[{"dbId":9483,"shortName":"BATMAN-TCM","accession":"DBC009483","fullName":"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.","url":"http://bionet.ncpsb.org.cn/batman-tcm/","foundedYear":"2016","hostInstitution":"Beijing Institute of Lifeomics","address":"No.5, No.1 Beichen West Road, Chaoyang District, Beijing, China","city":"Beijing","province":"","country":"China","currentVersion":"v2.0","contactName":"Zhongyang Liu","contactEmail":"liuzy1984@163.com","availableProtocol":"1","lastUpdate":"2024-01","age":10,"citation":594,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1721114176000,"lastModified":"2025-10-11 16:48:16","dataTypeList":[{"id":30231,"datatypeName":"DNA","lastModified":1724491573000},{"id":30232,"datatypeName":"Protein","lastModified":1724491573000}],"categoryList":[{"id":36831,"name":"Gene genome and annotation","lastModified":1724491573000},{"id":36832,"name":"Health and medicine","lastModified":1724491573000}],"keywordsList":[{"id":54216,"name":"traditional Chinese medicine (TCM)","lastModified":1724491573000},{"id":54217,"name":"target protein","lastModified":1724491573000},{"id":54218,"name":"interaction","lastModified":1724491573000},{"id":54219,"name":"drug discovery","lastModified":1724491573000}],"dataObjectList":[{"id":27459,"name":"NA","lastModified":1724491573000}],"publicationList":[{"id":78553,"pmid":"37904598","title":"BATMAN-TCM 2.0: an enhanced integrative database for known and predicted interactions between traditional Chinese medicine ingredients and target proteins.","author":"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","journal":"Nucleic Acids Res","year":"2024","issue":"D1","volume":"52","abst":"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.<br>","citation":106,"citationDate":"2026-05-02","lastModified":1777687763000,"createDate":1720512634000,"citationsList":"41970029,41824223,41825769,41762613,41722249,41722459,41654607,41588523,41574553,41657773,41546107,41540492,41585878,41506303,41483174,41243954,41473336,41599630,41430741,41386308,41361572,41397932,41331739,41241204,41365194,41788588,41322003,41220417,41188309,41260787,41239601,41300746,PPR1109745,41111909,PPR1096066,41261601,41180795,41150757,41069602,40795588,40800606,41052279,40754381,40778401,40732361,40703642,40682943,40678730,40712283,40729050,40631551,40586853,40661082,40732222,40626310,PPR1037130,40505263,40535764,40530435,40381707,40260541,40317435,40318773,40246868,40303920,40249926,40258762,40230684,40131994,40112539,40143189,40129983,40129771,40098618,39686653,39972480,39955364,39947372,39833846,39800680,39623712,38847263,38693741,39723533,39684661,39568012,39566862,39606633,39534925,39467716,39472740,39519004,39474612,39392404,39354431,39355231,39334727,39253011,39095509,39130628,38998977,38966421,38740106,38766523,38519956,38467948","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":null,"pubMonth":null,"firstPub":null},{"id":79015,"pmid":"26879404","title":"BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine.","author":"Liu Z, Guo F, Wang Y, Li C, Zhang X, Li H, Diao L, Gu J, Wang W, Li D, He F.","journal":"Sci Rep","year":"2016","issue":null,"volume":"6","abst":"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.","citation":539,"citationDate":"2026-05-02","lastModified":1777688250000,"createDate":null,"citationsList":"41770426,41650101,41657773,41549304,41547709,41507801,41560738,41473244,41329690,41304986,41322308,41212495,41226607,PPR1109745,41152387,41053833,40968251,41113022,40921925,40958250,40949293,40784529,40640294,40630680,40688586,40542274,40522426,40524966,40510335,41608209,40398514,40450987,40391189,40324631,40295796,40260263,40225864,40142979,39987176,39985335,39910202,39973856,39312276,39940967,39940699,39843552,39867868,39749683,39745279,41127994,40237055,40033508,39917918,39806972,39492771,39400011,38676497,38379403,39861077,39730024,39705287,39577557,39969310,39609491,39660000,39576697,39565148,39564108,40037544,39641032,39465696,39337710,39355777,39398618,39264139,39192219,39241387,39178683,39120856,39170438,PPR888319,39068852,39066667,39253696,38971780,39035991,39015338,39029075,PPR875334,38904095,38940090,38905402,38775721,38709282,38738181,38643449,38694920,PPR838687,39606260,38608086,38583348,38675376,38486764,38405483,38390212,38329441,38352962,38348705,38213248,38322942,38313313,38910482,38415453,37904598,37855349,37340752,36861803,38145012,38107658,38176264,38163225,38050310,37606264,36546685,38382279,38035021,38005265,38034785,37924136,38013284,37986356,37933017,37895953,37808899,37915641,37794689,37849727,37788594,37679988,37893458,37770919,37357557,37771609,37728545,37809603,37713995,37719108,37773840,37682161,37680700,37598188,37664753,37637410,37597360,37575147,37600392,37528325,37653805,37623830,37486750,37529338,37385213,37449101,37373516,37350984,37367071,37361229,37347115,37265745,37305432,37274217,37193294,37155147,PPR655823,37123969,37032511,37064951,PPR641895,37113393,37180669,37083798,37109624,36982981,37007025,37000099,36875720,37396157,37397412,37057280,36774724,36818229,36640003,36770995,36743462,36762105,36685422,36685421,36872359,36045534,36593870,36816233,36561604,36825182,36569327,36499711,36624942,34962453,36506308,36506508,36394096,36465462,36457705,36452327,36374307,36408344,36386710,36349188,36345477,36368285,36277473,36248423,36249768,36246605,36225565,36210811,36182651,36235337,36248435,36134852,36465851,36118098,36181021,35880436,36071733,36514753,36091822,36059953,36063745,35967794,35362201,35915795,36118001,35858880,35838029,35865997,35818037,35845577,35801781,35872979,35841663,35860733,35543243,35780747,35717786,35754689,35754951,35720023,35672815,35672755,35672528,35813340,35669396,35668772,35596156,35591866,35586697,35571728,35533913,35722393,35535155,35566179,35517983,35548340,35383784,35520289,35479514,35463075,35427726,35449823,35449811,35396886,35432526,35462897,35366129,35656081,35399630,35401884,35399830,35399637,35386850,35401181,35430443,35306140,35305385,35359830,35356545,35303581,35258759,35280511,35265147,35281906,35281886,35181715,35210754,35176999,35173140,35173416,35114343,35114443,35140607,35097123,35127697,35068944,35033647,35341135,35082676,35046814,34933331,34493195,34382512,34992452,34952191,34959737,34975499,34956381,36303742,34955724,34950028,34875999,34875251,35071471,34931923,34925035,34176428,34098848,33784489,34845218,34799616,34867329,34819854,34697550,34641869,34627325,34659577,34600579,34606948,34593896,34670180,34621323,34646130,34544480,34530875,34484411,34432202,34432201,34434246,34419734,34394386,35069753,34394393,34381520,34532487,34349502,PPR374916,34322321,34303037,34282381,34246740,34232166,34185887,34273705,34153045,34177580,34114461,34091181,34054530,34045964,34026596,33963245,33962310,33976706,33959188,33897417,33854318,33859874,33795629,33811957,33771644,34221858,33824873,33743701,33778069,33746756,33746755,32662814,33727915,33746604,33681222,33609729,33708876,33506873,33300033,33564316,33513128,33513419,33746744,33505310,33422675,33569466,33509748,32838712,32767929,33456481,33456482,33251769,33665096,33362562,33196098,32608342,35573878,33313323,33273808,33292335,33187508,33224254,33163124,33193800,33098971,33101439,33082908,33061308,32956722,32938944,33014099,32918992,32963568,32896625,32866138,32874205,32908557,32825325,32798277,32848800,32730293,32687952,32714405,32655662,32625232,32561477,32617108,32521813,32566871,32595734,32505821,32554251,32374895,32388823,32454869,32345291,32351618,32382293,32362827,32293408,32294506,32273767,32122353,32565596,32114589,31964464,32101775,38757042,32089647,32028240,32166674,31938806,31935895,31899674,31612829,31949472,31446830,31819371,31824322,31765763,31814838,31683034,31781287,31715498,31781263,31638231,31546083,31572193,31612073,31564827,31534865,31465829,31411813,31412658,31341240,31348992,31255722,31281407,31053932,31024317,30891809,30911319,30906412,30906409,30764831,30809144,30754631,30854000,30809532,30792744,30357356,30216226,30568725,30502478,30232231,30464399,30385774,30317606,30230922,29986408,29973199,30034946,29850479,35540854,29517941,29420025,29106634,29344417,29177114,29138518,29066842,28947774,28915268,28752861,28604846,29069769","isNew":0,"isParse":0,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":"10.1038/srep21146","pubMonth":"2","firstPub":"2016-02-16"}],"ratingList":[],"organismList":[{"id":38707,"organismName":"NA","lastModified":1724491573000}],"biodbRanks":[],"themeList":[],"zindex":59.4,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:53","ess":0},{"dbId":6146,"shortName":"ETCM","accession":"DBC006146","fullName":"The