{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T20:01:39Z","timestamp":1757620899052,"version":"3.44.0"},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["No. 62006109"],"award-info":[{"award-number":["No. 62006109"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Stable Support Plan Program of Shenzhen Natural Science Fund","award":["20220814165010001"],"award-info":[{"award-number":["20220814165010001"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"DOI":"10.1186\/s12859-025-06237-7","type":"journal-article","created":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T12:13:14Z","timestamp":1754050394000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Literature data-based de novo candidates for drug repurposing"],"prefix":"10.1186","volume":"26","author":[{"given":"Xianglong","family":"Liang","sequence":"first","affiliation":[]},{"given":"Xin","family":"Jiang","sequence":"additional","affiliation":[]},{"given":"Yifang","family":"Ma","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,8,1]]},"reference":[{"key":"6237_CR1","doi-asserted-by":"publisher","first-page":"844","DOI":"10.1001\/jama.2020.1166","volume":"323","author":"OJ Wouters","year":"2020","unstructured":"Wouters OJ, McKee M, Luyten J. Estimated research and development investment needed to bring a new medicine to market, 2009\u20132018. JAMA. 2020;323:844\u201353.","journal-title":"JAMA"},{"issue":"6","key":"6237_CR2","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1111\/j.1476-5381.2010.01127.x","volume":"162","author":"J Hughes","year":"2011","unstructured":"Hughes J, Rees S, Kalindjian S, Philpott K. Principles of early drug discovery. Br J Pharmacol. 2011;162(6):1239\u201349.","journal-title":"Br J Pharmacol"},{"issue":"2","key":"6237_CR3","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1093\/biostatistics\/kxx069","volume":"20","author":"CH Wong","year":"2018","unstructured":"Wong CH, Siah KW, Lo AW. Estimation of clinical trial success rates and related parameters. Biostatistics. 2018;20(2):273\u201386.","journal-title":"Biostatistics"},{"key":"6237_CR4","doi-asserted-by":"publisher","first-page":"114239","DOI":"10.1016\/j.ejmech.2022.114239","volume":"234","author":"H Yi","year":"2022","unstructured":"Yi H, Xiaowen D, Yuan X, Guomeng X, Haichun L, Tao L, Yadong C, Yanmin Z. Drug repositioning: progress and challenges in drug discovery for various diseases. Eur J Med Chem. 2022;234:114239.","journal-title":"Eur J Med Chem"},{"issue":"9","key":"6237_CR5","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1111\/jphp.13273","volume":"72","author":"J-P Jourdan","year":"2020","unstructured":"Jourdan J-P, Bureau R, Rochais C, Dallemagne P. Drug repositioning: a brief overview. J Pharm Pharmacol. 2020;72(9):1145\u201351.","journal-title":"J Pharm Pharmacol"},{"key":"6237_CR6","doi-asserted-by":"publisher","first-page":"628144","DOI":"10.3389\/fmolb.2021.628144","volume":"8","author":"BM Sahoo","year":"2021","unstructured":"Sahoo BM, Ravi KBVV, Sruti J, Mahapatra MK, Banik BK, Borah P. Drug repurposing strategy (DRS): emerging approach to identify potential therapeutics for treatment of novel coronavirus infection. Front Mol Biosci. 2021;8:628144.","journal-title":"Front Mol Biosci"},{"issue":"3","key":"6237_CR7","first-page":"110","volume":"18","author":"L Zhichao","year":"2013","unstructured":"Zhichao L, Hong F, Kelly R, Xiaowei X, Donna LM, William S, Weida T. In silico drug repositioning\u2014what we need to know. Drug Discov Today. 2013;18(3):110\u20135.","journal-title":"Drug Discov Today"},{"issue":"5","key":"6237_CR8","first-page":"10-11280042218","volume":"3","author":"PT Ryan","year":"2018","unstructured":"Ryan PT, Paul MD, Edward MS, Stephen LK, Hani AA. A high-throughput screening approach to repurpose fda-approved drugs for bactericidal applications against staphylococcus aureus small-colony variants. MSphere. 2018;3(5):10-11280042218.","journal-title":"MSphere"},{"issue":"1","key":"6237_CR9","doi-asserted-by":"publisher","first-page":"10331","DOI":"10.1038\/ncomms10331","volume":"7","author":"E Guney","year":"2016","unstructured":"Guney E, Menche J, Vidal M, Bar\u00e1basi A-L. Network-based in silico drug efficacy screening. Nat Commun. 2016;7(1):10331.","journal-title":"Nat Commun"},{"issue":"2","key":"6237_CR10","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nbt1284","volume":"25","author":"MJ Keiser","year":"2007","unstructured":"Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotechnol. 