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GOSAP: Gene Ontology Based Semantic Alignment of Biological Pathways
University of Skövde, School of Humanities and Informatics.
University of Skövde, School of Humanities and Informatics.
2005 (English)Report (Other academic)
Abstract [en]

A large number of biological pathways have been assembled in later years, and are being stored in databases. Hence, the need for methods to analyse these pathways has emerged. One class of methods compares pathways, in order to discover parts that are evolutionary conserved between species or to discover intra-species similarites. Most previous work has been focused on methods targeted at metabolic pathways utilising the EC enzyme hierarchy. Here, we propose a Gene Ontology (GO) based approach for finding semantic local alignments when comparing paths in biological pathways where the nodes are gene products. The method takes advantage of all three sub-ontologies, and uses a measure of semantic similarity to calculate a match score between gene products. Our proposed method is applicable to all types of biological pathways, where nodes are gene products, e.g. regulatory pathways, signalling pathways and metabolic enzyme-to-enzyme pathways. It would also be possible to extend the method to work with other types of nodes, as long as there is an ontology or abstraction hierarchy available for categorising the nodes. We demonstrate that the method is useful for studying protein regulatory pathways in S. cerevisiae, as well as metabolic pathways for the same organism.

Place, publisher, year, edition, pages
Skövde: Institutionen för kommunikation och information , 2005. , 8 p.
Series
IKI Technical Reports, HS-IKI-TR-05-005
National Category
Information Science
Identifiers
URN: urn:nbn:se:his:diva-1260OAI: oai:DiVA.org:his-1260DiVA: diva2:2396
Available from: 2008-06-17 Created: 2008-06-17 Last updated: 2012-12-17Bibliographically approved

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fulltext(105 kB)348 downloads
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ac7e438cc138ed114f922f365acf00d5a62d628885396e5f9663348d75ee24ea3466b2dd
Type fulltextMimetype application/pdf

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Gamalielsson, JonasOlsson, Björn
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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