TCM‐Suite: A comprehensive and holistic platform for Traditional Chinese Medicine component identification and network pharmacology analysis
Pengshuo Yang,
Jidong Lang,
Hongjun Li,
Jinxiang Lu,
Hanyang Lin,
Geng Tian,
Hong Bai,
Jialiang Yang,
Kang Ning
Affiliations
Pengshuo Yang
Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology College of Life Science and Technology, Huazhong University of Science and Technology Wuhan China
Jidong Lang
Geneis Beijing Co., Ltd. Beijing China
Hongjun Li
Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology College of Life Science and Technology, Huazhong University of Science and Technology Wuhan China
Jinxiang Lu
Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology College of Life Science and Technology, Huazhong University of Science and Technology Wuhan China
Hanyang Lin
Sequenxe Biological Technology Co., Ltd. Xiamen China
Geng Tian
Geneis Beijing Co., Ltd. Beijing China
Hong Bai
Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology College of Life Science and Technology, Huazhong University of Science and Technology Wuhan China
Jialiang Yang
Geneis Beijing Co., Ltd. Beijing China
Kang Ning
Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology College of Life Science and Technology, Huazhong University of Science and Technology Wuhan China
Abstract DNA‐based biological ingredient identification and downstream pharmacology network analysis are commonly used in research for Traditional Chinese Medicine preparations (TCM formulas). Advancements in bioinformatics tools and the accumulation of related data have become driving forces for progress in this field. However, a lack of a platform integrating biological ingredient identification and downstream pharmacology network analysis hinders the deep understanding of TCM. In this study, we developed the TCM‐Suite platform composed of two sub‐databases, Holmes‐Suite and Watson‐Suite, for TCM biological ingredient identification and network pharmacology investigation, respectively, both are among the most complete: In the Holmes‐Suite, we collected and processed six types of marker gene sequences, accounting for 1,251,548 marker gene sequences. In the Watson‐Suite, we curated and integrated a massive number of entries from more than 10 public databases. Importantly, we developed a comprehensive pipeline to integrate TCM biological ingredient identification and downstream network pharmacology research, allowing users to simultaneously identify components of a TCM formula and analyze its potential pharmacology mechanism. Furthermore, we designed search engines and a user‐friendly platform to better search and visualize these rich resources. TCM‐Suite is a comprehensive and holistic platform for TCM‐based drug discovery and repurposing. TCM‐Suite website: http://TCM-Suite.AImicrobiome.cn.
