Using views of Systems Biology Cloud: application for model building

Abstract

A large and growing network ("cloud") of interlinked terms and records of items of Systems Biology knowledge is available from the web. These items include pathways, reactions, substances, literature references, organisms, and anatomy, all described in different data sets. Here, we discuss how the knowledge from the cloud can be molded into representations (views) useful for data visualization and modeling. We discuss methods to create and use various views relevant for visualization, modeling, and model annotations, while hiding irrelevant details without unacceptable loss or distortion. We show that views are compatible with understanding substances and processes as sets of microscopic compounds and events respectively, which allows the representation of specializations and generalizations as subsets and supersets respectively. We explain how these methods can be implemented based on the bridging ontology Systems Biological Pathway Exchange (SBPAX) in the Systems Biology Linker (SyBiL) we have developed.