Figure 1. Formulation and use of GEMs as a four-step process.

Formulation and use of GEMs as a four-step process. Step 1, the process is based on a variety of high-throughput data sets (i.e., omics data) and a comprehensive assessment of the literature (i.e., bibliomic data). Step 2, all of the data types are used to reconstruct the list of biochemical transformations that make up a network as well as their genetic basis¹. In principal, the network is unique. Step 3, the data contained in the reconstruction can be formally represented (i.e., in the form of matrices and logical statements) that can be mathematically characterized by a variety of methods. Step 4, the computational model enables a broad spectrum of applications, as reviewed in this article. Figure adapted from²