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BioPatML : pattern sharing for the genomic sciences

Maetschke, Stefan, Towsey, Michael W., & Hogan, James M. (2008) BioPatML : pattern sharing for the genomic sciences. In 2008 Microsoft eScience Workshop, 7-9 December 2008., University Place Conference Center & Hotel, Indianapolis. (Unpublished)

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Abstract

Computational biology increasingly demands the sharing of sophisticated data and annotations between research groups. Web 2.0 style sharing and publication requires that biological systems be described in well-defined, yet flexible and extensible formats which enhance exchange and re-use. In contrast to many of the standards for exchange in the genomic sciences, descriptions of biological sequences show a great diversity in format and function, impeding the definition and exchange of sequence patterns. In this presentation, we introduce BioPatML, an XML-based pattern description language that supports a wide range of patterns and allows the construction of complex, hierarchically structured patterns and pattern libraries. BioPatML unifies the diversity of current pattern description languages and fills a gap in the set of XML-based description languages for biological systems. We discuss the structure and elements of the language, and demonstrate its advantages on a series of applications, showing lightweight integration between the BioPatML parser and search engine, and the SilverGene genome browser. We conclude by describing our site to enable large scale pattern sharing, and our efforts to seed this repository.

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ID Code: 27327
Item Type: Conference Item (Presentation)
Keywords: Computational biology, genomics, pattern definition, XML
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400) > Genome Structure and Regulation (060407)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Past > Schools > School of Software Engineering & Data Communications
Copyright Owner: Copyright 2008 [please consult the authors]
Deposited On: 11 Sep 2009 07:53
Last Modified: 10 Jun 2010 00:00

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