In response, several software projects became available to offer computer-assisted data and software integration. Notable among these are G2N, GeneMANIA, STRING, Ingenuity,Tenuifoliside-C and pISTiL softwares. Though, most of them show some limitations. pISTil works well on chromatograms processing and partial annotation, but lacks the connection to visualization and analysis of interaction networks. The other software work well on the integration of a variety of bioinformatic tools with focus on the interaction networks, but lack the chromatograms processing feature or are restricted to a small number of model organisms and types of molecules. Here we present the Integrated Interactome System, a new platform integrating a variety of tools and data sources used in systems biology analyses. It comprises a pipeline that receives raw sequence data from screening methods based on Sanger sequencing, like yeast two-hybrid system, or lists of proteins/genes, metabolites and drugs of interest, which are automatically processed, annotated and linked to interaction networks that can be Sibiricose-A6 filtered by the scoring system proposed by mathematical approaches, and evaluated according to expression/concentration fold change values and to the enriched biological processes and pathways in the network. As major advantages over other systems, IIS supports the entire data analysis of experiments such as two-hybrid assays, besides other omics approaches, from the sequencing all the way to generating publication-ready interaction networks and annotation tables. In the process, all the challenges related to this type of experiment are addressed: processing/assembling reads, mapping them to the correct gene, automatically retrieving annotations from multiple resources and interactors from nine public databases, assigning annotations and interactions via orthologs if required, and building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization, topological metrics and enriched biological processes and pathways. Each one of those tasks being very time-consuming and hard to manually integrate using separate different tools.