An ontological framework for the formalization, organization and usage of TCM-Knowledge

Long, Hai; Zhu, Yan; Liu, Jia; Gao, Bo; Liu, Jing; Herre, Heinrich

doi:10.1186/s12911-019-0760-9

Cited by 11 publications

(14 citation statements)

References 6 publications

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“…In our work we developed a domain ontology for syndrome differentiation of psoriasis vulgaris. For this purpose, we used the ontology-editor Protégé and applied a top-down approach which adopts the framework of general formal ontology (GFO) and its middle-level core ontology GFO-TCM described in [17][18][19][20] .…”

Section: Construction Of Domain Ontology For Syndrome Differentiationmentioning

confidence: 99%

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Towards an ontology-based decision support system for syndrome-differentiation and treatment of Psoriasis Vulgaris in Traditional Chinese Medicine

Long¹,

Wang²,

Cui³

et al. 2020

Preprint

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Background: Psoriasis is a chronic, non-communicable, painful, disfiguring and disabling disease, which is not curable and strongly declines the patients’ quality of life (QoL). However, diagnose and treatment in traditional Chinese medicine (TCM) based on syndrome differentiation has been used in practice for a long time and has also achieved some effect. Though, up to now, only few studies are available reporting on the use of semantic technologies and pertain to knowledge systems that use TCM-syndrome differentiation for information retrieval and automated reasoning. Nowadays, the diagnosis in TCM relies mainly on the personal expertise and clinical experience of the doctors. For various reasons, misdiagnoses or missed diagnoses cannot be completely excluded, leading to unexpected results.Methods In the present paper, we developed a domain ontology for syndrome differentiation of psoriasis vulgaris (PV). For this purpose, we used the ontology editor Protégé and applied a top-down approach which adopts the framework of general formal ontology (GFO) and its middle-level core ontology GFO-TCM. Furthermore, we implemented a prototype which is based on this ontology. Additionally, we also used a case-database for CBR (Case Based Reasoning) combined with fuzzy pattern recognition.Results: A prototype for diagnosis and treatment of psoriasis vulgaris, named ONTOPV-system, is proposed which is based on the principle of syndrome differentiation and treatment in TCM; this system realizes an expert-assisted decision support method which relies on a domain ontology, uses fuzzy logic reasoning, and case retrieval and is intended to support clinical diagnostic decisions for TCM practitioners.Conclusions: We designed and implemented a prototype for psoriasis diagnosis in terms of syndrome differentiation. The system realizes the basic functionalities of data collection, querying, browsing and navigation, and supports rule-based knowledge reasoning and integrates approximative reasoning, based on CBR and fuzzy logic. The system provides users with clinical decision support for TCM syndrome differentiation in diagnosis of psoriasis. In addition, it comprises a domain knowledge base of psoriasis, which is developed in the GFO framework with good extensibility.

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Section: Construction Of Domain Ontology For Syndrome Differentiationmentioning

confidence: 99%

“…shows the basic hierarchy of the ontology. The relevant concepts has been explicitly introduced in our former papers [19][20] .…”

Section: ) Basic Conceptual Hierarchymentioning

confidence: 99%

Towards an ontology-based decision support system for syndrome-differentiation and treatment of Psoriasis Vulgaris in Traditional Chinese Medicine

Long¹,

Wang²,

Cui³

et al. 2020

Preprint

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“…One of the most comprehensive works in this regard is the traditional Chinese Medicine Language System (TCMLS), with over 120,000 concepts, 300,000 terms, and 1.27 million semantic relational links [ 7 ]. TCMLS is an extensive semantic network and thesaurus, which has recently been used to create a middle-level ontology of TCM concepts to strengthen the foundations for natural language processing, semantic retrieval, clinical decision making in traditional Chinese medicine [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

IrGO: Iranian traditional medicine General Ontology and knowledge base

et al. 2021

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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. Conclusion We 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.

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“…In their system, ontology was used to transform the implicit relations among syndromes into a machine-interpretable model and support diagnosis in traditional Chinese medicine. In order to explore the solution of integrating existing TCM terminologies, Long et al reported an ontological framework in 2019 for the formalization and organization of the TCM knowledge [ 17 ]. Their system, called GFO-TCM, is based on the framework of the General Formal Ontology (GFO), a top-level ontology that integrates Object and Process.…”

Section: Introductionmentioning

confidence: 99%

“…Their system, called GFO-TCM, is based on the framework of the General Formal Ontology (GFO), a top-level ontology that integrates Object and Process. A formal middle-level ontology that is compatible with both the TCM terminology and modern medical terminology standards is then proposed [ 17 ]. Compared to GFO, the Basic Formal Ontology (BFO) [ 18 ] is another top-level ontology that has recently been accepted as an ISO/IEC top-level ontology standard 21838 ( https://www.iso.org/standard/74572.html ).…”

Section: Introductionmentioning

confidence: 99%

TCDO: A Community-Based Ontology for Integrative Representation and Analysis of Traditional Chinese Drugs and Their Properties

Zhu

Gao

Liu

et al. 2021

Evidence-Based Complementary and Alternative Medicine

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Traditional Chinese drugs (TCDs) have been widely used in clinical practice in China and many other regions for thousands of years. Nowadays TCD’s bioactive ingredients and mechanisms of action are being identified. However, the lack of standardized terminologies or ontologies for the description of TCDs has hindered the interoperability and deep analysis of TCD knowledge and data. By aligning with the Basic Formal Ontology (BFO), an ISO-approved top-level ontology, we constructed a community-driven TCD ontology (TCDO) with the aim of supporting standardized TCD representation and integrated analysis. TCDO provides logical and textual definitions of TCDs, TCD categories, and the properties of TCDs (i.e., nature, flavor, toxicity, and channel tropism). More than 400 popular TCD decoction pieces (TCD-DPs) and Chinese medicinal materials (CMMs) are systematically represented. The logical TCD representation in TCDO supports computer-assisted reasoning and queries using tools such as Description Logic (DL) and SPARQL queries. Our statistical analysis of the knowledge represented in TCDO revealed scientific insights about TCDs. A total of 36 TCDs with medium or high toxicity are most densely distributed, primarily in Aconitum genus, Lamiids clade, and Fabids clade. TCD toxicity is mostly associated with the hot nature and pungent or bitter flavors and has liver, kidney, and spleen channel tropism. The three pairs of TCD flavor-nature associations (i.e., bitter-cold, pungent-warm, and sweet-neutral) were identified. The significance of these findings is discussed. TCDO has also been used to support the development of a web-based traditional Chinese medicine semantic annotation system that provides comprehensive annotation for individual TCDs. As a novel formal TCD ontology, TCDO lays out a strong foundation for more advanced TCD studies in the future.

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An ontological framework for the formalization, organization and usage of TCM-Knowledge

Cited by 11 publications

References 6 publications

Towards an ontology-based decision support system for syndrome-differentiation and treatment of Psoriasis Vulgaris in Traditional Chinese Medicine

Towards an ontology-based decision support system for syndrome-differentiation and treatment of Psoriasis Vulgaris in Traditional Chinese Medicine

IrGO: Iranian traditional medicine General Ontology and knowledge base

TCDO: A Community-Based Ontology for Integrative Representation and Analysis of Traditional Chinese Drugs and Their Properties

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