Encyclopedia of Traditional Chinese Medicine","description":"ETCM 2.0 provides the most comprehensive list of 48,442 TCM formulas and 9872 Chinese patent drugs with the standardized clinical data, the chemical and target profilings, as well as the quantitative information of marker ingredients and functional information.","url":"http://www.tcmip.cn/ETCM2/front/#/","foundedYear":"2019","hostInstitution":"Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences","address":"Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China","city":"Beijing","province":"Beijing","country":"China","currentVersion":"v2.0","contactName":"Hai-Yu Xu","contactEmail":"hyxu@icmm.ac.cn","availableProtocol":"1","lastUpdate":"2022-06","age":7,"citation":579,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1546531430000,"lastModified":"2025-10-11 16:43:25","dataTypeList":[{"id":26336,"datatypeName":"Other","lastModified":1693979825000}],"categoryList":[{"id":31689,"name":"Health and medicine","lastModified":1693979825000}],"keywordsList":[{"id":45514,"name":"traditional chinese medicine","lastModified":1693979825000}],"dataObjectList":[{"id":23866,"name":"NA","lastModified":1693979825000}],"publicationList":[{"id":67442,"pmid":"30365030","title":"ETCM: an encyclopaedia of traditional Chinese medicine.","author":"Xu HY, Zhang YQ, Liu ZM, Chen T, Lv CY, Tang SH, Zhang XB, Zhang W, Li ZY, Zhou RR, Yang HJ, Wang XJ, Huang LQ.","journal":"Nucleic Acids Res","year":"2019","issue":"D1","volume":"47","abst":"Traditional Chinese medicine (TCM) is not only an effective solution for primary health care, but also a great resource for drug innovation and discovery. To meet the increasing needs for TCM-related data resources, we developed ETCM, an Encyclopedia of Traditional Chinese Medicine. ETCM includes comprehensive and standardized information for the commonly used herbs and formulas of TCM, as well as their ingredients. The herb basic property and quality control standard, formula composition, ingredient drug-likeness, as well as many other information provided by ETCM can serve as a convenient resource for users to obtain thorough information about a herb or a formula. To facilitate functional and mechanistic studies of TCM, ETCM provides predicted target genes of TCM ingredients, herbs, and formulas, according to the chemical fingerprint similarity between TCM ingredients and known drugs. A systematic analysis function is also developed in ETCM, which allows users to explore the relationships or build networks among TCM herbs, formulas,ingredients, gene targets, and related pathways or diseases. ETCM is freely accessible at http://www.nrc.ac.cn:9090/ETCM/. We expect ETCM to develop into a major data warehouse for TCM and to promote TCM related researches and drug development in the future.<br>","citation":555,"citationDate":"2026-05-02","lastModified":1777675625000,"createDate":1613162927000,"citationsList":"41780827,41762613,41672401,41616564,40598731,41452443,41473336,41473244,41368819,41498040,41471355,41243489,41328642,41367024,41239042,41213440,41322003,41240538,41203071,41182350,41305716,41260778,41239601,PPR1111825,41226607,41152614,41300276,41205526,41135273,41155084,41061588,40921925,41011202,40988117,40901370,40977901,40854970,40783635,40784529,41004131,40695405,40703642,40683424,40724927,40718791,40645540,40682943,40632498,40631551,40596421,40577270,40571901,40544322,40626310,40522426,40575773,40524966,40519656,40599314,40496730,40451357,40495892,40426157,40453667,40386636,40391004,40391580,40356964,40339536,40224393,40239538,40190815,40168944,40170727,40166460,40142979,39956299,39953430,39937393,39929402,39312276,39940967,39871254,39843552,39833846,39714965,39800680,39803604,39778593,39839391,39802510,39765297,39866448,39819538,39558177,38920066,35770417,39705287,39704481,39712520,PPR955798,39617279,39669205,39558555,39561883,41169938,39606633,39605916,39534925,39313870,39527891,40037544,40007160,39512686,39488872,39413937,39423481,39390901,39506958,39382678,39524885,39524713,39404324,39430861,39355231,39326289,39311834,39299361,39289763,39305743,39336138,39323837,39241972,39252243,39281275,39338294,39123236,39120856,39127288,39170438,39276046,39148543,39135796,39066667,39130628,39108744,39044161,39064786,39062817,39006190,39073832,39011503,38967379,38950838,39005933,38940332,38974913,38888753,38928028,38841513,38693521,38738181,38630770,38680873,38622983,39606260,38504542,38574427,38561057,38583348,38552763,38675376,38583347,PPR823073,38484140,38460201,38429802,38471318,38476329,PPR954316,38435751,38344924,38396803,38310985,38363941,38348705,38322942,PPR792809,38328576,39257141,38920073,38902931,38415453,38213161,37859322,37475552,37309760,38707921,38145859,38102686,38375054,38050310,37674371,37386769,36546685,38019769,38089052,38213899,38035021,37962031,37957642,38074898,37941061,38197310,38027004,37890804,37880698,37847347,37813291,37904411,37861538,37895859,37893319,37777031,37770919,37357557,PPR728534,37799727,37682161,37759595,37615817,37611839,37664753,37631075,37829020,37570816,37546617,37495029,37486750,37467820,37458182,37459834,37456759,37393026,37385213,37449101,37413835,37446547,37350984,37383718,37719385,37347115,37264453,37305432,37244433,37242550,37236139,37189139,37170366,37138292,37245871,37094153,37081536,37089716,37043698,37089916,37086361,36997527,36989725,36882903,37425046,36949297,37007025,36948142,36982389,36969211,36898572,36896476,36969029,36937833,37000099,36719094,36875720,36858276,37397412,36903262,36874030,36795011,36818229,38327605,38868333,36845103,36814500,36736970,36716903,36670282,36777831,36713827,36684691,38868426,36321231,36045534,35392781,36608500,36593772,36563052,36561604,36484971,36503032,36523421,36545315,36482532,36479314,36479181,36506573,36483951,36410574,36430747,36382875,36408344,36401485,36326669,36353164,36345477,PPR559209,36288650,36345486,36278162,36263126,36304327,36204124,36193286,36225565,36193202,36193133,36182651,36248435,36134852,36186074,36133786,36133785,39666297,36139041,36110515,36105213,36091823,36091794,36063700,38867910,36046748,36034874,36003508,35990498,36245702,36006844,35953761,35935870,35935848,35891565,35910835,35818037,35873573,35810695,35780747,35799788,35811865,35688255,35672815,35672755,35610020,35749826,35681322,35656312,35646921,35567927,35586697,35547656,35383784,35468451,35427726,35405252,35462897,35406976,35287559,35541911,35401166,35360660,35