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Recently, studies of traditional Chinese medicine (TCM) have increasingly turned to high-throughput transcriptomic screens for molecular effects of herbs\/ingredients. And numerous studies have examined gene targets for herbs\/ingredients, and link herbs\/ingredients to various modern diseases. However, there is currently no systematic database organizing these data for TCM. Therefore, we built HERB, a high-throughput experiment- and reference-guided database of TCM, with its Chinese name as BenCaoZuJian. We re-analyzed 6164 gene expression profiles from 1037 high-throughput experiments evaluating TCM herbs\/ingredients, and generated connections between TCM herbs\/ingredients and 2837 modern drugs by mapping the comprehensive pharmacotranscriptomics dataset in HERB to CMap, the largest such dataset for modern drugs. Moreover, we manually curated 1241 gene targets and 494 modern diseases for 473 herbs\/ingredients from 1966 references published recently, and cross-referenced this novel information to databases containing such data for drugs. Together with database mining and statistical inference, we linked 12 933 targets and 28 212 diseases to 7263 herbs and 49 258 ingredients and provided six pairwise relationships among them in HERB. In summary, HERB will intensively support the modernization of TCM and guide rational modern drug discovery efforts. And it is accessible through http:\/\/herb.ac.cn\/.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1063","type":"journal-article","created":{"date-parts":[[2020,10,28]],"date-time":"2020-10-28T08:11:42Z","timestamp":1603872702000},"page":"D1197-D1206","source":"Crossref","is-referenced-by-count":579,"title":["HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine"],"prefix":"10.1093","volume":"49","author":[{"given":"ShuangSang","family":"Fang","sequence":"first","affiliation":[{"name":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China"}]},{"given":"Lei","family":"Dong","sequence":"additional","affiliation":[{"name":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China"}]},{"given":"Liu","family":"Liu","sequence":"additional","affiliation":[{"name":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China"}]},{"given":"JinCheng","family":"Guo","sequence":"additional","affiliation":[{"name":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China"}]},{"given":"LianHe","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China"}]},{"given":"JiaYuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China"}]},{"given":"DeChao","family":"Bu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China"}]},{"given":"XinKui","family":"Liu","sequence":"additional","affiliation":[{"name":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China"}]},{"given":"PeiPei","family":"Huo","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China"}]},{"given":"WanChen","family":"Cao","sequence":"additional","affiliation":[{"name":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China"}]},{"given":"QiongYe","family":"Dong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China"}]},{"given":"JiaRui","family":"Wu","sequence":"additional","affiliation":[{"name":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China"}]},{"given":"Xiaoxi","family":"Zeng","sequence":"additional","affiliation":[{"name":"West China Biomedical Big Data Center, Division of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China"}]},{"given":"Yang","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China"}]},{"given":"Yi","family":"Zhao","sequence":"additional","affiliation":[{"name":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China"},{"name":"Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China"}]}],"member":"286","published-online":{"date-parts":[[2020,12,2]]},"reference":[{"key":"2021010313135858300_B1","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1038\/s41587-020-0502-7","article-title":"Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker","volume":"38","author":"Duran-Frigola","year":"2020","journal-title":"Nat. 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