TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis

By Ruichao Xue, Zhao Fang, Meixia Zhang, Z. Yi, Chengping Wen, Tieliu Shi. Nucleic Acids Res., 2012

551 citations recorded by the source corpus.

As an alternative to modern western medicine, Traditional Chinese Medicine (TCM) is receiving increasingly attention worldwide. Great efforts have been paid to TCM’s modernization, which tries to bridge the gap between TCM and modern western medicine. As TCM and modern western medicine share a common aspect at molecular level that the compound(s) perturb human’s dysfunction network and restore human normal physiological condition, the relationship between compounds (in herb, refer to ingredients) and their targets (proteins) should be the key factor to connect TCM and modern medicine. Accordingly, we construct this Traditional Chinese Medicine Integrated Database (TCMID, http://www.megabionet.org/tcmid/), which records TCM-related information collected from different resources and through text-mining method. To enlarge the scope of the TCMID, the data have been linked to common drug and disease databases, including Drugbank, OMIM and PubChem. Currently, our TCMID contains ∼47 000 prescriptions, 8159 herbs, 25 210 compounds, 6828 drugs, 3791 diseases and 17 521 related targets, which is the largest data set for related field. Our web-based software displays a network for integrative relationships between herbs and their treated diseases, the active ingredients and their targets, which will facilitate the study of combination therapy and understanding of the underlying mechanisms for TCM at molecular level.

Subfields: Computational Theory and Mathematics, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/76883c8a18f0b58d486b6dc0fdb9331f3bda6360

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Run-zhi Zhang
2. Xue Zhu
3. Kang Ning
4. Hong Bai
5. Chao Huang
6. Shufeng Zhou
7. Yi Zhao
8. Yonghua Wang

In Molecular Biology

1. Xiu-Jie Wang
2. Shufeng Zhou
3. Tieliu Shi
4. Yi Zhao
5. Run-zhi Zhang
6. Xue Zhu
7. Bo Zhang
8. Kang Ning

In Pharmacology

1. Run-zhi Zhang
2. Xue Zhu
3. Kang Ning
4. Hong Bai
5. Shufeng Zhou
6. Bo Zhang
7. Shao Li

Citations in the corpus

• New Perspectives on How to Discover Drugs from Herbal Medicines: CAM's Outstanding Contribution to Modern Therapeutics (2013, background): “Indian origin with anticancer activity via 32 descriptive fields [148, 149].”
• Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment (2019, background): “Although TCMID is available for multiple inputs, including compound name, STITCH database ID, and CAS number, when searching for ingredients, it is not sufficiently comprehensive, and many compounds are searched without a related network in TCMID.”
• ETCM: an encyclopaedia of traditional Chinese medicine (2018, background): “The recent development of several TCM-related databases, such as HIT (7), TCMGeneDIT (8), TCMMESH (9), TCM-ID (10), TCMSP (11), TCMID (12,13), *To whom correspondence should be addressed.”
• TCMID 2.0: a comprehensive resource for TCM (2017, background): “Comprehensive integration of various data resources, including Database@Taiwan (1), HIT (2) makes TCMID as the largest database of TCM in related field with over 49 000 prescriptions, 8159 herbs, 25 210 ingredients, 3791 diseases, 6828 drugs and 17 521 targets (3).”
• BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine (2016, methodology): “…diseases among the potential targets of TCM construct the connection between TCM and diseases by targets and disease-related genes, not only bridging the gap between TCM and modern western medicine but also providing clues for exploring novel diseases on which the TCM has therapeutic effects 6 .”
• TCMSP: a database of systems pharmacology for drug discovery from herbal medicines (2014, background): “TCMID [16] comprises TCM formulae, herbs, ingredients and the targets and diseases.”
• The Traditional Medicine and Modern Medicine from Natural Products (2016, background): “Traditional Chinese medicine (TCM) [26,28,40–43] ‚ China ‚ Thousands of years ago.”
• SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping (2018, background): “As TCM is based on a holistic philosophy that differs substantially from that of MM (9), this task can be accomplished only by experts who are trained in TCM and familiar with MM.”
• How Can Synergism of Traditional Medicines Benefit from Network Pharmacology? (2017, background): “Recent studies of traditional Chinese medicine (TCM) found that more than 12,000 species of plants and animals and tens of thousands of prescriptions are used in the practice of TCM [14,15].”
• Traditional Chinese medicine network pharmacology: theory, methodology and application. (2013, background): “Meanwhile, with the availability of various databases and data resources related to TCM and biological systems [52-64] (Table 2), many researchers have continued to modernize TCM in the context of network pharmacology.”
• TCM network pharmacology: A new trend towards combining computational, experimental and clinical approaches. (2021, unknown): “Information in protein-protein interaction databases such as STRING [46] and HPRD [47] serves as a bridge between drugs and diseases for the construction of drug intervention networks for diseases.”
• HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine (2020, background): “In HERB, we first prepared a list of herbs and ingredients and determined their relationships by integrating multiple TCM databases including SymMap (21), TCMID 2.0 (22), TCMSP 2.3 (23) and TCM-ID (24).”