Computational framework for developing molecular connectivity maps. The framework consists of three major components: disease protein network, disease-disease network and disease biomarker network. The first component takes the inputs from database and literature and outputs a disease protein network (DPN). The second component takes the input from DPN and generates the output of positively scored disease-disease network (DDN) using scoring algorithm. Further, the second component was used to generate sub-component of common pathway network (CPN). The final disease biomarker network (DBN) component was generated from DPN showing proteins specific to diseases.