{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T05:24:27Z","timestamp":1774329867581,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T00:00:00Z","timestamp":1740700800000},"content-version":"vor","delay-in-days":98,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Fund of China","doi-asserted-by":"crossref","award":["82274363"],"award-info":[{"award-number":["82274363"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Fund of China","doi-asserted-by":"crossref","award":["82025036"],"award-info":[{"award-number":["82025036"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Fund of China","doi-asserted-by":"crossref","award":["22338004"],"award-info":[{"award-number":["22338004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Fundamental Research Program of Shanxi Province","award":["20210302124129"],"award-info":[{"award-number":["20210302124129"]}]},{"name":"Distinguished and Excellent Young Scholars Cultivation Project of Shanxi Agricultural University","award":["2022YQPYGC09"],"award-info":[{"award-number":["2022YQPYGC09"]}]},{"name":"Postgraduate Research Innovation Project of Shanxi Province","award":["2023KY322"],"award-info":[{"award-number":["2023KY322"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The biological targets of traditional Chinese medicine (TCM) are the core effectors mediating the interaction between TCM and the human body. Identification of TCM targets is essential to elucidate the chemical basis and mechanisms of TCM for treating diseases. Given the chemical complexity of TCM, both in silico high-throughput compound-target interaction predicting models and biological profile-based methods have been commonly applied for identifying TCM targets based on the structural information of TCM chemical components and biological information, respectively. However, the existing methods lack the integration of TCM chemical and biological information, resulting in difficulty in the systematic discovery of TCM action pathways. To solve this problem, we propose a novel target identification model NP-TCMtarget to explore the TCM target path by combining the overall chemical and biological profiles. First, NP-TCMtarget infers TCM effect targets by calculating associations between herb\/disease inducible gene expression profiles and specific gene signatures for 8233 targets. Then, NP-TCMtarget utilizes a constructed binary classification model to predict binding targets of herbal ingredients. Finally, we can distinguish TCM direct and indirect targets by comparing the effect targets and binding targets to establish the action pathways of herbal component\u2014direct target\u2014indirect target by mapping TCM targets in the biological molecular network. We apply NP-TCMtarget to the formula XiaoKeAn to demonstrate the power of revealing the action pathways of herbal formula. We expect that this novel model could provide a systematic framework for exploring the molecular mechanisms of TCM at the target level. NP-TCMtarget is available at http:\/\/www.bcxnfz.top\/NP-TCMtarget.<\/jats:p>","DOI":"10.1093\/bib\/bbaf078","type":"journal-article","created":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T22:18:31Z","timestamp":1741126711000},"source":"Crossref","is-referenced-by-count":9,"title":["NP-TCMtarget: a network pharmacology platform for exploring mechanisms of action of traditional Chinese medicine"],"prefix":"10.1093","volume":"26","author":[{"given":"Aoyi","family":"Wang","sequence":"first","affiliation":[{"name":"Shanxi Key Lab for Modernization of TCVM, College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haoyang","family":"Peng","sequence":"additional","affiliation":[{"name":"Shanxi Key Lab for Modernization of TCVM, College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yingdong","family":"Wang","sequence":"additional","affiliation":[{"name":"Shanxi Key Lab for Modernization of TCVM, College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haoran","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shanxi Key Lab for Modernization of TCVM, College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caiping","family":"Cheng","sequence":"additional","affiliation":[{"name":"Shanxi Key Lab for Modernization of TCVM, College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinzhong","family":"Zhao","sequence":"additional","affiliation":[{"name":"Shanxi Key Lab for Modernization of TCVM, College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wuxia","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shanxi Key Lab for Modernization of TCVM, College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianxin","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine , 11 North Third Ring Road East, Chaoyang District, Beijing 100029 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8858-8106","authenticated-orcid":false,"given":"Peng","family":"Li","sequence":"additional","affiliation":[{"name":"Shanxi Key Lab for Modernization of