Abstract: The present application relates to methods and systems of identifying molecules or processes of biological interest by using knowledge discovery in biological data. In particular, the present application describes new methods of creating a biological map, new methods of codifying such map, new methods of analyzing such map and new methods of identifying molecules and processes of biological interest. The present application provides methods and systems to identify new and useful direct or indirect therapeutic targets, molecular modulators, adverse events effectors, disease biomarkers, genetic biomarkers, safety-related biomarkers, diagnostic molecules, hormones, metabolites, or metabolic effectors of any type.