Systems biology resources arising from the human metabolome project

Abstract

This chapter provides an overview of a number of the on-line, open-access databases that have arisen from the Human Metabolome Project (HMP). It is primarily intended to show how these resources can be used to easily link genetic, proteomic or physiological data to human metabolomic data. The HMP was started in 2005 and continues to this day. It was mandated to use advanced experimental methods along with literature/data mining to quantitatively characterize and describe as many human metabolites in common biofluids and tissues as possible. The HMP was also tasked with linking this metabolomic information to diseases, mechanisms, genes/proteins and pathways. These data sets have been made public through a variety of on-line, continuously updated databases including the Human Metabolome Database (HMDB), DrugBank, the Toxin, Toxin-Target Database (T3DB), FooDB and the Small Molecule Pathway Database (SMPDB). The integration of such a large quantity of proteomic, genomic and metabolomic data on humans has made these resources particular valuable for wide ranging applications from systems biology to medicine.