BATMAN-TCM


37904598	BATMAN-TCM 2.0: an enhanced integrative database for known and predicted interactions between traditional Chinese medicine ingredients and target proteins. [PMID: 37904598] Xiangren Kong, Chao Liu, Zuzhen Zhang, Meiqi Cheng, Zhijun Mei, Xiangdong Li, Peng Liu, Lihong Diao, Yajie Ma, Peng Jiang, Xiangya Kong, Shiyan Nie, Yingzi Guo, Ze Wang, Xinlei Zhang, Yan Wang, Liujun Tang, Shuzhen Guo, Zhongyang Liu, Dong Li Abstract Traditional Chinese medicine (TCM) is increasingly recognized and utilized worldwide. However, the complex ingredients of TCM and their interactions with the human body make elucidating molecular mechanisms challenging, which greatly hinders the modernization of TCM. In 2016, we developed BATMAN-TCM 1.0, which is an integrated database of TCM ingredient-target protein interaction (TTI) for pharmacology research. Here, to address the growing need for a higher coverage TTI dataset, and using omics data to screen active TCM ingredients or herbs for complex disease treatment, we updated BATMAN-TCM to version 2.0 (http://bionet.ncpsb.org.cn/batman-tcm/). Using the same protocol as version 1.0, we collected 17 068 known TTIs by manual curation (with a 62.3-fold increase), and predicted ∼2.3 million high-confidence TTIs. In addition, we incorporated three new features into the updated version: (i) it enables simultaneous exploration of the target of TCM ingredient for pharmacology research and TCM ingredients binding to target proteins for drug discovery; (ii) it has significantly expanded TTI coverage; and (iii) the website was redesigned for better user experience and higher speed. We believe that BATMAN-TCM 2.0, as a discovery repository, will contribute to the study of TCM molecular mechanisms and the development of new drugs for complex diseases. Nucleic Acids Res. 2024:52(D1) \| 22 Citations (from Europe PMC, 2025-03-15)
26879404	BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine. [PMID: 26879404] Liu Z, Guo F, Wang Y, Li C, Zhang X, Li H, Diao L, Gu J, Wang W, Li D, He F. Abstract Traditional Chinese Medicine (TCM), with a history of thousands of years of clinical practice, is gaining more and more attention and application worldwide. And TCM-based new drug development, especially for the treatment of complex diseases is promising. However, owing to the TCM's diverse ingredients and their complex interaction with human body, it is still quite difficult to uncover its molecular mechanism, which greatly hinders the TCM modernization and internationalization. Here we developed the first online Bioinformatics Analysis Tool for Molecular mechANism of TCM (BATMAN-TCM). Its main functions include 1) TCM ingredients' target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient-target-pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. Finally, we applied BATMAN-TCM to Qishen Yiqi dripping Pill (QSYQ) and combined with subsequent experimental validation to reveal the functions of renin-angiotensin system responsible for QSYQ's cardioprotective effects for the first time. BATMAN-TCM will contribute to the understanding of the "multi-component, multi-target and multi-pathway" combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM's molecular mechanism. BATMAN-TCM is available at http://bionet.ncpsb.org/batman-tcm. Sci Rep. 2016:6() \| 399 Citations (from Europe PMC, 2025-03-15)

BATMAN-TCM 2.0: an enhanced integrative database for known and predicted interactions between traditional Chinese medicine ingredients and target proteins. [PMID: 37904598]

Xiangren Kong, Chao Liu, Zuzhen Zhang, Meiqi Cheng, Zhijun Mei, Xiangdong Li, Peng Liu, Lihong Diao, Yajie Ma, Peng Jiang, Xiangya Kong, Shiyan Nie, Yingzi Guo, Ze Wang, Xinlei Zhang, Yan Wang, Liujun Tang, Shuzhen Guo, Zhongyang Liu, Dong Li

Abstract

Traditional Chinese medicine (TCM) is increasingly recognized and utilized worldwide. However, the complex ingredients of TCM and their interactions with the human body make elucidating molecular mechanisms challenging, which greatly hinders the modernization of TCM. In 2016, we developed BATMAN-TCM 1.0, which is an integrated database of TCM ingredient-target protein interaction (TTI) for pharmacology research. Here, to address the growing need for a higher coverage TTI dataset, and using omics data to screen active TCM ingredients or herbs for complex disease treatment, we updated BATMAN-TCM to version 2.0 (http://bionet.ncpsb.org.cn/batman-tcm/). Using the same protocol as version 1.0, we collected 17 068 known TTIs by manual curation (with a 62.3-fold increase), and predicted ∼2.3 million high-confidence TTIs. In addition, we incorporated three new features into the updated version: (i) it enables simultaneous exploration of the target of TCM ingredient for pharmacology research and TCM ingredients binding to target proteins for drug discovery; (ii) it has significantly expanded TTI coverage; and (iii) the website was redesigned for better user experience and higher speed. We believe that BATMAN-TCM 2.0, as a discovery repository, will contribute to the study of TCM molecular mechanisms and the development of new drugs for complex diseases.

Nucleic Acids Res. 2024:52(D1) | 22 Citations (from Europe PMC, 2025-03-15)

BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine. [PMID: 26879404]

Liu Z, Guo F, Wang Y, Li C, Zhang X, Li H, Diao L, Gu J, Wang W, Li D, He F.

Abstract

Traditional Chinese Medicine (TCM), with a history of thousands of years of clinical practice, is gaining more and more attention and application worldwide. And TCM-based new drug development, especially for the treatment of complex diseases is promising. However, owing to the TCM's diverse ingredients and their complex interaction with human body, it is still quite difficult to uncover its molecular mechanism, which greatly hinders the TCM modernization and internationalization. Here we developed the first online Bioinformatics Analysis Tool for Molecular mechANism of TCM (BATMAN-TCM). Its main functions include 1) TCM ingredients' target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient-target-pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. Finally, we applied BATMAN-TCM to Qishen Yiqi dripping Pill (QSYQ) and combined with subsequent experimental validation to reveal the functions of renin-angiotensin system responsible for QSYQ's cardioprotective effects for the first time. BATMAN-TCM will contribute to the understanding of the "multi-component, multi-target and multi-pathway" combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM's molecular mechanism. BATMAN-TCM is available at http://bionet.ncpsb.org/batman-tcm.

Sci Rep. 2016:6() | 399 Citations (from Europe PMC, 2025-03-15)

URL:	http://bionet.ncpsb.org.cn/batman-tcm/
Full name:	A Bioinformatics Annotation daTabase for Molecular mechANism of Traditional Chinese Medicine
Description:	BATMAN-TCM is an integrative database that stores known and predicted interactions between TCM ingredients and target proteins, aiding in the exploration of TCM pharmacological mechanisms and drug discovery. The updated version 2.0 offers a significantly expanded TTI dataset and enhanced features, making it a valuable resource for understanding TCM's molecular mechanisms and developing new treatments for complex diseases.
Year founded:	2016
Last update:	2024-01
Version:	v2.0
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA Protein
Data object:	NA
Database category:	Gene genome and annotation Health and medicine
Major species:	NA
Keywords:	traditional Chinese medicine (TCM) target protein interaction drug discovery

University/Institution:	Beijing Institute of Lifeomics
Address:	No.5, No.1 Beichen West Road, Chaoyang District, Beijing, China
City:	Beijing
Province/State:
Country/Region:	China
Contact name (PI/Team):	Zhongyang Liu
Contact email (PI/Helpdesk):	liuzy1984@163.com

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