Dozens of drug terminologies and resources capture drug and/or drug class information; they range greatly in their coverage and their adequacy of representation. However, there are no transformative ways to link these resources together in a standard and formal fashion, which hinders data integration and data representation for supporting drug-related clinical and translational studies. In this study, we generated a standardized Pharmacological Class Profile Ontology, named PCPO, which integrates multiple drug resources in the Web Ontology Language (OWL). More specifically, we mapped two well-known drug class resources, Anatomical Therapeutic Chemical classification system (ATC) and National Drug File Reference Terminology (NDF-RT), as the pharmacological class backbone. Furthermore we extended the PCPO with individual clinical drug information extracted from RxNorm and Structured Product Labeling. In parallel, we calculated and compared chemical structure similarity for each drug pair from ATC and NDF-RT, and re-grouped drugs with a similar structure into a same drug class. PCPO will not only present big drug data into well-organized formal form, OWL with possible inference capability, but also potentially support computational drug repurposing application development.