Drug discovery is a lengthy, expensive and difficult process. Indentifying and understanding the hidden relationships among drugs, genes, proteins, and diseases will expedite the process of drug discovery. In this paper, we propose an effective methodology to discover drug-related semantic relationships over large-scale distributed web data in medicine, pharmacology and biotechnology. By utilizing semantic web and distributed system technologies, we developed a novel hierarchical knowledge abstraction and an efficient relation discovery protocol. Our approach effectively facilitates the realization of the full potential of harnessing the collective power and utilization of the drug-related knowledge scattered over the Internet.