| Literature DB >> 33863373 |
Ayeh Naghizadeh1, Mahdi Salamat1, Donya Hamzeian1, Shaghayegh Akbari1, Hossein Rezaeizadeh1, Mahdi Alizadeh Vaghasloo1, Reza Karbalaei2, Mehdi Mirzaie3, Mehrdad Karimi1, Mohieddin Jafari4.
Abstract
BACKGROUND: Iranian 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 CONTENT: Makhzan 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 DISCUSSION: The 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.Entities:
Keywords: Herbal medicine; Iranian traditional medicine; Knowledge base; Mizaj; Ontology; Persian medicine; Unani medicine
Year: 2021 PMID: 33863373 PMCID: PMC8052758 DOI: 10.1186/s13326-021-00237-1
Source DB: PubMed Journal: J Biomed Semantics
Fig. 1Mizaj types. The vertical axis is an indicator of active qualities with points lower than balanced being cold and higher points being hot. The horizontal axis displays passive qualities, with the dry quality to the left. The nine main mizaj types of ITM include balanced, hot, cold, dry, wet, hot-wet, cold-wet, hot-dry, cold-dry. Other Mizaj types illustrated in the second and third inner circles of the figure are more precise indications of degrees used in descriptions of the Mizaj of drugs in Makhzan al-Advieh with the green zone in the balanced region and the light red/blue zones counting as unbalanced in one active/passive quality. Smaller icons of qualities demonstrate a balanced-inclined (slight) quality while larger ones are indicative of an unbalanced quality, which can lie in a range between first to fourth degree. Mizaj types with horizontal stripes are unbalanced in one of the passive qualities, while the vertically-striped are unbalance in an active quality. The four checkered Mizaj types are unbalanced in both their active and passive quality
Fig. 2Degrees of qualities. The degrees used to describe each of the four qualities (hotness, coldness, wetness, dryness) range from slight to maximum in fourth degree. This classification based on the potency to induce changes in Mizaj and body functions of a young, healthy person upon consumption
Fig. 3Upper level classes of Iranian traditional medicine general ontology (IrGO) incorporated into Basic Formal Ontology (BFO). The number of direct and total subclasses have been specified for each class
Fig. 4A conspectus of Iranian traditional medicine general ontology (IrGO), illustrating upper classes in taxonomies of Mizaj, action, disease, and body entity along with properties relating them to medicinal substances. The annotation properties provided for IrGO classes are depicted in the bottom diagram
Base metrics of IrGO calculated by Ontometrics
| Metrics | Mizaj | Action | Body entity | Disease | IrGO |
|---|---|---|---|---|---|
| Axiom | 1046 | 4273 | 1698 | 13,562 | 20,903 |
| Logical axiom count | 143 | 614 | 384 | 2455 | 3627 |
| Class count | 123 | 609 | 289 | 2435 | 3521 |
| Object property count | 13 | ||||
| Data property count | 2 | ||||
| Annotation property count | 11 | ||||
| Class axioms | |||||
| SubClassOf | 131 | 607 | 376 | 2448 | 3615 |
| Disjoint classes axioms count | 4 | ||||
| Object property axioms | |||||
| SubObjectPropertyOf axioms count | 4 | ||||
| Inverse object properties axioms count | 2 | ||||
| Asymmetric object property axioms count | 2 | ||||
| Annotation axioms | |||||
| Annotation assertion | 764 | 3034 | 1008 | 8656 | 13,741 |
| Inheritance richness | 1.06 | 1.00 | 1.30 | 1.01 | 1.02 |
| Relationship richness | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 |
| Axiom/class ratio | 8.50 | 7.01 | 5.87 | 5.56 | 5.94 |
| Calss/relation | 0.83 | 1.00 | 0.76 | 0.99 | 0.97 |
Fig. 5Pairwise calculation of intersect actions between drugs with cold dry Mizaj (coldness and dryness both in third degree) and sample drugs. Mean intersect for each group (1.18 for selection versus 0.52 for sample) is demonstrated as a dashed line