TCMID 2.0: a Comprehensive Resource for TCM

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2017 Nov 7

PMID 29106634

Citations 169

Authors

Lin Huang

Duoli Xie

Yiran Yu

Huanlong Liu

Yan Shi

Tieliu Shi

Chengping Wen

Affiliations

Soon will be listed here.

Abstract

As a traditional medical intervention in Asia and a complementary and alternative medicine in western countries, Traditional Chinese Medicine (TCM) is capturing worldwide attention in life science field. Traditional Chinese Medicine Integrated Database (TCMID), which was originally launched in 2013, was a comprehensive database aiming at TCM's modernization and standardization. It has been highly recognized among pharmacologists and scholars in TCM researches. The latest release, TCMID 2.0 (http://www.megabionet.org/tcmid/), replenished the preceding database with 18 203 herbal ingredients, 15 prescriptions, 82 related targets, 1356 drugs, 842 diseases and numerous new connections between them. Considering that chemical changes might take place in decocting process of prescriptions, which may result in new ingredients, new data containing the prescription ingredients was collected in current version. In addition, 778 herbal mass spectrometry (MS) spectra related to 170 herbs were appended to show the variation of herbal quality in different origin and distinguish genuine medicinal materials from common ones while 3895 MS spectra of 729 ingredients were added as the supplementary materials of component identification. With the significant increase of data, TCMID 2.0 will further facilitate TCM's modernization and enhance the exploration of underlying biological processes that are response to the diverse pharmacologic actions of TCM.

Citing Articles

Herb-disease association prediction model based on network consistency projection.

Chen L, Zhang S, Zhou B Sci Rep. 2025; 15(1):3328.

PMID: 39865145 PMC: 11770172. DOI: 10.1038/s41598-025-87521-7.

Using network pharmacology and molecular docking technology, proteomics and experiments were used to verify the effect of Yigu decoction (YGD) on the expression of key genes in osteoporotic mice.

Yan K, Zhang R, Wang J, Chen H, Zhang Y, Cheng F Ann Med. 2025; 57(1):2449225.

PMID: 39749683 PMC: 11703118. DOI: 10.1080/07853890.2024.2449225.

Unveiling the Anti-Obesity Potential of Thunder God Vine: Network Pharmacology and Computational Insights into Celastrol-like Molecules.

Zheng S, Yang H, Zheng J, Wang Y, Jia B, Li W Int J Mol Sci. 2024; 25(23).

PMID: 39684213 PMC: 11641352. DOI: 10.3390/ijms252312501.

Identification for metabolism profiles and pharmacokinetic studies of tradition Chinese prescription Ji-Ming-San and its major metabolites in rats by UHPLC-Q-TOF-MS/MS and UHPLC-MS/MS.

Hsieh C, Wang C, Tayo L, Tsai P, Lee C J Food Drug Anal. 2024; 31(3):502-518.

PMID: 39666275 PMC: 10629916. DOI: 10.38212/2224-6614.3473.

Exploration of compatibility rules and discovery of active ingredients in TCM formulas by network pharmacology.

Liu Y, Li X, Chen C, Ding N, Ma S, Yang M Chin Herb Med. 2024; 16(4):572-588.

PMID: 39606260 PMC: 11589340. DOI: 10.1016/j.chmed.2023.09.008.

References

Huang L, Lv Q, Liu F, Shi T, Wen C . A Systems Biology-Based Investigation into the Pharmacological Mechanisms of Sheng-ma-bie-jia-tang Acting on Systemic Lupus Erythematosus by Multi-Level Data Integration. Sci Rep. 2015; 5:16401. PMC: 4642335. DOI: 10.1038/srep16401. View

Kim J, Ha W, Park J, Lee G, Choi G, Lee S . Influence of herbal combinations on the extraction efficiencies of chemical compounds from Cinnamomum cassia, Paeonia lactiflora, and Glycyrrhiza uralensis, the herbal components of Gyeji-tang, evaluated by HPLC method. J Pharm Biomed Anal. 2016; 129:50-59. DOI: 10.1016/j.jpba.2016.06.044. View

