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Using an ontology to enhance metabolic or signaling pathway comparisions by biological and chemical knowledge
University of Skövde, School of Humanities and Informatics.
2006 (English)Student thesis
Abstract [en]

Motivation:

As genome-scale efforts are ongoing to investigate metabolic networks of miscellaneous organisms the amount of pathway data is growing. Simultaneously an increasing amount of gene expression data from micro arrays becomes available for reverse engineering, delivering e.g. hypothetical regulatory pathway data. To avoid outgrowing of data and keep control of real new informations the need of analysis tools arises. One vital task is the comparison of pathways for detection of similar functionalities, overlaps, or in case of reverse engineering, detection of known data corroborating a hypothetical pathway. A comparison method using ontological knowledge about molecules and reactions will feature a more biological point of view which graph theoretical approaches missed so far. Such a comparison attempt based on an ontology is described in this report.

Results:

An algorithm is introduced that performs a comparison of pathways component by component. The method was performed on two selected databases and the results proved it to be not satisfying using it as stand-alone method. Further development possibilities are suggested and steps toward an integrated method using several approaches are recommended.

Availability:

The source code, used database snapshots and pictures can be requested from the author.

Place, publisher, year, edition, pages
Skövde: Institutionen för kommunikation och information , 2006. , 17 p.
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:his:diva-32OAI: oai:DiVA.org:his-32DiVA: diva2:2683
Presentation
(English)
Uppsok
Physics, Chemistry, Mathematics
Supervisors
Examiners
Available from: 2006-11-06 Created: 2006-11-06 Last updated: 2009-12-11

Open Access in DiVA

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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • 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