Supplementary Documents Supplementary Figure S1. The affiliation network of THM-NP studies. Circles represent the affiliations. The size of the circles and squares reflect the number of occurrences in the THM-NP studies. Nodes that appeared fewer than 3 times were removed. The box to the right of the network represents the index for the pie chart and the outline of the circle. Supplementary Table 1. Selected THM-NP studies. The Methods The Methods The Methods for for for Target Title Year Author Affiliation References Constructing Constructing C- Network H-C Network T Network Interpretation Drug-target network and polypharmacology studies Jiangyong Gu, Hu Beilstein Zhang, Lirong Chen, Peking University, database, Molecular of a Traditional Chinese 2011 . [1] Medicine for type II Shun Xu, Gu Yuan, Zhengzhou University Chinese herbal docking diabetes mellitus Xiaojie Xu drug database Potential synergistic and multitarget effect of herbal Beilstein pair Chuanxiong Rhizome- Hongzhi Ye, Chunsong Fujian University of database, Zheng, Xiaojie Xu, Traditional Chinese Chinese herbal Molecular Paeonia Albifora Pall on 2011 . [2] osteoarthritis disease: a Mingxia Wu, Medicine, Peking drug database, docking computational Xianxiang Liu University Literature pharmacology approach mining Xiuxiu Li, Xue Xu, A System-Level Chinese Jinan Wang, Hua Yu, Chinese Academy of Investigation into the Academy of Xia Wang, Hongjun Medical Sciences, Mechanisms of Chinese Sciences PharmMapper, TTD, Yang, Haiyu Xu, Northwest A&F Traditional Medicine; 2012 Chemistry Molecular PharmGkb, [3] Shihuan Tang, Yan Li, University, Dalian Compound Danshen database, docking Drugbank Ling Yang, Luqi University of Formula for Cardiovascular Chinese Herbal Huang, Yonghua Technology Disease Treatment Drug Database Wang, Shengli Yang A Systems Biology Bohui Li, Xue Xu, Xia Approach to Wang, Hua Yu, Xiuxiu Northwest A&F TCMSP, Understanding the 2012 Li, Weiyang Tao, University, Chinese TCMSP Molecular KEGG [4] Mechanisms of Action of Yonghua Wang, Ling Academy Sciences docking Chinese Herbs for Yang Treatment of Cardiovascular Disease Northwest A&F A systems biology University, Dalian University of approach to uncovering Xia Wang, Xue Xu, Technology, Chinese pharmacological synergy in Weiyang Tao, Yan Li, PharmGkb, 2012 Academy of Sciences, TCMSP TCMSP [5] herbal medicines with Yonghua Wang, Ling TTD China Academy of applications to Yang cardiovascular disease. Chinese Medical Sciences, Chinese Academy of Sciences Pathway-pathway network- based study of the Li Ye, Yuan He, Hao Ye, Shanghai Center for therapeutic mechanisms by Xueping Liu, Linlin Bioinformation Molecular 2012 . [6] which salvianolic acid B Yang, Zhiwei Cao, Technology, Tongji docking regulates cardiovascular Kailin Tang University diseases Second Military Medical University, Therapeutic effects of Jing Zhao, Pengyuan Shanghai Center for astragaloside IV on Yang, Fan Li, Lin Tao, Bioinformation Molecular myocardial injuries: multi- 2012 Hong Ding, Yaocheng . [7] Technology, Tongji docking target identification and Rui, Zhiwei Cao, University, Logistical network analysis Weidong Zhang Engineering University Understanding the China Academy of molecular mechanism of Chinese Medical Miao Jiang, Cheng Lu, interventions in treating Sciences, Hubei Gao Chen, Cheng Xiao, rheumatoid arthritis University, China- 2012 Qinglin Zha, Xuyan TCMGeneDIT TCMGeneDIT Gene ontology [8] patients with Japan Friendship Niu, Shilin Chen, corresponding traditional Hospital, Jiangxi Aiping Lu chinese medicine patterns University of Chinese based on bioinformatics Medicine, Hong Kong approach Baptist University Northwest A&F Deciphering the Yao Yao, Xiaodong University, Zhejiang combination principles of Zhang, Zhenzhong Jinju Chemcial Traditional Chinese Wang, Chunli Zheng, Corporation, Jiangsu TCMSP, Medicine from a systems 2013 Peng Li, Chao Huang, Kanion TCMSP Molecular TTD [9] pharmacology perspective Weiyang Tao, Wei Xiao, Pharmaceutical docking based on Ma-huang Yonghua Wang, Luqi Corporation, Chinese Decoction Huang, Ling Yang Academy of Sciences, Northwest University Chinese Network pharmacology- Academy of based prediction of the Northwest A&F Sciences Weiyang Tao, Xue Xu, active ingredients and University, Dalian Chemistry TCMSP, Xia Wang, Bohui Li, TTD, potential targets of Chinese 2013 University of database, Molecular [10] Yonghua Wang, Yan Li, PharmGkb herbal Radix Curcumae Technology, Chinese Chinese Herbal docking Ling Yang formula for application to Academy of Sciences Drug Database, cardiovascular disease Literature mining Systems approaches and polypharmacology for drug Hui Liu, Jinan Wang, Chinese Academy of TCMSP, TTD, discovery from herbal 2013 Wei Zhou, Yonghua Sciences, Northwest TCMSP Molecular [11] PharmGkb medicines: An example Wang, Ling Yang A&F University docking using licorice Systems pharmacology uncovers Janus functions of Xia Wang, Xue Xu, Yan Chinese Academy of TCMSP, botanical drugs; activation Li, Xiuxiu Li, Weiyang 2013 Sciences, Northwest TCMSP Molecular TTD, KEGG [12] of host defense system and Tao, Bohui Li, Yonghua A&F University docking inhibition of influenza Wang, Ling Yang virus replication. Material basis of Chinese Shanghai University of herbal formulas explored Lixia Pei, Yuanwu Bao, NCBI's entrez Traditional Chinese by combining 2013 Sheng Liu, Jin Zheng, HPLC gene, Pubmed, . [13] Medicine, University pharmacokinetics with Xiuping Chen CNKI network pharmacology of Macau A network pharmacology approach to evaluating the Zhejiang University, Leihong Wu, Yi Wang, efficacy of chinese medicine Chiatai Qingchunbao 2013 Jing Nie, Xiaohui Fan, HPLC Microarray KEGG [14] using genome-wide Pharmaceutical Yiyu Cheng transcriptional expression Corporation data A Systems Biology-Based Investigation into the Pharmacological Yanqiong Zhang, Danhua Wang, China Academy of TCM Mechanisms of Wu Tou TTD, Molecular Drugbank, 2013 Shufang Tan, Haiyu Chinese Medical Database@taiwa [15] Tang Acting on docking KEGG Rheumatoid Arthritis by Xu, Chunfang Liu, And Sciences n Integrating Network Na Lin Analysis An Integrative Platform of Tianjin International TCM Network Joint Academy of HerBiomap, Bo Zhang, Xu Wang, Pharmacology and Its 2013 Biotechnology & Literature drugCIPHER Gene ontology [16] Shao Li Application on a Herbal Medicine, Tsinghua mining Formula, Qing-Luo-Yin University Network pharmacology- Chinese Herbal Chun-Song Zheng, based prediction of the Fujian University of Drug Database, Xiao-Jie Xu, Hong-Zhi multi-target capabilities of Traditional Chinese Handbook of Molecular 2013 Ye, Guang-Wen Wu, TTD [17] the compounds in Taohong Medicine, Peking the Chemical docking Xi-Hai Li, Hui-Feng Siwu decoction, and their University Constutuents in Xu, Xian-Xiang Liu application in osteoarthritis Chinese Cerb Original Plants Pathway Pattern-based Wen Dai, Jianxin Chen, Chinese Academy of prediction of active drug Peng Lu, Yibo Gao, Lin Comparative Sciences, Beijing components and gene Chen, Xi Liu, Jianglong Toxicogenomics University of Chinese Literature targets from H1N1 2013 Song, Haiyu Xu, Di Database, KEGG [18] Medicine, China mining influenza's treatment with Chen, Yiping Yang, Molecular Academy of Chinese maxingshigan-yinqiaosan Hongjun Yang, Luqi docking Medical Sciences formula Huang Chinese Nanjing University of Academy of The multi-target Shitang Ma, Chengtao Chinese Medicine, Sciences capabilities of the Feng, Xiaolin Zhang, Anhui Science and Chemistry Guoliang Dai, Technology database, Dr. Molecular compounds in a TCM used 2013 RCSB PDB [19] to treat sepsis and their in Changyin Li, Xiaogui University, Huainan Duke's docking silico pharmacology. Cheng, Peixun Liu, Union University, phytochemical Wenzheng Ju, Hao Yu Chinese Academy of and Medical Sciences ethnobotanical database TCM-ID, Towards a bioinformatics Yi Sun, Ruixin Zhu, Tongji University, Pharmacopoeia analysis of anti-Alzheimer's Hao Ye, Kailin Tang, Shanghai Center for 2013 of the People's HIT HIT, KEGG [20] herbal medicines from a Jing Zhao, Yujia Chen, Bioinformation Republic of target network perspective Qi Liu, Zhiwei Cao Technology China, pubmed Dalian University of Yan Li, Chunxiao Han, Investigation into the Technology, Jiangsu Jinghui Wang, Wei mechanism of Eucommia Kanion TCMSP, Xiao, Zhenzhong ulmoides Oliv. based on a 2014 Pharmaceutical TCMSP Molecular TTD [21] Wang, Jingxiao Zhang, systems pharmacology Corporation, Graduate docking Yinfeng Yang, Shuwei approach School of the Chinese Zhang, Chunzhi Ai Academy of Sciences Systems pharmacology- Bohui Li, Weiyang Tao, Northwest A&F TCMSP, TTD, 2014 TCMSP [22] based approach for Chunli Zheng, Piar University Molecular PharmGkb dissecting the addition and Sharali, Chao Huang, docking subtraction theory of Yingxue Fu, Yonghua traditional Chinese Wang medicine: An example using Xiao-Chaihu- Decoction and Da-Chaihu- Decoction A network pharmacology approach to understanding Shaohua Shi, Yuepiao Cai, Xiaojun Cai, Comprehensive the mechanisms of action of Central South Xiaoyong Zheng, natural Molecular Drugbank, traditional medicine: 2014 University, Wenzhou [23] Dongsheng Cao, products in docking KEGG Bushenhuoxue formula for Medical University treatment of chronic kidney Faqing Ye, Zheng TCM, Reaxys disease Xiang A novel network pharmacology approachto HerBiomap, Xujun Liang, Huiying TCM Gene ontology, analyse traditional herbal 2014 Tsinghua University drugCIPHER [24] formulae; the Liu-Wei-Di- Li, Shao Li Database@taiwa KEGG Huang pill as a case study n Institute of Chinese