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.