TCVM, College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,2,28]]},"reference":[{"key":"2025030422173260200_ref1","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1038\/448126a","article-title":"Traditional medicine: A culture in the balance","volume":"448","author":"Qiu","year":"2007","journal-title":"Nature"},{"key":"2025030422173260200_ref2","doi-asserted-by":"publisher","first-page":"S90","DOI":"10.1038\/480S90a","article-title":"Modernization: One step at a time","volume":"480","author":"Xu","year":"2011","journal-title":"Nature"},{"key":"2025030422173260200_ref3","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1038\/nchembio.118","article-title":"Network pharmacology: The next paradigm in drug discovery","volume":"4","author":"Hopkins","year":"2008","journal-title":"Nat Chem Biol"},{"key":"2025030422173260200_ref4","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/S1875-5364(13)60037-0","article-title":"Traditional Chinese medicine network pharmacology: Theory, methodology and application","volume":"11","author":"Li","year":"2013","journal-title":"Chin J Nat Med"},{"key":"2025030422173260200_ref5","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1007\/s11655-019-3064-0","article-title":"Network pharmacology in research of Chinese medicine formula: Methodology, application and prospective","volume":"26","author":"Luo","year":"2020","journal-title":"Chin J Integr Med"},{"key":"2025030422173260200_ref6","doi-asserted-by":"publisher","first-page":"123","DOI":"10.3389\/fphar.2019.00123","article-title":"Network pharmacology databases for traditional Chinese medicine: Review and assessment","volume":"10","author":"Zhang","year":"2019","journal-title":"Front Pharmacol"},{"key":"2025030422173260200_ref7","doi-asserted-by":"publisher","first-page":"687","DOI":"10.2174\/1389557515666150219143933","article-title":"Network based approach to drug discovery: A mini review","volume":"15","author":"Li","year":"2015","journal-title":"Mini Rev Med Chem"},{"key":"2025030422173260200_ref8","doi-asserted-by":"publisher","first-page":"D1110","DOI":"10.1093\/nar\/gky1021","article-title":"SymMap: An integrative database of traditional Chinese medicine enhanced by symptom mapping","volume":"47","author":"Wu","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025030422173260200_ref9","doi-asserted-by":"publisher","first-page":"21146","DOI":"10.1038\/srep21146","article-title":"BATMAN-TCM: A bioinformatics analysis tool for molecular mechANism of traditional Chinese medicine","volume":"6","author":"Liu","year":"2016","journal-title":"Sci Rep"},{"key":"2025030422173260200_ref10","doi-asserted-by":"publisher","first-page":"D1055","DOI":"10.1093\/nar\/gkq1165","article-title":"HIT: Linking herbal active ingredients to targets","volume":"39","author":"Ye","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2025030422173260200_ref11","doi-asserted-by":"publisher","first-page":"D1089","DOI":"10.1093\/nar\/gks1100","article-title":"TCMID: Traditional Chinese medicine integrative database for herb molecular mechanism analysis","volume":"41","author":"Xue","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2025030422173260200_ref12","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1758-2946-6-13","article-title":"TCMSP: A database of systems pharmacology for drug discovery from herbal medicines","volume":"6","author":"Ru","year":"2014","journal-title":"J Chem"},{"key":"2025030422173260200_ref13","doi-asserted-by":"publisher","first-page":"D976","DOI":"10.1093\/nar\/gky987","article-title":"ETCM: An encyclopaedia of traditional Chinese medicine","volume":"47","author":"Xu","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025030422173260200_ref14","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1016\/j.csbj.2018.11.002","article-title":"YaTCM: Yet another traditional Chinese medicine database for drug discovery","volume":"16","author":"Li","year":"2018","journal-title":"Comput Struct Biotechnol J"},{"key":"2025030422173260200_ref15","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad518","article-title":"Network pharmacology: Towards the artificial intelligence-based precision traditional Chinese medicine","volume":"25","author":"Zhang","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025030422173260200_ref16","doi-asserted-by":"publisher","first-page":"1989","DOI":"10.1038\/s41467-023-37572-z","article-title":"Improving the generalizability of protein-ligand binding predictions with AI-bind","volume":"14","author":"Chatterjee","year":"2023","journal-title":"Nat Commun"},{"key":"2025030422173260200_ref17","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1038\/nchembio.1199","article-title":"Target identification and mechanism of action in chemical biology and drug discovery","volume":"9","author":"Schenone","year":"2013","journal-title":"Nat Chem Biol"},{"key":"2025030422173260200_ref18","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1126\/science.1132939","article-title":"The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease","volume":"313","author":"Lamb","year":"2006","journal-title":"Science"},{"key":"2025030422173260200_ref19","doi-asserted-by":"publisher","first-page":"1437","DOI":"10.1016\/j.cell.2017.10.049","article-title":"A