Cellular functions rely on the interactions of their chemical constituents. Various high-throughput experimental methods now allow us to determine the chemical composition of cells on a genome-scale. These methods include whole-genome sequencing and annotation (genomics), the measurement of the messenger RNA molecules that are synthesized under a given condition (transcriptomics), the protein abundance, interactions, and functional states (proteomics),measurements of the presence and concentration of metabolites (metabolomics), and metabolic fluxes (fluxomics). In addition, methods now exist to determine the binding sites of proteins on the DNA (location analysis), to determine transcription start sites (TSSs), transcription breakage points, and the location of ribosomes on the transcripts. Furthermore, the physical location of protein products and segments of the DNA can be determined using various fluorescent reporting molecules. All these omic data types along with bibliomic data (primary literature information) enable the reconstruction of the biochemical reaction networks that operate in cells. Part I will discuss the process of network reconstruction, that effectively amounts to a 2D annotation of genomes.