Huang L, Lv Q, Xie D, Shi T, Wen C . Deciphering the Potential Pharmaceutical Mechanism of Chinese Traditional Medicine (Gui-Zhi-Shao-Yao-Zhi-Mu) on Rheumatoid Arthritis. Sci Rep. 2016; 6:22602. PMC: 4776278. DOI: 10.1038/srep22602. View

Melchart D, Hager S, Dai J, Weidenhammer W . Quality Control and Complication Screening Programme of Chinese Medicinal Drugs at the First German Hospital of Traditional Chinese Medicine - A Retrospective Analysis. Forsch Komplementmed. 2016; 23 Suppl 2:21-8. DOI: 10.1159/000444983. View

Zhen G, Zhang L, Du Y, Yu R, Liu X, Cao F . De novo assembly and comparative analysis of root transcriptomes from different varieties of Panax ginseng C. A. Meyer grown in different environments. Sci China Life Sci. 2015; 58(11):1099-110. DOI: 10.1007/s11427-015-4961-x. View

Chatr-Aryamontri A, Breitkreutz B, Oughtred R, Boucher L, Heinicke S, Chen D . The BioGRID interaction database: 2015 update. Nucleic Acids Res. 2014; 43(Database issue):D470-8. PMC: 4383984. DOI: 10.1093/nar/gku1204. View

Liu Z, Guo F, Wang Y, Li C, Zhang X, Li H . BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine. Sci Rep. 2016; 6:21146. PMC: 4754750. DOI: 10.1038/srep21146. View

. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2012; 41(Database issue):D8-D20. PMC: 3531099. DOI: 10.1093/nar/gks1189. View

Xue R, Fang Z, Zhang M, Yi Z, Wen C, Shi T . TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2012; 41(Database issue):D1089-95. PMC: 3531123. DOI: 10.1093/nar/gks1100. View

10.

Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A . DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res. 2010; 39(Database issue):D1035-41. PMC: 3013709. DOI: 10.1093/nar/gkq1126. View

11.

Szklarczyk D, Santos A, von Mering C, Jensen L, Bork P, Kuhn M . STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res. 2015; 44(D1):D380-4. PMC: 4702904. DOI: 10.1093/nar/gkv1277. View

12.

Ye H, Ye L, Kang H, Zhang D, Tao L, Tang K . HIT: linking herbal active ingredients to targets. Nucleic Acids Res. 2010; 39(Database issue):D1055-9. PMC: 3013727. DOI: 10.1093/nar/gkq1165. View

13.

Baxevanis A . Searching Online Mendelian Inheritance in Man (OMIM) for information on genetic loci involved in human disease. Curr Protoc Hum Genet. 2012; Chapter 9:9.13.1-9.13.10. DOI: 10.1002/0471142905.hg0913s73. View

14.

Jiang W, Li S, Li X . Therapeutic potential of berberine against neurodegenerative diseases. Sci China Life Sci. 2015; 58(6):564-9. PMC: 5823536. DOI: 10.1007/s11427-015-4829-0. View

15.

Gao H, Wang Z, Li Y, Qian Z . Overview of the quality standard research of traditional Chinese medicine. Front Med. 2011; 5(2):195-202. DOI: 10.1007/s11684-011-0134-x. View

16.

Sun Y, Liu Y, Chen K . Roles and mechanisms of ginsenoside in cardiovascular diseases: progress and perspectives. Sci China Life Sci. 2016; 59(3):292-8. DOI: 10.1007/s11427-016-5007-8. View

17.

Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V . ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2015; 44(D1):D1214-9. PMC: 4702775. DOI: 10.1093/nar/gkv1031. View

18.

Wang M, Carver J, Phelan V, Sanchez L, Garg N, Peng Y . Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016; 34(8):828-837. PMC: 5321674. DOI: 10.1038/nbt.3597. View

19.

Chen C . TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico. PLoS One. 2011; 6(1):e15939. PMC: 3017089. DOI: 10.1371/journal.pone.0015939. View

20.

Wang F, Chen H, Yan Y, Liu Y, Zhang S, Liu D . Baicalein protects against the development of angiotensin II-induced abdominal aortic aneurysms by blocking JNK and p38 MAPK signaling. Sci China Life Sci. 2016; 59(9):940-9. DOI: 10.1007/s11427-015-0277-8. View