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Design and Development of Novel Metabolomic Databases and Tools Open Access


Other title
Systems Biology
Metabolic Pathways
Drug Metabolism
Saccharomyces cerevisiae
Type of item
Degree grantor
University of Alberta
Author or creator
Jewison, Timothy
Supervisor and department
Wishart, David (Computing Science)
Examining committee member and department
Lin, Guohui (Computing Science)
Joel, Weiner (Biochemistry)
Wishart, David (Computing Science)
Department of Computing Science

Date accepted
Graduation date
Master of Science
Degree level
Metabolomics involves the high throughput characterization of small molecules or metabolites in cells, tissues and organisms. To interpret, store and exchange metabolomic data it is necessary to have comprehensive, electronically accessible databases that can be used to handle both the experimental data and the associated biological and chemical information needed to identify, quantify and interpret the meaning of those metabolites. As the field of metabolomics matures the need for improved databases is growing rapidly. In particular, there is a serious shortage of organism-specific metabolomic databases and a significant bottleneck with regard to the breadth and depth of known metabolic pathways needed to interpret metabolomic data. Consequently the main objective of my thesis project was to develop novel software and innovative databases to address these two metabolomics bottlenecks. In particular, I focused on the development of (i) species specific compound databases, (ii) the creation of graphical pathway databases and (iii) the design and implementation of innovative pathway visualization techniques and tools. This thesis describes the design and implementation of the Yeast Metabolome Database (YMDB) (
) an example of an organism-specific metabolomic database, and the Small Molecule Pathway Database (SMPDB) ( http://smpdb
. ca) an example of a comprehensive graphical pathway database. It also describes the PathWhiz system, a novel web server for the creation and visualization of biological pathways.

Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication
Jewison T, Knox C, Neveu V, Djoumbou Y, Guo AC, Lee J, Liu P, Mandal R, Krishnamurthy R, Sinelnikov I, Wilson M, Wishart DS. (2012) YMDB: the Yeast Metabolome Database. Nucleic Acids Res. 40(Database issue):D815-20.Jewison T, Su Y, Disfany FM, Liang Y, Knox C, Maciejewski A, Poelzer J, Huynh J, Zhou Y, Arndt D, Djoumbou Y, Liu Y, Deng L, Guo AC, Han B, Pon A, Wilson M, Rafatnia S, Liu P, Wishart DS. (2014) SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database. Nucleic Acids Res. 42(1):D478-84.

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