Abstract
BackgroundIranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unified language system has been proposed for the concepts of this medicine up to the present time. Considering the extensive terminology in the numerous textbooks written by the scholars over centuries, comprehending the totality of concepts is obviously a very challenging task. To resolve this issue, overcome the obstacles, and code the concepts in a reusable manner, constructing an ontology of the concepts of Iranian traditional medicine seems a necessity.Construction and contentMakhzan al-Advieh, an encyclopedia of materia medica compiled by Mohammad Hossein Aghili Khorasani, was selected as the resource to create an ontology of the concepts used to describe medicinal substances. The steps followed to accomplish this task included (1) compiling the list of classes via examination of textbooks, and text mining the resource followed by manual review to ensure comprehensiveness of extracted terms; (2) arranging the classes in a taxonomy; (3) determining object and data properties; (4) specifying annotation properties including ID, labels (English and Persian), alternative terms, and definitions (English and Persian); (5) ontology evaluation. The ontology was created using Protégé with adherence to the principles of ontology development provided by the Open Biological and Biomedical Ontology (OBO) foundry.Utility and discussionThe ontology was finalized with inclusion of 3521 classes, 15 properties, and 20,903 axioms in the Iranian traditional medicine General Ontology (IrGO) database, freely available at http://ir-go.net/. An indented list and an interactive graph view using WebVOWL were used to visualize the ontology. All classes were linked to their instances in UNaProd database to create a knowledge base of ITM materia medica.ConclusionWe constructed an ontology-based knowledge base of ITM concepts in the domain of materia medica to help offer a shared and common understanding of this concept, enable reuse of the knowledge, and make the assumptions explicit. This ontology will aid Persian medicine practitioners in clinical decision-making to select drugs. Extending IrGO will bridge the gap between traditional and conventional schools of medicine, helping guide future research in the process of drug discovery.
Highlights
Iranian traditional medicine, known as Persian Medicine, is a holistic school of medicine with a long prolific history
One of the best and most comprehensive resources of Iranian traditional medicine (ITM), this semi-structured encyclopedia includes 1741 principal herbal, animal, and mineral preliminary monographs. They are described by their identity, Mizaj, actions and medicinal uses, dosage, adverse effects, substitutes, and corrigents
We constructed an ontology-based knowledge base of ITM concepts in the domain of materia medica to standardize and clearly demarcate concepts in this regard. This was accomplished according to the principles provided by the Open Biological and Biomedical Ontology (OBO) foundry using Protégé 5.5.0
Summary
We constructed an ontology-based knowledge base of ITM concepts in the domain of materia medica to standardize and clearly demarcate concepts in this regard. Molecular properties of herbal compounds have recently been studies by machine learning approaches and found to have associations with meridians in TCM, providing a deeper insight and rationales for classifications of this traditional medical system [38, 39] It seems that the knowledge and experience provided by ITM can help reduce the expenses and time consumed in the process of developing new drugs from natural sources. The efficacy of this method would be even higher in a more organized and standardized model of traditional medicine. IrGO can be used to investigate similarities in chemical
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