From knowledge networks to biological models

Chapters in this book describe building mechanistic models for various human diseases and conditions. While each chapter provides novel insights into the disease mechanism and should be of interest to any expert in this disease, we note that the authors in this book have never published articles about the disease described in their chapter and have never performed any experiments to study the disease. All authors have learned and advanced the understanding of the disease mechanism either through analysis of knowledge networks or through analysis of publicly available gene expression datasets using knowledge networks. All chapters also have in common the use of Pathway Studio software from Ariadne Genomics. Pathway Studio provides access to the biological knowledge networks and tools for their navigation and analysis. Most knowledge in the Pathway Studio database is extracted automatically from scientific literature using MedScan information extraction technology. While MedScan is thoroughly described in publications from Ariadne Genomics, the goal of this book is to show how to use the extracted information for knowledge inference, for building mechanistic models, and for learning how to use the model and knowledge networks to make more informed predictions about disease targets and biomarkers. We emphasize that while every model in this book required MedScan-extracted knowledge networks, Pathway Studio also allows import and navigation of additional knowledge from other sources and databases. Some examples of additional knowledge - protein homology network or network of physical interaction imported from public PINA database - are described in the chapters about cholestasis and gastric cancer models.