Ariadne's ChemEffect and Pathway Studio knowledge base.

IMPORTANCE OF THE FIELD: Drug discovery and development is a very complex and costly process. Understanding the detailed molecular mechanisms of a disease and drug actions can make it more efficient not only for new target discovery but also for lead prioritization, drug repositioning and development of biomarkers for drug efficacy and safety. Access to formalized knowledge about functions of proteins and small molecules is crucial for rationalization of the drug development process, and scientific publications are the main source of this knowledge. Protein knowledge networks capturing protein functions, protein-protein relations and organization of proteins in complex cellular sub-systems are making their way into modern drug discovery. Chemical networks representing multiple aspects of chemical functional information integrated into a protein systems biology network is even more advanced and promising paradigm. AREAS COVERED IN THIS REVIEW: This review describes utilization of literature-derived protein and chemical functional knowledge bases in drug development. WHAT THE READER WILL GAIN: Readers will gain an understanding of how integrated protein and chemical knowledge networks can be used for understanding and building the models of cellular events, disease mechanisms, and drug actions, finding biomarkers of drug efficacy and safety, as well as interpretation of high-throughput gene expression, proteomic and metabolomic experiments. TAKE HOME MESSAGE: Integrated literature-derived protein and chemical knowledge bases can rationalize many aspects of drug development process including drug repositioning and biomarker design.