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Traditional Chinese Medicine Multidimensional Knowledge Graph
<h3>Overview of the Traditional Chinese Medicine Multi-dimensional Knowledge Graph (TCM-MKG)</h3> <p>The <strong>Traditional Chinese Medicine Multi-dimensional Knowledge Graph (TCM-MKG)</strong> is a comprehensive, open-source data platform developed by Jingqi Zeng in November 2024. This platform aims to integrate and standardize a vast array of data from multiple sources, encompassing both traditional Chinese medicine (TCM) and modern biomedical sciences. By organizing and linking this diverse information, TCM-MKG acts as a bridge that connects the ancient wisdom of TCM with contemporary medical research and applications.</p> <h3>Key Features and Objectives:</h3> <ul> <li> <p><strong>Multi-source Data Integration</strong>: TCM-MKG consolidates data from over 30 authoritative resources, covering a broad spectrum of topics, including TCM terminology, Chinese patent medicines (CPM), Chinese herbal pieces (CHP), natural products (NP), chemical components, disease targets, and more. These data sources are carefully curated and interlinked, ensuring a rich, multi-dimensional view of TCM in relation to modern biomedical research. The platform incorporates data from reputable databases such as DrugBank, BioGRID, DisGeNET, STRING, and many others, ensuring that the TCM knowledge is not only expansive but also scientifically robust and cross-referenced with global biomedical standards.</p> </li> <li> <p><strong>Standardized Design for Global Interoperability</strong>: TCM-MKG adheres to international data standards and integrates with widely-used global medical classification systems such as ICD-11, UMLS, MeSH, and DOID. This ensures that the platform’s data is globally comparable and facilitates easy integration with international research efforts, promoting collaboration and knowledge exchange across the fields of TCM and modern medicine.</p> </li> <li> <p><strong>Open Source and Collaborative</strong>: In line with its mission to enhance transparency and accessibility, TCM-MKG is open-sourced in a structured tabular format. This allows researchers worldwide to freely access, contribute to, and expand upon the data, fostering interdisciplinary collaboration and accelerating innovation in both TCM research and modern medicine.</p> </li> <li> <p><strong>Advanced Analytical Capabilities</strong>: By leveraging the power of knowledge graph technology and graph-based intelligence algorithms, TCM-MKG supports deep data mining and relational reasoning. Researchers can uncover hidden associations between TCM components, diseases, and targets, providing insights into the mechanisms of herbal interactions and offering new pathways for drug discovery and therapeutic research.</p> </li> </ul> <h3>Personal Research Application:</h3> <p>Using the TCM-MKG platform, I conducted a study titled <strong>"Graph Neural Networks for Quantifying Compatibility Mechanisms in Traditional Chinese Medicine."</strong> This research applied advanced graph intelligence algorithms to quantitatively assess the compatibility mechanisms of Chinese herbal formulas (CHF). The study provides fresh insights into the underlying principles of TCM herbal combinations.</p> <p>This research has been published:</p> <p><strong>Zeng, J., & Jia, X. (2025). Quantifying compatibility mechanisms in traditional Chinese medicine with interpretable graph neural networks. <em>Journal of Pharmaceutical Analysis</em>, 101342. <a href="https://doi.org/10.1016/j.jpha.2025.101342">https://doi.org/10.1016/j.jpha.2025.101342</a></strong></p> <p>The code and methodology for this research have been open-sourced and are available on <a href="https://github.com/ZENGJingqi/GraphAI-for-TCM" target="_new" rel="noopener">GitHub</a>.</p> <h3>Acknowledgments:</h3> <p>This work benefited from the integration of data from numerous open-access and authoritative databases. We acknowledge the valuable contributions of resources such as DrugBank, BindingDB, BioGRID, DisGeNET, and many others. These datasets provided essential insights into TCM, modern drug chemistry, genetics, diseases, and related fields, forming the foundation for the traditional Chinese medicine multi-dimensional knowledge graph (TCM-MKG) used in this study. Furthermore, we utilized the PSICHIC model (https://github. com/huankoh/PSICHIC) to analyze the binding interactions between components and targets. Full citations for these resources are included.</p> <h3>Contact Information:</h3> <p>For further inquiries or more detailed information, please feel free to contact:<br><strong>Email</strong>: <a rel="noopener">zjingqi@163.com</a></p> <p> </p>
Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales
<p>A better understanding of the relationship between plant specialized metabolism and traditional medicine has the potential to aid in bioprospecting and untangling of cross-cultural use patterns. However, given the limited information available for metabolites in most plant species, understanding medicinal use-metabolite relationships can be difficult. The order Caryophyllales has a unique pattern of lineages of tyrosine- or phenylalanine-dominated specialized metabolism, represented by mutually exclusive anthocyanin and betalain pigments, making Caryophyllales a compelling system to explore the relationship between medicine and metabolites by using pigment as a proxy for tyrosine- vs phenylalanine-dominant metabolism. We compiled a list of medicinal species in select tyrosine- or phenylalanine-dominant families of Caryophyllales (Nepenthaceae, Polygonaceae, Simmondsiaceae, Microteaceae, Caryophyllaceae, Amaranthaceae, Limeaceae, Molluginaceae, Portulacaceae, Cactaceae, and Nyctaginaceae) by searching scientific literature until no new medicinal uses were recovered. We then tested for phylogenetic clustering of uses using a "hot nodes" approach. To test potential non-metabolite drivers of medicinal use, like how often humans encounter a species (apparency), we repeated the analysis using only North American species across the entire order and performed phylogenetic generalized least squares regression (PGLS) with occurrence data from the Global Biodiversity Information Facility (GBIF). We hypothesized families with tyrosine-enriched metabolism would show clustering of different types of medicinal use compared to phenylalanine-enriched metabolism. Instead, wide-ranging, apparent clades in Polygonaceae and Amaranthaceae are overrepresented across nearly all types of medicinal use. Our results suggest that apparency is a better predictor of medicinal use than metabolite profile, although metabolism type may still be a contributing factor.</p>
Home and hub: pet trade and traditional medicine impact reptile populations in source locations and destinations
<p>The pet trade and Traditional Chinese Medicine (TCM) consumption are major drivers of global biodiversity loss. Tokay geckos (<em>Gekko gecko</em>) are among the most traded reptile species worldwide. In Hong Kong, pet and TCM markets sell tokay geckos while wild populations also persist. To clarify connections between trade sources and destinations, we compared genetics and stable isotopes of wild tokays in local and nonlocal populations to dried individuals from TCM markets across Hong Kong. We found that TCM tokays are likely not of local origin. Most wild tokays were related to individuals in South China, indicating a probable natural origin. However, two populations contained individuals more similar to distant populations, indicating pet trade origins. Our results highlight the complexity of wildlife trade impacts within trade hubs. Such trade dynamics complicate local legal regulation when endangered species are protected, but the same species might also be non-native and possibly damaging to the environment.</p>
Fig. 3 in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa
Fig. 3. Traditional healer's regalia. A, wrist-band from Pondoland made from shells of the gastropod Nerita albicilla (the black and white coloration symbolising the black and white components of many traditional remedies); B, diviner's necklace with glass beads and marine shells, Mtubatuba area, Zululand (Natal Museum 7147).
Fig. 2 in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa
Fig. 2. Samples of invertebrate animals for sale in market. A, dried, live-collected chitons of the genera Chiton, Dinoplax and Onithochiton; B, ring cowries (Cypraea annulus), many with dried bodies inside; C, organ-pipe coral (Tubipora musica) from localities as much as 2000 km distant in northern Mozambique; D, starfish (Protoreaster lincki) collected alive in sheltered localities in Mozambique.
Fig. 1 in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa
Fig. 1. Stalls in the Warwick Triangle market, Durban. A, typical stall selling a wide range of products, nearly all of animal origin; B, neatly organised stall of a Mozambican trader, displaying a range of animal products, many of tropical origin. Note Cypraea annulus head-bands in foreground.
Fig. 5. Traditional nomenclature - isongololo. A in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa
Fig. 5. Traditional nomenclature - isongololo. A, isongololo, the well-known juliform millipedes and B, isongololo lasolwandle, the shell of the cephalopod mollusc Spirula spirula.
Fig. 4. Traditional nomenclature - imfinyezi. A, a in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa
Fig. 4. Traditional nomenclature - imfinyezi. A, a chiton imfinyezi yasolwandle (Dinoplax sp.) and B, a pill millipede imfinyezi yentaba or imfinyezi yangaphandle (Sphaerotherium sp.), showing the superficially similar shape and body segmentation.
Spanish wild plants traditionally used as medicine
<p>List of Spanish wild plant species with the ethnobotanical references in which they have been reported as medicinal and their cultural importance index (CI). Accompanied as well by data about origin (wild or cultivated), abundance, occupancy area, endemicity, conservation status, protection status. We also provide the complete list of references and legislation used.</p> <p>The excel file has five tabs: 1. Ethnobotanical references, 2. Medicinal species, 3. Legislation, 4. Protection, 5. Protection categories.</p>
Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales
Open the record for dataset details and reuse information.