next generation connectivity map: L1000 platform and the first 1,000,000 profiles","volume":"171","author":"Subramanian","year":"2017","journal-title":"Cell"},{"key":"2025030422173260200_ref20","doi-asserted-by":"publisher","first-page":"474267","DOI":"10.3389\/fphar.2021.474267","article-title":"The advantages of connectivity map applied in traditional Chinese medicine","volume":"12","author":"Jiang","year":"2021","journal-title":"Front Pharmacol"},{"key":"2025030422173260200_ref21","doi-asserted-by":"publisher","first-page":"D1197","DOI":"10.1093\/nar\/gkaa1063","article-title":"HERB: A high-throughput experiment- and reference-guided database of traditional Chinese medicine","volume":"49","author":"Fang","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025030422173260200_ref22","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad027","article-title":"Exploring pharmacological active ingredients of traditional Chinese medicine by pharmacotranscriptomic map in ITCM","volume":"24","author":"Tian","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025030422173260200_ref23","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab542","article-title":"TMNP: A transcriptome-based multi-scale network pharmacology platform for herbal medicine","volume":"23","author":"Li","year":"2022","journal-title":"Brief Bioinform"},{"key":"2025030422173260200_ref24","doi-asserted-by":"publisher","first-page":"e2003213","DOI":"10.1371\/journal.pbio.2003213","article-title":"Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the connectivity map","volume":"15","author":"Smith","year":"2017","journal-title":"PLoS Biol"},{"key":"2025030422173260200_ref25","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025030422173260200_ref26","doi-asserted-by":"publisher","first-page":"5545","DOI":"10.1093\/bioinformatics\/btaa1005","article-title":"DeepPurpose: A deep learning library for drug-target interaction prediction","volume":"36","author":"Huang","year":"2021","journal-title":"Bioinformatics"},{"key":"2025030422173260200_ref27","doi-asserted-by":"publisher","first-page":"1803","DOI":"10.1016\/S0140-6736(22)01655-5","article-title":"Type 2 diabetes","volume":"400","author":"Ahmad","year":"2022","journal-title":"Lancet"},{"key":"2025030422173260200_ref28","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1038\/aps.2014.138","article-title":"Deciphering the therapeutic mechanisms of Xiao-Ke-an in treatment of type 2 diabetes in mice by a Fangjiomics approach","volume":"36","author":"Yang","year":"2015","journal-title":"Acta Pharmacol Sin"},{"key":"2025030422173260200_ref29","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1186\/s12906-015-0785-2","article-title":"Evaluating the antidiabetic effects of Chinese herbal medicine: Xiao-Ke-an in 3T3-L1 cells and KKAy mice using both conventional and holistic omics approaches","volume":"15","author":"Yang","year":"2015","journal-title":"BMC Complement Altern Med"},{"key":"2025030422173260200_ref30","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1038\/s12276-021-00561-7","article-title":"Advanced glycation end products (AGEs) and other adducts in aging-related diseases and alcohol-mediated tissue injury","volume":"53","author":"Rungratanawanich","year":"2021","journal-title":"Exp Mol Med"},{"key":"2025030422173260200_ref31","doi-asserted-by":"publisher","first-page":"37","DOI":"10.3389\/fcvm.2020.00037","article-title":"Receptor for advanced glycation end products (RAGE) and mechanisms and therapeutic opportunities in diabetes and cardiovascular disease: Insights from human subjects and animal models","volume":"7","author":"Ega\u00f1a-Gorro\u00f1o","year":"2020","journal-title":"Front Cardiovasc Med"},{"key":"2025030422173260200_ref32","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/j.jocn.2021.09.012","article-title":"Alzheimer's disease, Huntington's disease and cancer","volume":"93","author":"Panegyres","year":"2021","journal-title":"J Clin Neurosci"},{"key":"2025030422173260200_ref33","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1016\/j.drudis.2018.01.039","article-title":"The rise of deep learning in drug discovery","volume":"23","author":"Chen","year":"2018","journal-title":"Drug Discov Today"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/1\/bbaf078\/62206650\/bbaf078.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/1\/bbaf078\/62206650\/bbaf078.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T22:18:38Z","timestamp":1741126718000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf078\/8046257"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,22]]},"references-count":33,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,11,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf078","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2024,11,22]]},"article-number":"bbaf078"}}