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An Extension of XQuery for Graph Analysis of Biological Pathways
Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology. (IDA/ADIT)
Rostock University.
2009 (English)In: Proc. The First International Conference on Advances in Databases, Knowledge, and Data Applications, DBKDA 2009,, 2009, 22-27 p.Conference paper, Published paper (Refereed)
Abstract [en]

 The vast quantity of scientific data produced in life sciences demands the use of sophisticated storage and analysis techniques. In particular, for biological pathways graph analysis plays an important role and data is commonly available in XML-based formats. Thus, there is a growing need to make analysis capabilities available through query languages for XML. This paper presents an approach to extend XQuery for graph analysis with focus on data for biological pathways. A graph model is introduced within the XQuery environment. New built-in functions define the available operations on the graph model. XQuery expressions can be utilized to populate graphs with data and execute graph algorithms. Graph data and results of algorithms can be accessed in an XML representation for further processing. In addition, a reference mechanism can be used to preserve associations from graph data to the original XML data. The approach has been implemented as an extension to exist. First evaluations of the implementation show that the introduced approach is practical and efficient for reaction networks with several thousand vertices and edges.

Place, publisher, year, edition, pages
2009. 22-27 p.
Keyword [en]
Biological Pathways, XML, XQuery, Graph Management, Databases
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:liu:diva-60207DOI: 10.1109/DBKDA.2009.16ISBN: 978-0-7695-3550-0 (print)OAI: oai:DiVA.org:liu-60207DiVA: diva2:355664
Conference
Proc. The First International Conference on Advances in Databases, Knowledge, and Data Applications, DBKDA 2009
Available from: 2010-10-07 Created: 2010-10-07 Last updated: 2010-10-12

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Strömbäck, Lena

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CiteExportLink to record
Permanent link

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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf