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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>
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>
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>
FIGURE 3 in Phylogeny and morphology reveal two new species of Diaporthe from Traditional Chinese Medicine in Northeast China
FIGURE 3. Morphology of Diaporthe schisandrae from Schisandra chinensis (BJFC-S1370). A: Habit of conidiomata on branches. B: Longitudinal section of conidioma. C: Transverse section of conidioma. D, E: Conidia. F: Conidiophores. G: Colonies on PDA at 30 days. Scale bars: B–C = 200 μm; D–F = 10 μm.
FIGURE 2 in Phylogeny and morphology reveal two new species of Diaporthe from Traditional Chinese Medicine in Northeast China
FIGURE 2. Morphology of Diaporthe Sambucusii from Sambucus williamsii (BJFC-S1368). A, B: Habit of conidiomata on branches. C: Transverse section of conidioma. D, E, G: Conidia. F: Conidiophores. H: Colonies on PDA at 30 days. Scale bars: B–C = 500 μm; D, G = 5 μm; E–F = 10 μm.
TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis
<p><strong>ABSTRACT: </strong>Traditional Chinese Medicines Integrated Database and the description about Chinese herbs, including English and Latin names, properties, meridians, medicinal parts, herbal effect and indication. Traditional Chinese Medicine (TCM) is a system of healthcare and healing that has been practiced for thousands of years in China. It is based on a holistic approach that views the human body and its various systems as interconnected. TCM encompasses a wide range of practices, including herbal medicine, acupuncture, massage (tui na), exercise (qigong), and dietary therapy.</p> <p><strong>Instruction: </strong></p> <p>Data was cleaned and duplicates were removed.</p> <p><strong>Inspiration: </strong>The dataset was uploaded to UBRITE for "DGR_DEPOT" summer 2023 team project</p> <p><strong>Acknowledgements: </strong>Ruichao Xue 1, Zhao Fang, Meixia Zhang, Zhenghui Yi, Chengping Wen, Tieliu Shi</p> <p>TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2013 Jan;41(Database issue):D1089-95. doi: 10.1093/nar/gks1100. Epub 2012 Nov 29. PMID: 23203875; PMCID: PMC3531123.</p> <p><strong>U-BRITE LAST UPDATED June 19, 2023</strong></p>
Fig. 6 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge
Fig. 6. Characterization of Aa7DR1 as a 7-dehydrocholesterol reductase 1 from A. asphodeloides Bunge.
Fig. 4 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge
Fig. 4. Transcriptional levels of candidate 7-DR genes involved in timosaponin biosynthesis by RT-qPCR. The characters on the X-axis indicate the roots (R), shortening stem (S) and leaves (L). The Y-axis represents the fold change in gene expression. The ubiquitin gene was used as an internal reference.
Fig. 5. 7 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge
Fig. 5. 7-dehydrocholesterol reductase (7-DR) are involved in cholesterol and phytosterol biosynthesis. CAS: cycloartenol synthase; LAS: lansterol synthase; SMT: sterol C-24 methyltransferase; SSR: sterol side chain reductase; Erg1:squalene epoxidase; Erg5: sterol C-22 desaturase; Erg4: C-24 sterol reductase.
Fig. 3 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge
Fig. 3. Content analyses of steroidal saponins (A) and phytosterols in different organs of A. asphodeloides Bunge. Corresponding histograms indicate the difference in concentration among the different organs. Three biological replicates were performed for each sample.
Fig. 7 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge
Fig. 7. Phylogenetic tree of 7-dehydrocholesterol reductase. Sequences from the following species were represented: A. asphodeloides Bunge (Aa), Arabidopsis thaliana L. (Brassicaceae) (At), Brachypodium distachyon L. (Poaceae) (Bd), Capsicum annuum L. (Solanaceae) (Ca), Chlamydomonas reinhardtii (Cr), Homo sapiens (Hs), Medicago truncatula Gaetn (Leguminosae) (Mt), Nicotiana. Benthamiana Domin (Solanaceae) (Nb), Ostreococcus lucimarinus (Ol), Oryza sativa L. (Poaceae) (Os), Ostreococcus tauri (Ot), Physcomitrella patens (Pp), Sorghum bicolor L. (Poaceae) (Sb), Saccharomyces cerevisiae (Sc), Solanum lycopersicum L. (Solanaceae) (Sl), Solanum melongena L. (Solanaceae) (Sm), Solanum tuberosum L. (Solanaceae) (St), Volvax carteri (Vc), Vitis vinifera L. (Vitaceae) (Vv) and Zea mays L. (Poaceae) (Zm).
A Clinical Evaluation on Traditional Chinese Medicine Diagnosis and Treatment Program Blocking and Reversing Hepatitis B-related Liver Fibrosis - a Randomized, Controlled, Double-blind, Multi-center C
ClinicalTrials.gov study NCT01965418. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Efficacy and Safety Evaluation of Traditional Chinese Medicine in the Treatment of Advanced Colorectal Cancer
ClinicalTrials.gov study NCT02923622. IPD Sharing: NO. Countries: 1. Publications: 1.
Therapeutic Effects of Traditional Chinese Medicine, Shen-Mai San in Cancer Patient Undergoing Chemotherapy or Radiotherapy
ClinicalTrials.gov study NCT01580358. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Series of N-of-1 Trials of Traditional Chinese Medicine Based on Bayesian Method
ClinicalTrials.gov study NCT04601792. IPD Sharing: YES. Countries: 1. Publications: 6.
Cohort Study on Treatment of Cardiovascular Diseases With Traditional Chinese Medicine
ClinicalTrials.gov study NCT05309343. IPD Sharing: YES. Countries: 1. Publications: 1.
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