Iranian traditional medicine, an elaborate holistic system of healing, is grounded in a philosophical basis. The numerous concepts and their intricate relationships are described in numerous textbooks by the scholars. However, embracing the totality of this rich school of thought is challenging due to the large amount of data in various time periods and ambiguities resulting from lack of consensus or semantic change and the evolution of word usage. In order to arrange for an explicit, shared and common understanding of Iranian traditional medicine concepts and facilitate connection with contemporary medicine to offer potentials for future research, the ontology of the key concepts mentioned in descriptions of materia medica will be extracted. Subontologies include mizaj, actions, functions, dosage, harms, substitutes, and enhancements and will be based on the 1744 monographs described in Makhzan-al-Adviah, an encyclopedia of materia medica compiled by Mohammad Hossein Aghili Khorasani in the 18th century. Iranian traditional medicine general ontology (IrGO) will enable reuse of the knowledge in this field, make the assumptions explicit and finally gain new knowledge by analyzing the concepts and their relationships.