430443,35401186,35303280,35306140,35370677,35283292,35356545,35303581,35591924,35260672,35258759,35256851,35265147,35281906,35177987,35155889,35114443,35092825,35103067,35097123,35087623,35075364,35115923,35069756,35069542,34980163,34664659,34493195,35115127,34975502,34955724,34950027,34875251,35655909,34899351,34887747,34799616,34826774,34867413,34859062,34836709,34754316,34715778,34702323,34632655,34528665,34607274,34603473,34512320,34484411,34432201,34457214,34434246,34419734,34413968,34394900,34381520,34532487,34393777,34325669,34349502,34349833,34302944,34322321,34335236,34246740,36118930,34306165,34183011,34273705,34257679,34194519,34729303,34149422,34051074,34122100,34093718,33931876,34045964,34040514,33972672,34046076,34025416,33963245,33953309,34055017,34007289,33995004,33981239,33986941,33968984,33897431,33854318,33831468,33839698,33795629,34221858,33824873,33729688,33762941,33647426,33615709,33681222,33658934,33679403,33633573,33603663,33584273,33513419,33551818,33551800,33628171,33585398,33441867,33516447,33264402,33358854,33426081,33381214,33296090,33363710,33338839,33273808,33299447,33163124,33193800,33193802,33173434,33192528,33178009,33178024,33039419,33123002,33209439,33014098,33041827,33014099,32978039,32949888,32849901,32727531,34277118,32600331,32670064,32559618,32450873,32477148,32457601,32360484,32345291,32382293,32344708,32351982,32307268,32328128,33431011,32198544,32197305,32208163,PPR117589,32126522,31982775,31892257,31614129,31348992,31379593,31379563,30936832","isNew":0,"isParse":0,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":"10.1093/nar/gky987","pubMonth":"1","firstPub":"2019-01-01"},{"id":74821,"pmid":"37425046","title":"ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine.","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","journal":"Acta Pharm Sin B","year":"2023","issue":"6","volume":"13","abst":"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.<br>","citation":73,"citationDate":"2026-05-02","lastModified":1777684756000,"createDate":1692176309000,"citationsList":"41970029,41793523,41742706,41722249,41588523,41657773,41501158,41483174,41498040,41331836,41291896,41322003,41184845,41260787,41260788,41260785,PPR1109745,41167569,41205526,41101073,41057911,41155084,41180795,40901370,40822477,40732361,40695405,40634546,40729050,40597357,40626310,40481553,40573220,40499219,40470052,40381707,40893436,40421208,40345271,40335461,40031344,40303920,40635974,40052602,39947372,39820731,39800680,40574364,39558177,40823261,39577557,39466576,39458516,39355231,39123236,39095509,39175133,38929100,38799163,38716617,38898979,38621329,38519956,38471316,38238785,37904598,38037139,PPR766756,38035021,37733919,37860777,37280673,37264453","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":null,"pubMonth":null,"firstPub":null}],"ratingList":[],"organismList":[{"id":33656,"organismName":"NA","lastModified":1693979825000}],"biodbRanks":[{"id":4935,"zindex":2.0,"citations":2,"year":2019,"month":11,"updateDate":1573450317000,"lastModified":1573450317000}],"themeList":[],"zindex":82.7143,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:34","ess":0},{"dbId":7435,"shortName":"HERB","accession":"DBC007435","fullName":"A high-throughput experiment- and reference-guided database of traditional Chinese medicine","description":"HERB database integrates four types of evidence for TCM: (i) we curated 8558 clinical trials and 8032 meta-analyses information for TCM and extracted clear clinical conclusions for 1941 clinical trials and 593 meta-analyses with companion supporting papers. (ii) we updated experimental evidence for TCM, increased the number of high-throughput experiments to 2231, and curated references to 6 644. We newly added high-throughput experiments for 376 diseases and evaluated all pairwise similarities among TCM herbs/ingredients/formulae, modern drugs and diseases. (iii) we provide an automatic analyzing interface for users to upload their gene expression profiles and map them to our curated datasets. (iv) we built knowledge graph representations of HERB entities and relationships to retrieve TCM knowledge better. ","url":"http://herb.ac.cn/v2","foundedYear":"2021","hostInstitution":"Beijing University of Chinese Medicine","address":"Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China.","city":"Beijing","province":"Beijing","country":"China","currentVersion":"2.0","contactName":"Yi Zhao","contactEmail":"biozy@ict.ac.cn","availableProtocol":"1","lastUpdate":"2024-11-18","age":5,"citation":405,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1634626786000,"lastModified":"2025-10-11 16:45:12","dataTypeList":[{"id":34044,"datatypeName":"DNA","lastModified":1754536831000}],"categoryList":[{"id":42270,"name":"Health and medicine","lastModified":1754536831000},{"id":42271,"name":"Metadata","lastModified":1754536831000}],"keywordsList":[{"id":62400,"name":"Pharmacotranscriptomics","lastModified":1754536831000},{"id":62401,"name":"TCM","lastModified":1754536831000},{"id":62402,"name":"traditional chinese medicine","lastModified":1754536831000}],"dataObjectList":[{"id":31223,"name":"NA","lastModified":1754536831000}],"publicationList":[{"id":71824,"pmid":"33264402","title":"HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine.","author":"Fang S, Dong L, Liu L, Guo J, Zhao L, Zhang J, Bu D, Liu X, Huo P, Cao W, Dong Q, Wu J, Zeng X, Wu Y, Zhao Y.","journal":"Nucleic Acids Res","year":"2021","issue":"D1","volume":"49","abst":"Pharmacotranscriptomics has become a powerful approach for evaluating the therapeutic efficacy of drugs and discovering new drug targets. 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/.<br>","citation":444,"citationDate":"2026-05-02","lastModified":1777681609000,"createDate":1613629626000,"citationsList":"41970029,41865191,41850640,41790377,41762613,41690431,41673882,41651870,41650101,41674937,41588256,41588523,41657773,41562296,41508020,41983820,41662351,41582741,41531391,40947735,41421687,41418643,41411324,41471391,41386308,41368332,41471355,41353393,41243489,41397932,41367024,41383484,41314435,41357186,41357200,41270909,41231334,41225027,41222694,41322003,41226241,41305835,41305716,41260787,41260788,41260785,41226607,41202382,PPR1109745,41145778,41205526,41135615,41155659,41155084,41261601,41189264,41054059,40968251,41011235,40945847,40794009,40948754,40932836,40916282,40815948,40784529,40779843,40843378,40759079,40800606,40754381,40778401,40792149,40718724,40741600,40732361,40684964,40668407,40634546,40633860,40624153,40605371,40725959,40631551,40491254,40577270,40626310,40580693,40607002,40513940,40513920,40481474,40530435,40521559,41608209,40409102,40381707,40421208,40348996,40031344,40319129,40503414,40406134,40309305,PPR1009762,40382816,40286672,40303920,40296871,40286748,40221773,40211760,40635974,40238509,40215819,40196753,40172120,40271912,40258762,40169534,40133701,40191596,40138971,40076984,40057142,40050654,40050387,40054637,40032878,40037475,40183906,40142979,39998991,40076790,40026302,39994309,40227198,40092104,39955364,40017515,39947372,39973856,39928794,39876048,39865865,39865145,39844171,39843552,39828895,39800680,39772836,39762416,39752106,40357772,40033508,39558177,39495135,38676511,38551057,38379403,39730024,39724681,40823261,39577557,39617279,40171446,39600675,39582813,39659916,39516633,40037544,39544939,39488872,39462106,39461014,39444311,39443630,39464340,39428405,39474612,39474608,39382736,39378530,39640819,39392404,39408591,39355231,39329977,39386883,39398618,39328786,39296670