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Towards rule-based metabolic databases: a requirement analysis based on KEGG
Stockholm University, Faculty of Science, Stockholm Resilience Centre.
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Number of Authors: 5
2015 (English)In: International journal of data mining and bioinformatics, ISSN 1748-5673, Vol. 13, no 3, 289-319 p.Article in journal (Refereed) Published
Abstract [en]

Knowledge of metabolic processes is collected in easily accessable online databases which are increasing rapidly in content and detail. Using these databases for the automatic construction of metabolic network models requires high accuracy and consistency. In this bipartite study we evaluate current accuracy and consistency problems using the KEGG database as a prominent example and propose design principles for dealing with such problems. In the first half, we present our computational approach for classifying inconsistencies and provide an overview of the classes of inconsistencies we identified. We detected inconsistencies both for database entries referring to substances and entries referring to reactions. In the second part, we present strategies to deal with the detected problem classes. We especially propose a rule-based database approach which allows for the inclusion of parameterised molecular species and parameterised reactions. Detailed case-studies and a comparison of explicit networks from KEGG with their anticipated rule-based representation underline the applicability and scalability of this approach.

Place, publisher, year, edition, pages
2015. Vol. 13, no 3, 289-319 p.
Keyword [en]
metabolism, database, rule-based modelling, inconsistency check, cell models, KEGG, reaction balance, pathway analysis, ontology
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-123876DOI: 10.1504/IJDMB.2015.072103ISI: 000364232000005PubMedID: 26547981OAI: oai:DiVA.org:su-123876DiVA: diva2:878344
Available from: 2015-12-08 Created: 2015-12-08 Last updated: 2015-12-08Bibliographically approved

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Fetzer, Ingo
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Stockholm Resilience Centre
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