Molecular Biology and Pathogenicity of Mycoplasmas (PDF)

for the biological researcher. In this chapter, we provide an overview of available data resources and relevant tools for extracting pathway-related information from the most widely used databases and briefly explain their usage. We will also discuss some of the systems and methods, both established and new, to support the process of examination and understanding of the data. We will revise several of the methods and problems related to the integration, handling and interpretation of biochemical data. As an introduction to data modelling, we present a small example related to the modelling of enzymatic reactions. This is meant to raise awareness of the importance of structuring data. It should give researchers, who have no experience in creating databases, a rough idea of what they could gain from putting their data into an integrated system.

2. BIOCHEMICAL DATABASES

The genomes of Mycoplasma pneumoniae (M.pn.) and Mycoplasma genitalium (M.gen.) are widely viewed as a blueprint for a cell with a minimal metabolism. The availability of data generated from the sequencing of their genomes and results from both comparative genome analysis and experiments, such as global transposon mutagenesis (14), make them a sensible choice to study methods for pathway analysis and data integration. There are several databases – accessible through the World Wide Web (WWW) – that contain information about biochemical pathways, to different extends and with different focuses (see Appendix). With the growing amount of information related to biochemical reactions and thus with the growing interest towards the study of biochemical networks, the number of projects and databases (or data collections)i dealing with biochemical pathways is rapidly expanding. This means that, like any other study, this short description of some of the existing biochemical pathway databases can only be a snapshot of the current stand. We will mention a few of these databases, not all of which contain explicit information about mycoplasmas.