,41399784,39329129,39318781,39247430,39217296,39216402,39197801,PPR900861,39180998,39211446,39095509,39151530,39002826,39006190,39026676,39175133,38967229,38693787,38968792,38924866,39353880,38974913,38884700,38837094,38776291,38835215,38753250,38766523,38705430,38701256,38738181,38757105,38681206,PPR838687,38680873,39850603,38698802,38704357,38561057,38519984,38583347,38711369,38476329,38726425,PPR954316,38344924,38396803,38326539,38310985,38661582,38363941,38363936,38213248,38328576,38272335,38229051,38215156,38234923,39092733,38867534,38747231,38571354,38343057,38181263,38178682,37904598,37897343,37340752,38707921,38145345,38102686,38156015,38694562,38069658,38061471,38149194,38115276,38048229,38019798,38213899,37984544,38035021,37963492,38074898,37941061,38197310,38013344,37933017,37992493,37865148,PPR739799,37814323,37793997,37832105,37800842,37770919,37808199,37701046,37682161,37615817,37611839,37664753,37631075,37580684,PPR706435,37583907,37829020,37490124,37495029,37488546,37485340,37393234,37315647,37374083,37233762,37251843,PPR661374,37335709,37245871,37168258,37028096,37086361,37113393,37012370,36997527,36972781,37425046,36949297,37101493,37007025,36896476,36969029,36936437,36719094,36858276,36841364,36845041,36795011,36805225,36879883,36827014,36800601,36777631,36716957,PPR608729,36654765,36661523,36598916,PPR592158,37817527,36625159,36581492,36477977,PPR581019,36523421,36624942,36533181,36506559,36506308,36467554,36440293,36345477,36386126,36389722,PPR559209,36304143,36200679,36248430,36581570,36249800,36171401,36162550,36193202,36182651,PPR549138,36185677,36160715,36148321,36133786,PPR542076,36267750,36058476,35880436,36119473,36062176,36091823,35995784,36016675,36245702,35959419,35991881,36006844,35910835,35873910,35838029,35874515,35793597,35774609,35720023,35688255,35721171,35694259,35664944,35615578,35586682,35509624,35529440,35531567,35406976,35287559,35370688,35306140,35283292,35591924,35260672,35177987,35164167,35153764,35140607,35127696,35095490,34986599,34933331,34664659,35115127,35002704,34992531,34975502,34898475,34802380,34662244,34867405,34824593,34705126,34702323,34753029,34622844,34557547,34433871,34400263,34422068,34413968,34422028,34378141,34394377,34321866,34335855,34239596,33957833,33968984,33850275,33363710","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":"10.1093/nar/gkaa1063","pubMonth":"1","firstPub":"2021-01-01"},{"id":81236,"pmid":"39558177","title":"HERB 2.0: an updated database integrating clinical and experimental evidence for traditional Chinese medicine.","author":"Gao K, Liu L, Lei S, Li Z, Huo P, Wang Z, Dong L, Deng W, Bu D, Zeng X, Li C, Zhao Y, Zhang W, Wang W, Wu Y.","journal":"Nucleic Acids Res","year":"2025","issue":"D1","volume":"53","abst":"Clinical trials and meta-analyses are considered high-level medical evidence with solid credibility. However, such clinical evidence for traditional Chinese medicine (TCM) is scattered, requiring a unified entrance to navigate all available evaluations on TCM therapies under modern standards. Besides, novel experimental evidence has continuously accumulated for TCM since the publication of HERB 1.0. Therefore, we updated the HERB database to integrate four types of evidence for TCM: (i) we curated 8558 clinical trials and 8032 meta-analyses information for TCM and extracted clear clinical conclusions for 1941 clinical trials and 593 meta-analyses with companion supporting papers. (ii) we updated experimental evidence for TCM, increased the number of high-throughput experiments to 2231, and curated references to 6 644. We newly added high-throughput experiments for 376 diseases and evaluated all pairwise similarities among TCM herbs/ingredients/formulae, modern drugs and diseases. (iii) we provide an automatic analyzing interface for users to upload their gene expression profiles and map them to our curated datasets. (iv) we built knowledge graph representations of HERB entities and relationships to retrieve TCM knowledge better. In summary, HERB 2.0 represents rich data type, content, utilization, and visualization improvements to support TCM research and guide modern drug discovery. It is accessible through http://herb.ac.cn/v2 or http://47.92.70.12.","citation":24,"citationDate":"2026-05-02","lastModified":1777689532000,"createDate":null,"citationsList":"41991344,41970029,41955698,41850640,41657773,41563450,41547391,41590654,41206750,41359225,41409597,41383484,PPR1109745,41102805,41173671,41155084,41180795,41069602,40971773,40945847,40729050,40554052,40893436,PPR1002444","isNew":0,"isParse":0,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":"10.1093/nar/gkae1037","pubMonth":"1","firstPub":"2025-01-01"}],"ratingList":[],"organismList":[{"id":43606,"organismName":"NA","lastModified":1754536831000}],"biodbRanks":[],"themeList":[],"zindex":81.0,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:42","ess":0},{"dbId":7890,"shortName":"NPCDR","accession":"DBC007890","fullName":"Natural product-based drug combination and its disease-specific molecular regulation","description":"This database was unique in (a) providing the comprehensive information of NP-based drug combinations & describing their clinically or experimentally validated therapeutic effect, (b) giving the disease-specific molecular regulation data for a number of NP-based drug combinations, (c) fully referencing all NPs, drugs, regulated molecules/pathways by cross-linking them to the available databases describing their biological or pharmaceutical characteristics. ","url":"https://idrblab.org/npcdr","foundedYear":"2022","hostInstitution":"Hangzhou Normal University","address":"","city":"","province":"","country":"China","currentVersion":"","contactName":"Feng ZHU","contactEmail":"zhufeng@zju.edu.cn","availableProtocol":"1","lastUpdate":"","age":4,"citation":29,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1650602680000,"lastModified":"2025-10-11 16:45:51","dataTypeList":[{"id":23151,"datatypeName":"Other","lastModified":1659256916000}],"categoryList":[{"id":27479,"name":"Health and medicine","lastModified":1659256916000},{"id":27480,"name":"Pathway","lastModified":1659256916000}],"keywordsList":[{"id":38665,"name":"drug","lastModified":1659256916000},{"id":38666,"name":"drug combination","lastModified":1659256916000},{"id":38667,"name":"pharmacology","lastModified":1659256916000}],"dataObjectList":[{"id":20605,"name":"NA","lastModified":1659256916000}],"publicationList":[{"id":74377,"pmid":"34664659","title":"NPCDR: natural product-based drug combination and its disease-specific molecular regulation.","author":"Xueni Sun, Yintao Zhang, Ying Zhou, Xichen Lian, Lili Yan, Ting Pan, Ting Jin, Han Xie, Zimao Liang, Wenqi Qiu, Jianxin Wang, Zhaorong Li, Feng Zhu, Xinbing Sui","journal":"Nucleic Acids Res","year":"2022","issue":"D1","volume":"50","abst":"Natural product (NP) has a long history in promoting modern drug discovery, which has derived or inspired a large number of currently prescribed drugs. Recently, the NPs have emerged as the ideal candidates to combine with other therapeutic strategies to deal with the persistent challenge of conventional therapy, and the molecular regulation mechanism underlying these combinations is crucial for the related communities. Thus, it is urgently demanded to comprehensively provide the disease-specific molecular regulation data for various NP-based drug combinations. However, no database has been developed yet to describe such valuable information. In this study, a newly developed database entitled 'Natural Product-based Drug Combination and Its Disease-specific Molecular Regulation (NPCDR)' was thus introduced. This database was unique in (a) providing the comprehensive information of NP-based drug combinations & describing their clinically or experimentally validated therapeutic effect, (b) giving the disease-specific molecular regulation data for a number of NP-based drug combinations, (c) fully referencing all NPs, drugs, regulated molecules/pathways by cross-linking them to the available databases describing their biological or pharmaceutical characteristics. Therefore, NPCDR is expected to have great implications for the future practice of network pharmacology, medical biochemistry, drug design, and medicinal chemistry. This database is now freely accessible without any login requirement at both official (https://idrblab.org/npcdr/) and mirror (http://npcdr.idrblab.net/) sites.