ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine
Existing traditional Chinese medicine (TCM)-related databases are still insufficient in data standardization, integrity and precision, and need to be updated urgently. Herein, an Encyclopedia of Traditional Chinese Medicine version 2.0 (ETCM v2.0, http://www.tcmip.cn/ETCM2/front/#/) was constructed...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | Acta Pharmaceutica Sinica B |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211383523001016 |
| _version_ | 1797791909467389952 |
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| author | Yanqiong Zhang Xin Li Yulong Shi Tong Chen Zhijian Xu Ping Wang Meng Yu Wenjia Chen Bing Li Zhiwei Jing Hong Jiang Lu Fu Wenjing Gao Yanhua Jiang Xia Du Zipeng Gong Weiliang Zhu Hongjun Yang Haiyu Xu |
| author_facet | Yanqiong Zhang Xin Li Yulong Shi Tong Chen Zhijian Xu Ping Wang Meng Yu Wenjia Chen Bing Li Zhiwei Jing Hong Jiang Lu Fu Wenjing Gao Yanhua Jiang Xia Du Zipeng Gong Weiliang Zhu Hongjun Yang Haiyu Xu |
| author_sort | Yanqiong Zhang |
| collection | DOAJ |
| description | Existing traditional Chinese medicine (TCM)-related databases are still insufficient in data standardization, integrity and precision, and need to be updated urgently. Herein, an Encyclopedia of Traditional Chinese Medicine version 2.0 (ETCM v2.0, http://www.tcmip.cn/ETCM2/front/#/) was constructed as the latest curated database hosting 48,442 TCM formulas recorded by ancient Chinese medical books, 9872 Chinese patent drugs, 2079 Chinese medicinal materials and 38,298 ingredients. To facilitate the mechanistic research and new drug discovery, we improved the target identification method based on a two-dimensional ligand similarity search module, which provides the confirmed and/or potential targets of each ingredient, as well as their binding activities. Importantly, five TCM formulas/Chinese patent drugs/herbs/ingredients with the highest Jaccard similarity scores to the submitted drugs are offered in ETCM v2.0, which may be of significance to identify prescriptions/herbs/ingredients with similar clinical efficacy, to summarize the rules of prescription use, and to find alternative drugs for endangered Chinese medicinal materials. Moreover, ETCM v2.0 provides an enhanced JavaScript-based network visualization tool for creating, modifying and exploring multi-scale biological networks. ETCM v2.0 may be a major data warehouse for the quality marker identification of TCMs, the TCM-derived drug discovery and repurposing, and the pharmacological mechanism investigation of TCMs against various human diseases. |
| first_indexed | 2024-03-13T02:25:31Z |
| format | Article |
| id | doaj.art-d299f57c38ca4aa287e7e5a87c02fd53 |
| institution | Directory Open Access Journal |
| issn | 2211-3835 |
| language | English |
| last_indexed | 2024-03-13T02:25:31Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Acta Pharmaceutica Sinica B |
| spelling | doaj.art-d299f57c38ca4aa287e7e5a87c02fd532023-06-30T04:21:59ZengElsevierActa Pharmaceutica Sinica B2211-38352023-06-0113625592571ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicineYanqiong Zhang0Xin Li1Yulong Shi2Tong Chen3Zhijian Xu4Ping Wang5Meng Yu6Wenjia Chen7Bing Li8Zhiwei Jing9Hong Jiang10Lu Fu11Wenjing Gao12Yanhua Jiang13Xia Du14Zipeng Gong15Weiliang Zhu16Hongjun Yang17Haiyu Xu18Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaState Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, ChinaNational Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, ChinaState Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaShaanxi Academy of Traditional Chinese Medicine, Xi'an 710003, ChinaState Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang 550004, ChinaState Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, ChinaChina Academy of Chinese Medical Sciences, Beijing 100700, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Corresponding author. Tel.: +86 10 84035184; fax: +86 10 64013996.Existing traditional Chinese medicine (TCM)-related databases are still insufficient in data standardization, integrity and precision, and need to be updated urgently. Herein, an Encyclopedia of Traditional Chinese Medicine version 2.0 (ETCM v2.0, http://www.tcmip.cn/ETCM2/front/#/) was constructed as the latest curated database hosting 48,442 TCM formulas recorded by ancient Chinese medical books, 9872 Chinese patent drugs, 2079 Chinese medicinal materials and 38,298 ingredients. To facilitate the mechanistic research and new drug discovery, we improved the target identification method based on a two-dimensional ligand similarity search module, which provides the confirmed and/or potential targets of each ingredient, as well as their binding activities. Importantly, five TCM formulas/Chinese patent drugs/herbs/ingredients with the highest Jaccard similarity scores to the submitted drugs are offered in ETCM v2.0, which may be of significance to identify prescriptions/herbs/ingredients with similar clinical efficacy, to summarize the rules of prescription use, and to find alternative drugs for endangered Chinese medicinal materials. Moreover, ETCM v2.0 provides an enhanced JavaScript-based network visualization tool for creating, modifying and exploring multi-scale biological networks. ETCM v2.0 may be a major data warehouse for the quality marker identification of TCMs, the TCM-derived drug discovery and repurposing, and the pharmacological mechanism investigation of TCMs against various human diseases.http://www.sciencedirect.com/science/article/pii/S2211383523001016Traditional Chinese medicineDatabaseTarget identificationNetwork visualizationNew drug research and developmentMolecular mechanism |
| spellingShingle | Yanqiong Zhang Xin Li Yulong Shi Tong Chen Zhijian Xu Ping Wang Meng Yu Wenjia Chen Bing Li Zhiwei Jing Hong Jiang Lu Fu Wenjing Gao Yanhua Jiang Xia Du Zipeng Gong Weiliang Zhu Hongjun Yang Haiyu Xu ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine Acta Pharmaceutica Sinica B Traditional Chinese medicine Database Target identification Network visualization New drug research and development Molecular mechanism |
| title | ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine |
| title_full | ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine |
| title_fullStr | ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine |
| title_full_unstemmed | ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine |
| title_short | ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine |
| title_sort | etcm v2 0 an update with comprehensive resource and rich annotations for traditional chinese medicine |
| topic | Traditional Chinese medicine Database Target identification Network visualization New drug research and development Molecular mechanism |
| url | http://www.sciencedirect.com/science/article/pii/S2211383523001016 |
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