Section 2: A framework for categorizing and classifying network biology approaches.
When conducting network-based omics analysis, the choice of prior knowledge network can impact the results of the analysis20. Given the multitude of network databases available, it is useful to have a framework that can guide researchers to make informed decisions. Herein we define three ‘tasks’ which describe the overarching goal(s) of network-based approaches to omics data analysis. These tasks include network inference, explanation extraction, and phenotype prediction. Additionally, we define a framework for classifying network models into five levels of increasing level of detail: Gene Sets, Interaction Networks, Activity Flow, Process Description, and Quantitative Models (Figure 2). Finally, we review a sampling of network-based approaches at each of these five levels to contextualize the framework. Our classification of networks and the approaches that use them is intentionally broad to provide a high-level organization allowing for nuances in this rapidly evolving area of research.