<br>","citation":31,"citationDate":"2026-05-02","lastModified":1777683731000,"createDate":1649238765000,"citationsList":"41243954,41206750,41260785,40634546,40341222,39708551,39164783,39002694,38795676,38494866,38579613,38372508,38711369,38049779,38005315,37663785,37486750,37514998,37245871,36951721,36795011,36805225,36660714,36364163,36234829,36142236,35994933,35820601,35890545,35508859,34986604","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":null,"pubMonth":null,"firstPub":null}],"ratingList":[],"organismList":[{"id":28490,"organismName":"NA","lastModified":1659256916000}],"biodbRanks":[],"themeList":[],"zindex":7.25,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:44","ess":0},{"dbId":7820,"shortName":"MCDB ","accession":"DBC007820","fullName":"","description":"MCDB is designed to provide centralized and comprehensive information on mitotic catastrophe-related genes, proteins and chemical interventions, as well as extended functions such as protein sequence similarity comparison and target prediction rested on compound structure similarity.","url":"http://www.combio-lezhang.online/MCDB/index_html","foundedYear":"2021","hostInstitution":"Sichuan University","address":"","city":"","province":"","country":"China","currentVersion":"","contactName":"Guan Wang","contactEmail":"guan8079@163.com","availableProtocol":"1","lastUpdate":"","age":5,"citation":24,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1650547241000,"lastModified":"2025-10-11 16:45:45","dataTypeList":[{"id":22730,"datatypeName":"DNA","lastModified":1655704096000},{"id":22731,"datatypeName":"Protein","lastModified":1655704096000}],"categoryList":[{"id":26916,"name":"Structure","lastModified":1655704096000},{"id":26917,"name":"Interaction","lastModified":1655704096000},{"id":26918,"name":"Literature","lastModified":1655704096000}],"keywordsList":[{"id":37846,"name":"mitotic catastrophe","lastModified":1655704096000}],"dataObjectList":[{"id":20101,"name":"NA","lastModified":1655704096000}],"publicationList":[{"id":74292,"pmid":"34729303","title":"MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction.","author":"Le Zhang, Lei Zhang, Yue Guo, Ming Xiao, Lu Feng, Chengcan Yang, Guan Wang, Liang Ouyang","journal":"Acta Pharm Sin B","year":"2021","issue":"10","volume":"11","abst":"Mitotic catastrophe (MC) is a form of programmed cell death induced by mitotic process disorders, which is very important in tumor prevention, development, and drug resistance. Because rapidly increased data for MC is vigorously promoting the tumor-related biomedical and clinical study, it is urgent for us to develop a professional and comprehensive database to curate MC-related data. Mitotic Catastrophe Database (MCDB) consists of 1214 genes/proteins and 5014 compounds collected and organized from more than 8000 research articles. Also, MCDB defines the confidence level, classification criteria, and uniform naming rules for MC-related data, which greatly improves data reliability and retrieval convenience. Moreover, MCDB develops protein sequence alignment and target prediction functions. The former can be used to predict new potential MC-related genes and proteins, and the latter can facilitate the identification of potential target proteins of unknown MC-related compounds. In short, MCDB is such a proprietary, standard, and comprehensive database for MC-relate data that will facilitate the exploration of MC from chemists to biologists in the fields of medicinal chemistry, molecular biology, bioinformatics, oncology and so on. The MCDB is distributed on http://www.combio-lezhang.online/MCDB/index_html/.<br>","citation":31,"citationDate":"2026-05-02","lastModified":1777683598000,"createDate":1649238730000,"citationsList":"41644632,41507521,41516175,41675595,41419001,PPR1130181,40789828,40664640,40580449,40414522,39290983,39142816,39015573,38544801,38374297,38323982,41676022,38238555,38003905,37625527,37234044,36825001,36649216,36543035,36421506,36815052,36186430,35805101,35538061,34908415,34764986","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":null,"pubMonth":null,"firstPub":null}],"ratingList":[],"organismList":[{"id":27862,"organismName":"NA","lastModified":1655704096000}],"biodbRanks":[],"themeList":[],"zindex":4.8,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:44","ess":0},{"dbId":8367,"shortName":"TCM2COVID","accession":"DBC008367","fullName":"Anti-COVID-19 effects and mechanisms of TCM","description":"TCM2COVID documents more than 280 anti-COVID TCM formulas and over 80 NPs that refer to over 300 herbs, all from the literature and public sources. Meanwhile, TCM2COVID launches a useful webserver for querying, analyzing and visualizing documented formulas similar to those supplied by the user.","url":"http://zhangy-lab.cn/tcm2covid","foundedYear":"2022","hostInstitution":"University of Traditional Chinese Medicine","address":"Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu China","city":"Chengdu","province":"Sichuan","country":"China","currentVersion":"","contactName":"Yang Zhang","contactEmail":"yangzhang@cdutcm.edu.cn","availableProtocol":"1","lastUpdate":"","age":4,"citation":24,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1692695644000,"lastModified":"2025-10-11 16:46:28","dataTypeList":[{"id":27222,"datatypeName":"Other","lastModified":1694700050000}],"categoryList":[{"id":32831,"name":"Health and medicine","lastModified":1694700050000}],"keywordsList":[{"id":47495,"name":"traditional Chinese medicine","lastModified":1694700050000},{"id":47496,"name":"COVID-19","lastModified":1694700050000},{"id":47497,"name":"SARS-CoV-2","lastModified":1694700050000}],"dataObjectList":[{"id":24700,"name":"Plant","lastModified":1694700050000},{"id":24701,"name":"Virus","lastModified":1694700050000}],"publicationList":[{"id":76216,"pmid":"36245702","title":"TCM2COVID: A resource of anti-COVID-19 traditional Chinese medicine with effects and mechanisms.","author":"Liping Ren, Yi Xu, Lin Ning, Xianrun Pan, Yuchen Li, Qi Zhao, Bo Pang, Jian Huang, Kejun Deng, Yang Zhang","journal":"Imeta","year":"2022","issue":null,"volume":null,"abst":"In China, traditional Chinese medicine (TCM) has been widely used for coronavirus infectious disease 2019 (COVID-19) prevention, treatment, and recovery and has played a part in the battle against the disease. A variety of TCM treatments have been recommended for different stages of COVID-19. But, to the best of our knowledge, a comprehensive database for storing and organizing anti-COVID TCM treatments is still lacking. Herein, we developed TCM2COVID, a manually curated resource of anti-COVID TCM formulas, natural products (NPs), and herbs. The current version of TCM2COVID (1) documents over 280 TCM formulas (including over 300 herbs) with detailed clinical evidence and therapeutic mechanism information; (2) records over 80 NPs with detailed potential therapeutic mechanisms; and (3) launches a useful web server for querying, analyzing and visualizing documented formulas similar to those supplied by the user (formula similarity analysis). In summary, TCM2COVD provides a user-friendly and practical platform for documenting, querying, and browsing anti-COVID TCM treatments, and will help in the development and elucidation of the mechanisms of action of new anti-COVID TCM therapies to support the fight against the COVID-19 epidemic. TCM2COVID is freely available at http://zhangy-lab.cn/tcm2covid/.