Home and hub: pet trade and traditional medicine impact reptile populations in source locations and destinations
Open the record for dataset details and reuse information.
Three-tiered authentication of herbal Traditional Chinese Medicine ingredients used in women's health provides progressive qualitative and quantitative insight - part 2/4
<p>Traditional Chinese Medicine herbal products are increasingly used in Europe but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients. </p>
Three-tiered authentication of herbal Traditional Chinese Medicine ingredients used in women's health provides progressive qualitative and quantitative insight - part 1/4
<p>Traditional Chinese Medicine herbal products are increasingly used in Europe but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients. </p>
Three-tiered authentication of herbal Traditional Chinese Medicine ingredients used in women's health provides progressive qualitative and quantitative insight - part 3/4
<p>Traditional Chinese Medicine herbal products are increasingly used in Europe but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.</p>
Three-tiered authentication of herbal Traditional Chinese Medicine ingredients used in women's health provides progressive qualitative and quantitative insight - part 4/4
<p>Traditional Chinese Medicine herbal products are increasingly used in Europe but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.</p>
Prevalence and Factors Associated with the Use of Traditional Medicine in Individuals with Hypercholesterolemia, Hyperglycaemia, and Arterial Hypertension in Ecuador: Results from a Population-based Study in Two Health Districts
Open the record for dataset details and reuse information.
Integrated Traditional Chinese Medicine Day Care Program for Metabolic Syndrome
ClinicalTrials.gov study NCT06703788. IPD Sharing: NO. Countries: 1. Publications: 2.
Identification of the Inhibition Mechanism of Fructooligosaccharide from Chinese Traditional Medicine Polygonatum sibiricum to Carbonic Anhydrase II
<p>The input files, parameter files, topology files, etc. of the MD simulation in the manuscript "Identification of the Inhibition Mechanism of Fructooligosaccharide from Chinese Traditional Medicine Polygonatum sibiricum to Carbonic Anhydrase II".</p>
Traditional use of medicinal plants among the indigenous communities in district Baramulla, Jammu and Kashmir, India
<p>A number of indigenous communities reside in the Himalayan belt of Baramulla, where the lack of modern health care facilities represents crucial problems to their survival. Therefore the current study was aimed at documenting traditional knowledge of medicinal plants in the region. Ethnomedicinal data was collected during 2018-2020. Fifty-one informants were interviewed in seventeen villages via questionnaires, semi-structured interviews and group discussions. Data was also analyzed by various ethnobotanical indices. A total of 85 plant species distributed in 40 families were documented. Asteraceae was reported to be the dominant plant family and leaves were the most frequently utilized plant part. Musculoskeletal disorder scored the highest ICF value (0.87). Colchicum luteum (0.61), Verbascum thapsus (0.59) reported highest UV and Viola odorata, Ajuga integrifolia had the highest FL of 100%. Of the documented species about 18 plants (21%) were reported for the first time to be used in the area. Medicinal plants still play an important role in the healthcare sector and the folk knowledge attached to them is remarkable in the region, although declining among the younger generations. Medicinal plants reported for the first time, needs to be studied pharmacologically.</p>
Tongue image dataset for Tri-Dhat classification in traditional Thai medicine
<p>Traditional Thai medicine (TTM) is an increasingly popular treatment option. Tongue diagnosis is a highly efficient method for determining overall health, as practiced by TTM practitioners. However, the diagnosis naturally varies depending on the practitioner's expertise. In this work, we propose tongue image analysis with raw pixels using artificial intelligence (AI) to support TTM diagnoses. The target classification of Tri-Dhat consists of three classes: Vata, Pitta, and Kapha. We utilized our own organized, genuine datasets collected from our university TTM hospital. Class balancing and data augmentation were conducted, and we present analysis approaches and experimental designs. Transfer learning techniques for various pretrained deep learning models were developed. We used two-tailed paired t-tests and single-factor ANOVA for performance comparisons. Our work demonstrated that the DenseNet121 and Xception models provided the most significant results with cropped image datasets, including DSLR-taken and mobile-taken images. Notably, model ensemble evaluations yielded the highest average predictions, achieving a precision of 0.94, an F1 score of 0.96, an accuracy of 0.96, a sensitivity of 0.96, and a specificity of 0.97, supported by a p-value of 0.0003 from ANOVA. We suggest that our methods could be effectively deployed in real-world scenarios to aid TTM practitioners in their diagnoses.</p>
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