WikiPathways: Integrating Pathway Knowledge with Clinical Data

Abstract

Throughout the chapters in this book, pathways are used to visualize how genetically inheritable metabolic disorders are related. These pathways provide common conceptual models which explain groups of chemical reactions within their biological context. Visual representations of the reactions in biological pathway diagrams provide intuitive ways to study the complex metabolic processes. In order to link (clinical) data to these pathways, they have to be understood by computers. Understanding how to move from a regular pathway drawing to its machine-readable counterpart is pertinent for creating proper models. This chapter outlines the various aspects of the digital counterparts of the pathway diagrams in this book, connecting them to databases and using them in data integration and analysis. This is followed by three examples of bioinformatics applications including a pathway enrichment analysis, a biological network extension, and a final example that integrates pathways with clinical biomarker data.