<br>","citation":25,"citationDate":"2026-05-02","lastModified":1777685849000,"createDate":1692176882000,"citationsList":"41588523,41052279,40626310,40635974,39780217,39769436,39578684,39578676,39337334,39095509,38953556,38900186,38789016,38406595,38188542,38094296,PPR706435,37510209,37315383,37125199,36926588,38868426,36752289,36203529,36245702","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":null,"pubMonth":null,"firstPub":null}],"ratingList":[],"organismList":[{"id":34777,"organismName":"Severe acute respiratory syndrome-related coronavirus","lastModified":1694700050000},{"id":34778,"organismName":"Cyrtomium fortunei","lastModified":1694700050000}],"biodbRanks":[],"themeList":[],"zindex":6.0,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:47","ess":0},{"dbId":8439,"shortName":"DCABM-TCM","accession":"DBC008439","fullName":" a Database of Constituents Absorbed into Blood and Metabolites of Traditional Chinese Medicine","description":"DCABM-TCM is a Database of Constituents Absorbed into Blood and Metabolites of Traditional Chinese Medicine, is the first database systematically collecting blood constituents of TCM prescriptions and herbs.  In current DCABM-TCM, 1816 blood constituents with chemical structures of 194 herbs and 192 prescriptions were manually mined from literature, together with the detailed experimental conditions under which the blood constituents were detected, including extraction method, experimental animal and animal model, administration method and dose, blood collection time and location etc. In addition, 1893 blood constituents without structures were also been recorded in the DCABM-TCM as they were given in the source publications.","url":"http://bionet.ncpsb.org.cn/dcabm-tcm/","foundedYear":"2021","hostInstitution":"Beijing Institute of Lifeomics","address":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.","city":"Beijing","province":"","country":"China","currentVersion":"v1.0","contactName":"Zhongyang Liu","contactEmail":"liuzy1984@163.com","availableProtocol":"1","lastUpdate":"2023-06","age":3,"citation":24,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1692705919000,"lastModified":"2025-10-11 16:46:36","dataTypeList":[{"id":26063,"datatypeName":"Other","lastModified":1693830150000}],"categoryList":[{"id":31339,"name":"Health and medicine","lastModified":1693830150000}],"keywordsList":[{"id":44939,"name":"traditional chinese medicine","lastModified":1693830150000},{"id":44940,"name":"blood constituents","lastModified":1693830150000},{"id":44941,"name":"drug discovery","lastModified":1693830150000}],"dataObjectList":[{"id":23601,"name":"Plant","lastModified":1693830150000}],"publicationList":[{"id":74731,"pmid":"37486750","title":"DCABM-TCM: A Database of Constituents Absorbed into the Blood and Metabolites of Traditional Chinese Medicine.","author":"Xinyue Liu, Jinying Liu, Bangze Fu, Ruzhen Chen, Jianzhou Jiang, He Chen, Runa Li, Lin Xing, Liying Yuan, Xuetai Chen, Jing Zhang, Honglei Li, Shuzhen Guo, Feifei Guo, Jiachen Guo, Yuan Liu, Yaning Qi, Biyue Yu, Feng Xu, Dong Li, Zhongyang Liu","journal":"J Chem Inf Model","year":"2023","issue":"15","volume":"63","abst":"Traditional Chinese medicine (TCM) not only maintains the health of Asian people but also provides a great resource of active natural products for modern drug development. Herein, we developed a Database of Constituents Absorbed into the Blood and Metabolites of TCM (DCABM-TCM), the first database systematically collecting blood constituents of TCM prescriptions and herbs, including prototypes and metabolites experimentally detected in the blood, together with the corresponding detailed detection conditions through manual literature mining. The DCABM-TCM has collected 1816 blood constituents with chemical structures of 192 prescriptions and 194 herbs and integrated their related annotations, including physicochemical, absorption, distribution, metabolism, excretion, and toxicity properties, and associated targets, pathways, and diseases. Furthermore, the DCABM-TCM supported two blood constituent-based analysis functions, the network pharmacology analysis for TCM molecular mechanism elucidation, and the target/pathway/disease-based screening of candidate blood constituents, herbs, or prescriptions for TCM-based drug discovery. The DCABM-TCM is freely accessible at http://bionet.ncpsb.org.cn/dcabm-tcm/. The DCABM-TCM will contribute to the elucidation of effective constituents and molecular mechanism of TCMs and the discovery of TCM-derived drug-like compounds that are both bioactive and bioavailable.<br>","citation":31,"citationDate":"2026-05-02","lastModified":1777684720000,"createDate":1692176271000,"citationsList":"41797446,41765716,41588523,41588462,41349710,41232630,41214635,41260788,41261625,40854416,40838302,41052279,41626567,40697595,40985417,40516490,40480395,40356679,40303920,40084567,40005250,39947372,39899688,39835270,PPR963509,39392404,39327620,39208658,38496269,38398522,38747231","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":null,"pubMonth":null,"firstPub":null}],"ratingList":[{"id":210,"ratingEmail":"1628549030@qq.com","dataScore":0,"contentScore":0,"systemScore":0,"ratingDate":1765284916000}],"organismList":[{"id":33344,"organismName":"Homo sapiens","lastModified":1693830150000}],"biodbRanks":[],"themeList":[],"zindex":8.0,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:47","ess":0},{"dbId":9577,"shortName":"TCMBank","accession":"DBC009577","fullName":"Traditional Chinese Medicine Bank","description":"TCMBank provides standardized information about traditional Chinese medicines, ingredients, diseases, and their corresponding gene targets, and establishes a comprehensive network containing six pairs of relationships.","url":"https://TCMBank.CN","foundedYear":"2023","hostInstitution":"Sun Yat-sen University","address":"No.66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, P.R. China","city":"","province":"Guangdong","country":"China","currentVersion":"v1.0","contactName":"Calvin Yu-Chian Chen","contactEmail":"chenyuchian@mail.sysu.edu.cn","availableProtocol":"1","lastUpdate":"","age":3,"citation":19,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1721133020000,"lastModified":"2025-10-11 16:48:26","dataTypeList":[{"id":30005,"datatypeName":"DNA","lastModified":1724465395000},{"id":30006,"datatypeName":"Other","lastModified":1724465395000}],"categoryList":[{"id":36464,"name":"Interaction","lastModified":1724465395000},{"id":36465,"name":"Pathway","lastModified":1724465395000},{"id":36466,"name":"Health and