Drug repositioning — detection of new uses of existing drugs — is an emerging trend in pharmaceutical industry. It essentially is a multiple aspect process of analyzing large-scale heterogeneous data for exploiting advantage of off-targets of the existing drugs. Three kinds of omics, phenomic and drug data are often integrated and used to study drug repositioning. The recent prevalence of electronic medical records (EMRs) makes it become an extremely significant resource of phenomic data for drug repositioning in the post-market stage. However, there is still no generic process and method to this end. This work aims to establish such a process and method. The paper addresses the solution of the first two problems in this complex process.