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Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology. (IDA/ADIT)ORCID iD: 0000-0002-9084-0470
2005 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, no 24, 4401-4407 p.Article in journal (Refereed) Published
Abstract [en]

Motivation: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. Results: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.

Place, publisher, year, edition, pages
Oxford University Press, 2005. Vol. 21, no 24, 4401-4407 p.
National Category
Computer Science
Identifiers
URN: urn:nbn:se:liu:diva-29663DOI: 10.1093/bioinformatics/bti718ISI: 000233849400013PubMedID: 16234320Local ID: 15044OAI: oai:DiVA.org:liu-29663DiVA: diva2:250480
Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2017-12-13Bibliographically approved

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Strömbäck, LenaLambrix, Patrick

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  • de-DE
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