medicine","lastModified":1724465395000}],"keywordsList":[{"id":53780,"name":"herb","lastModified":1724465395000},{"id":53781,"name":"ingredient","lastModified":1724465395000},{"id":53782,"name":"target protein","lastModified":1724465395000},{"id":53783,"name":"drug repurposing","lastModified":1724465395000}],"dataObjectList":[{"id":27261,"name":"NA","lastModified":1724465395000}],"publicationList":[{"id":78681,"pmid":"37829020","title":"TCMBank: bridges between the largest herbal medicines, chemical ingredients, target proteins, and associated diseases with intelligence text mining.","author":"Lv Q, Chen G, He H, Yang Z, Zhao L, Chen HY, Chen CY.","journal":"Chem Sci","year":"2023","issue":"39","volume":"14","abst":"Traditional Chinese Medicine (TCM) has long been viewed as a precious source of modern drug discovery. AI-assisted drug discovery (AIDD) has been investigated extensively. However, there are still two challenges in applying AIDD to guide TCM drug discovery: the lack of a large amount of standardized TCM-related information and AIDD is prone to pathological failures in out-of-domain data. We have released TCM Database@Taiwan in 2011, and it has been widely disseminated and used. Now, we developed TCMBank, the largest systematic free TCM database, which is an extension of TCM Database@Taiwan. TCMBank contains 9192 herbs, 61 966 ingredients (unduplicated), 15 179 targets, 32 529 diseases, and their pairwise relationships. By integrating multiple data sources, TCMBank provides 3D structure information of ingredients and provides a standard list and detailed information on herbs, ingredients, targets and diseases. TCMBank has an intelligent document identification module that continuously adds TCM-related information retrieved from the literature in PubChem. In addition, driven by TCMBank big data, we developed an ensemble learning-based drug discovery protocol for identifying potential leads and drug repurposing. We take colorectal cancer and Alzheimer's disease as examples to demonstrate how to accelerate drug discovery by artificial intelligence. Using TCMBank, researchers can view literature-driven relationship mapping between herbs/ingredients and genes/diseases, allowing the understanding of molecular action mechanisms for ingredients and identification of new potentially effective treatments. TCMBank is available at https://TCMBank.CN/.<br>","citation":28,"citationDate":"2026-05-02","lastModified":1777687907000,"createDate":1720512689000,"citationsList":"41881252,41770426,41668206,41588523,41508020,41501158,41260787,41260785,41057911,41004131,40668407,40634546,40624035,40893436,40303920,40635974,40038923,39754842,39609715,39355231,39267184,39438078,41550147,39253057,39095509,38730226,38193238,37829008","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":"chenyuchian@mail.sysu.edu.cn;;chenyuchian@mail.sysu.edu.cn;;chenyuchian@mail.sysu.edu.cn;;chenyuchian@mail.sysu.edu.cn;;chenyuchian@mail.sysu.edu.cn;;chenyuchian@mail.sysu.edu.cn","doi":null,"pubMonth":null,"firstPub":null}],"ratingList":[],"organismList":[{"id":38344,"organismName":"Punica granatum","lastModified":1724465395000},{"id":38345,"organismName":"Trachycarpus fortunei","lastModified":1724465395000}],"biodbRanks":[],"themeList":[],"zindex":6.33333,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:54","ess":0},{"dbId":8653,"shortName":"CPMCP","accession":"DBC008653","fullName":"Chinese patent medicine and compound prescription","description":"We established a database of Chinese patent medicine and compound prescription (CPMCP). It demonstrates the prescription information of Chinese patent medicines (CPMs) and ancient Chinese medicine prescriptions (CMPs). CPMCP reports their comprehensive and standardized information such as the components, indications and contraindications. It is worth mentioning that we organized relevant experts and spent lots of time manually mapping the functions of compound prescriptions in ancient Chinese to the standardized TCM symptom vocabularies, obtaining a total of 71 414 associations between compound prescriptions and TCM symptoms. ","url":"http://cpmcp.top","foundedYear":"2022","hostInstitution":"Nankai University","address":"Centre for Bioinformatics and Intelligent Medicine, Nankai University, No. 38 Tongyan Road, Tianjin 300071, China.","city":"","province":"","country":"China","currentVersion":"1.0","contactName":"jianliu","contactEmail":"jianliu@nankai.edu.cn","availableProtocol":"1","lastUpdate":"2022-08-25","age":4,"citation":9,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1692782320000,"lastModified":"2025-10-11 16:46:55","dataTypeList":[{"id":26408,"datatypeName":"Other","lastModified":1693990042000}],"categoryList":[{"id":31788,"name":"Literature","lastModified":1693990042000}],"keywordsList":[{"id":45660,"name":"Traditional Chinese Medicine (TCM)","lastModified":1693990042000},{"id":45661,"name":"Chinese Patent Medicine (CPM)","lastModified":1693990042000}],"dataObjectList":[{"id":23936,"name":"NA","lastModified":1693990042000}],"publicationList":[{"id":76486,"pmid":"36006844","title":"CPMCP: a database of Chinese patent medicine and compound prescription.","author":"Chang Sun, Jipeng Huang, Rong Tang, Minglei Li, Haili Yuan, Yuxiang Wang, Jin-Mao Wei, Jian Liu","journal":"Database (Oxford)","year":"2022","issue":null,"volume":"2022","abst":"Although several traditional Chinese medicine (TCM)-related databases have emerged, they focus on researching single medicinal materials, which is far from sufficient for clinical research and application. In comparison, compound prescriptions are more informative and meaningful in TCM, for they embody the information on the compatibility of TCM besides the relatively isolated information about single medicinal materials. The compatibility information is essential in TCM because it conveys not only what components are involved to treat special diseases but also how to combine these single medical materials. We established a database of Chinese patent medicine and compound prescription (CPMCP). It demonstrates the prescription information of Chinese patent medicines (CPMs) and ancient Chinese medicine prescriptions (CMPs). CPMCP reports their comprehensive and standardized information such as the components, indications and contraindications. It is worth mentioning that we organized relevant experts and spent lots of time manually mapping the functions of compound prescriptions in ancient Chinese to the standardized TCM symptom vocabularies, obtaining a total of 71 414 associations between compound prescriptions and TCM symptoms. In this way, CPMCP established the associations between TCM and modern medicine (MM) according to the associations between TCM symptoms and MM symptoms. In addition, to further exhibit the compatibility mechanism of compound prescriptions, CPMCP summarizes a set of common drug combination principles by analyzing the existing prescriptions. We believe that CPMCP can promote the modernization of TCM and make greater contributions to MM. Database URL http://cpmcp.top.