schemas for common bioinformatic data types and their application in workflow systems”, BMC Bioinformatics, vol. 7, 2006, : 490.
Seibel, P.N., Krüger, J., Hartmeier, S., Schwarzer, K., Löwenthal, K., Mersch, H., Dandekar, T., Giegerich, R.: XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics. 7, : 490 (2006).
Seibel, Philipp N., Krüger, Jan, Hartmeier, Sven, Schwarzer, Knut, Löwenthal, Kai, Mersch, Henning, Dandekar, Thomas, and Giegerich, Robert. “XML schemas for common bioinformatic data types and their application in workflow systems”. BMC Bioinformatics 7.1 (2006): 490.
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Wolf M, Achtziger M, Schultz J, Dandekar T, Muller T., RNA 11(11), 2005
PMID: 16244129
Wolf M, Achtziger M, Schultz J, Dandekar T, Muller T., RNA 11(11), 2005
PMID: 16244129
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.
Reeder J, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15294028
Reeder J, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15294028
REPuter: the manifold applications of repeat analysis on a genomic scale.
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R., Nucleic Acids Res. 29(22), 2001
PMID: 11713313
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R., Nucleic Acids Res. 29(22), 2001
PMID: 11713313
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