Metabolic Times

Two new computer databases relating to human metabolism appear to represent important contributions to the field of bioinformatics and will likely have a significant impact on disease diagnosis and treatment. Researchers with the University of Alberta have completed the first draft of the human metabolome, which forms part of the Human Metabolome Database (HMDB), and researchers with the University of California (UCSD) have recently released a computer model of human metabolism. Metabolism refers to the range of biochemical processes that take place within the human body. The byproduct of these biochemical processes are small-molecule chemicals or metabolites. The "metabolome" is the complete complement of all the metabolites found in, or produced by, an individual. The human metabolome is thus the chemical equivalent of the human genome. The Human Metabolome Project began in Canada in 2004, and involved the compilation and characterization of 2,500 metabolites, 1,200 drugs and 3,500 food components found in the human body. This data was entered into the HMDB, which is freely available on the Web. The HMDB also includes approximately 5500 protein (and DNA) sequences linked to the metabolite entries, together with two additional databases, DrugBank and FooDB. As suggested by their names, DrugBank contains information on drugs while FooDB contains information on food components and additives. The HMDB may be used to ascertain the molecular basis of a disease. For example, researchers can use the data in the HMDB to determine the particular metabolites associated with any disease, and the genes associated with each metabolite. As more information is added to the database, it is expected that the identification and diagnosis of diseases will occur more efficiently. The computer model of human metabolism completed by UCSD's researchers is also available on the Web and includes every known human gene, metabolic reaction and metabolic product, each associated together. As with the HMDB, researchers can use UCSD's computer model to better understand the molecular basis of disease. The creator of UCSD's computer model, Professor Palsson, is quoted as stating that it may help drug companies discover drug compounds which have the same effects as a competitor's drugs, but which could avoid the competitor's patents. While this is a much sought-after goal, companies should work closely with their patent counsel to minimize the risk of patent infringement. To review Professor Palsson's article, visit: http://www.technologyreview.com/Biotech/18142/ To access UCSD's computer model of metabolism, see: http://bigg.ucsd.edu/main.pl To access the HMDB, visit: http://www.hmdb.ca/ Summary by: Lenni Carreiro