<br>","citation":11,"citationDate":"2026-05-02","lastModified":1777686041000,"createDate":1692176993000,"citationsList":"41588523,41205526,41061906,40917854,40714300,40732361,40142979,39527891,38680873,PPR954316,38035021","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":null,"pubMonth":null,"firstPub":null}],"ratingList":[],"organismList":[{"id":33730,"organismName":"NA","lastModified":1693990042000}],"biodbRanks":[],"themeList":[],"zindex":2.25,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:48","ess":0},{"dbId":9222,"shortName":"TCMM","accession":"DBC009222","fullName":"Traditional Chinese medicine modernization","description":"TCMM is the currently largest modernized TCM database that integrates pioneering intelligent pipelines. It includes 20 types of TCM concepts and 46 biological relations, totaling 3,447,023 records. The database supports prescription generation and knowledge discovery, with outcomes consistent with biological experimental results.","url":"https://www.tcmm.net.cn","foundedYear":"2024","hostInstitution":"Anhui University of Science and Technology","address":"","city":"","province":"","country":"China","currentVersion":"v1.0","contactName":"Huan Xu","contactEmail":"xh890421@163.com","availableProtocol":"1","lastUpdate":"2024-04-15","age":2,"citation":4,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1721050355000,"lastModified":"2025-10-11 16:47:48","dataTypeList":[{"id":29961,"datatypeName":"Other","lastModified":1724387991000}],"categoryList":[{"id":36385,"name":"Interaction","lastModified":1724387991000},{"id":36386,"name":"Health and medicine","lastModified":1724387991000}],"keywordsList":[{"id":53659,"name":"traditional Chinese medicine","lastModified":1724387991000},{"id":53660,"name":"knowledge graph","lastModified":1724387991000},{"id":53661,"name":"graph neural network","lastModified":1724387991000},{"id":53662,"name":"deep learning","lastModified":1724387991000}],"dataObjectList":[{"id":27204,"name":"NA","lastModified":1724387991000}],"publicationList":[{"id":77584,"pmid":"38680873","title":"TCMM: A unified database for traditional Chinese medicine modernization and therapeutic innovations.","author":"Zhixiang Ren, Yiming Ren, Zeting Li, Huan Xu","journal":"Comput Struct Biotechnol J","year":"2024","issue":null,"volume":"23","abst":"Mining the potential of traditional Chinese medicine (TCM) in treating modern diseases requires a profound understanding of its action mechanism and a comprehensive knowledge system that seamlessly bridges modern medical insights with traditional theories. However, existing databases for modernizing TCM are plagued by varying degrees of information loss, which impede the multidimensional dissection of pharmacological effects. To address this challenge, we introduce traditional Chinese medicine modernization (TCMM), the currently largest modernized TCM database that integrates pioneering intelligent pipelines. By aligning high-quality TCM and modern medicine data, TCMM boasts the most extensive TCM modernization knowledge, including 20 types of modernized TCM concepts such as prescription, ingredient, target and 46 biological relations among them, totaling 3,447,023 records. We demonstrate the efficacy and reliability of TCMM with two features, prescription generation and knowledge discovery, the outcomes show consistency with biological experimental results. A publicly available web interface is at https://www.tcmm.net.cn/.<br>","citation":10,"citationDate":"2026-05-02","lastModified":1777687088000,"createDate":1720512210000,"citationsList":"41991344,41588523,41585934,41341446,41322003,41205526,40535109,40407387,40283917,40142979","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":null,"pubMonth":null,"firstPub":null}],"ratingList":[],"organismList":[{"id":38281,"organismName":"NA","lastModified":1724387991000}],"biodbRanks":[],"themeList":[],"zindex":2.0,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:51","ess":0},{"dbId":9117,"shortName":"ccTCM","accession":"DBC009117","fullName":"ccTCM","description":"ccTCM combines resource distribution, similarity analysis, and molecular mechanism analysis to leverage over 273 TCMs within one integrated portal. The platform integrates multiple databases to provide 40,767 compound-target pairs, supporting scientific and clinical studies of TCM by offering detailed quantitative data on bioactive ingredients.","url":"http://www.cctcm.org.cn","foundedYear":"2023","hostInstitution":"Nanjing University of Chinese Medicine","address":"School of Medicine & Holistic Integrative Medicine\r\nNanjing University of Chinese Medicine\r\n138 Xianlin Rd, Nanjing, 210023, China","city":"Nanjing","province":"Jiangsu","country":"China","currentVersion":"v1.0","contactName":"Yunan Zhao","contactEmail":"zhaoyunan-js@163.com","availableProtocol":"1","lastUpdate":"2023-11-20","age":3,"citation":2,"token":null,"expireDate":null,"ins":0,"groupEmail":null,"isPartner":0,"funding":"","submitter":null,"pv":null,"isNew":0,"bigsearchId":null,"recordCreated":1721033419000,"lastModified":"2025-10-11 16:47:37","dataTypeList":[{"id":31006,"datatypeName":"Other","lastModified":1724914121000}],"categoryList":[{"id":38031,"name":"Gene genome and annotation","lastModified":1724914121000},{"id":38032,"name":"Health and medicine","lastModified":1724914121000}],"keywordsList":[{"id":55926,"name":"bioactive ingredients","lastModified":1724914121000},{"id":55927,"name":"traditional Chinese medicine","lastModified":1724914121000},{"id":55928,"name":"compounds","lastModified":1724914121000}],"dataObjectList":[{"id":28098,"name":"Plant","lastModified":1724914121000}],"publicationList":[{"id":78126,"pmid":"38213899","title":"ccTCM: A quantitative component and compound platform for promoting the research of traditional Chinese medicine.","author":"Dongqing Yang, Zhu Zhu, Qi Yao, Cuihua Chen, Feiyan Chen, Ling Gu, Yucui Jiang, Lin Chen, Jingyuan Zhang, Juan Wu, Xingsu Gao, Junqin Wang, Guochun Li, Yunan Zhao","journal":"Comput Struct Biotechnol J","year":"2023","issue":null,"volume":"21","abst":"Traditional Chinese medicine (TCM) databases play a vital role in bridging the gap between TCM and modern medicine, as well as in promoting the popularity of TCM. Elucidating the bioactive ingredients of Chinese medicinal materials is key to TCM modernization and new drug discovery. However, one drawback of current TCM databases is the lack of quantitative data on the constituents of Chinese medicinal materials. Herein, we present ccTCM, a web-based platform designed to provide a component and compound-content-based resource on TCM and analysis services for medical experts. In terms of design features, ccTCM combines resource distribution, similarity analysis, and molecular-mechanism analysis to accelerate the discovery of bioactive ingredients in TCM. ccTCM contains 273 Chinese medicinal materials commonly used in clinical settings, covering 29 functional classifications. By searching and comparing, we finally adopted 2043 studies, from which we collected the compounds contained in each TCM with content greater than 0.001 %, and a total of 1449 were extracted. Subsequently, we collected 40,767 compound-target pairs by integrating multiple databases. Taken together, ccTCM is a versatile platform that can be used by TCM scientists to perform scientific and clinical TCM studies based on quantified ingredients of Chinese medicinal materials. ccTCM is freely accessible at http://www.cctcm.org.cn.<br>","citation":5,"citationDate":"2026-05-02","lastModified":1777687348000,"createDate":1720512448000,"citationsList":"41588462,41585934,41204032,41322003,39392404","isNew":0,"isParse":1,"isExclude":0,"isMultipleHttp":0,"affiliations":null,"doi":null,"pubMonth":null,"firstPub":null}],"ratingList":[],"organismList":[{"id":39490,"organismName":"NA","lastModified":1724914121000}],"biodbRanks":[],"themeList":[],"zindex":0.666667,"firstPublicationYear":0,"searchExample":null,"citedDate":"2026-01-04 00:00:51","ess":0}]