The Anatomical Therapeutic Chemical (ATC) classification system is frequently used to classify drugs according to an encoding system that considers the organ or system on which they act on and/or their therapeutic class and chemical characteristics. Motivated by the maintenance of a French drug database, we have transformed, using an inductive approach, the chemical layer of this classification into an OWL knowledge base. Using this knowledge base, we have been able to design interesting novel application functionalities. Nevertheless, these functionalities require that drugs are annotated in a different way than is generally done right now. In this paper, we highlight several French databases that are not fully benefiting from their ATC usage, present our annotation best practice and emphasize on the gains of its adoption.