Design and Development of Novel Metabolomic Databases and Tools

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) (http://ymdb.ca) 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.