Exposure to environmental chemicals and drugs may have a negative effect on human health. An essential step towards understanding the effect of chemicals on human health is to identify all possible molecular targets of a given chemical. Recently, various network-oriented chemical pharmacology approaches have been published. However, these methods limit the protein prediction to already known molecular drug targets. New findings can for example be made by using high-confidence protein-protein association databases. Here, we describe a generic, computational systems biology model with the aim of understanding the underlying molecular mechanisms of chemicals and the biological pathways they perturb. We present a novel and complementary approach to existing models by integrating toxicogenomics data, chemical structures, protein-protein interaction data, disease information and functional annotation of proteins. The high confidence protein-protein association network proposed reveals unexpected connections between chemicals and diseases or human proteins. We provide literature support to demonstrate the validity of some predictions, and thereby illustrate the power of an approach that integrates toxicogenomics data with other data types.