2007;25(2):197\u2013206.","journal-title":"Nat Biotechnol"},{"issue":"1","key":"6237_CR11","first-page":"15","volume":"14","author":"F Yang","year":"2022","unstructured":"Yang F, Zhang Q, Ji X, Zhang Y, Li W, Peng S, Xue F. Machine learning applications in drug repurposing. INSC. 2022;14(1):15\u201321.","journal-title":"INSC"},{"issue":"3","key":"6237_CR12","first-page":"488","volume":"18","author":"H-T Yang","year":"2016","unstructured":"Yang H-T, Ju J-H, Wong Y-T, Shmulevich I, Chiang J-H. Literature-based discovery of new candidates for drug repurposing. Brief Bioinform. 2016;18(3):488\u201397.","journal-title":"Brief Bioinform"},{"issue":"3","key":"6237_CR13","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1186\/s12859-020-03882-y","volume":"22","author":"H-C Yi","year":"2021","unstructured":"Yi H-C, You Z-H, Wang L, Su X-R, Zhou X, Jiang T-H. In silico drug repositioning using deep learning and comprehensive similarity measures. BMC Bioinform. 2021;22(3):293.","journal-title":"BMC Bioinform"},{"key":"6237_CR14","doi-asserted-by":"publisher","first-page":"272508","DOI":"10.3389\/fphar.2017.00298","volume":"8","author":"E March-Vila","year":"2017","unstructured":"March-Vila E, Pinzi L, Sturm N, Tinivella A, Engkvist O, Chen H, Rastelli G. On the integration of in silico drug design methods for drug repurposing. Front Pharmacol. 2017;8:272508.","journal-title":"Front Pharmacol"},{"issue":"9","key":"6237_CR15","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1080\/17460441.2021.1883585","volume":"16","author":"T Ziaurrehman","year":"2021","unstructured":"Ziaurrehman T, Markus V-K, Tero A. Artificial intelligence, machine learning, and drug repurposing in cancer. Expert Opin Drug Dis. 2021;16(9):977\u201389.","journal-title":"Expert Opin Drug Dis"},{"issue":"1","key":"6237_CR16","doi-asserted-by":"publisher","first-page":"2691","DOI":"10.1038\/s41467-018-05116-5","volume":"9","author":"F Cheng","year":"2018","unstructured":"Cheng F, Desai RJ, Handy DE, Wang R, Schneeweiss S, Barab\u00e1si A-L, Loscalzo J. Network-based approach to prediction and population-based validation of in silico drug repurposing. Nat Commun. 2018;9(1):2691.","journal-title":"Nat Commun"},{"issue":"3","key":"6237_CR17","first-page":"488","volume":"18","author":"H-T Yang","year":"2016","unstructured":"Yang H-T, Ju J-H, Wong Y-T, Shmulevich I, Chiang J-H. Literature-based discovery of new candidates for drug repurposing. Brief Bioinform. 2016;18(3):488\u201397.","journal-title":"Brief Bioinform"},{"issue":"10","key":"6237_CR18","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1089\/cmb.2020.0356","volume":"28","author":"J Gopal","year":"2021","unstructured":"Gopal J, Prakash Sinnarasan VS, Venkatesan A. Identification of repurpose drugs by computational analysis of disease\u2013gene\u2013drug associations. J Comput Biol. 2021;28(10):975\u201384.","journal-title":"J Comput Biol"},{"issue":"9","key":"6237_CR19","doi-asserted-by":"publisher","first-page":"2006643","DOI":"10.1371\/journal.pbio.2006643","volume":"16","author":"T Stoeger","year":"2018","unstructured":"Stoeger T, Gerlach M, Morimoto RI, Nunes Amaral LA. Large-scale investigation of the reasons why potentially important genes are ignored. PLoS Biol. 2018;16(9):2006643.","journal-title":"PLoS Biol"},{"issue":"7","key":"6237_CR20","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1016\/j.drudis.2016.05.015","volume":"21","author":"S Wei","year":"2016","unstructured":"Wei S, Philip ES, Wei Z. Drug combination therapy increases successful drug repositioning. Drug Discov Today. 2016;21(7):1189\u201395.","journal-title":"Drug Discov Today"},{"issue":"5","key":"6237_CR21","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1016\/j.drudis.2013.11.005","volume":"19","author":"G Jin","year":"2014","unstructured":"Jin G, Wong STC. Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. Drug Discov Today. 2014;19(5):637\u201344.","journal-title":"Drug Discov Today"},{"issue":"3","key":"6237_CR22","first-page":"110","volume":"18","author":"L Zhichao","year":"2013","unstructured":"Zhichao L, Hong F, Kelly R, Xiaowei X, Donna LM, William S, Weida T. In silico drug repositioning\u2014what we need to know. Drug Discov Today. 2013;18(3):110\u20135.","journal-title":"Drug Discov Today"},{"issue":"298","key":"6237_CR23","first-page":"272508","volume":"8","author":"E March-Vila","year":"2017","unstructured":"March-Vila E, Pinzi L, Sturm N, Tinivella A, Engkvist O, Chen H, Rastelli G. On the integration of in silico drug design methods for drug repurposing. Front Pharmacol. 2017;8(298):272508.","journal-title":"Front Pharmacol"},{"key":"6237_CR24","doi-asserted-by":"crossref","unstructured":"Li J, Lu Z. A new method for computational drug repositioning using drug pairwise similarity. In: 2012 IEEE international conference on bioinformatics and biomedicine; 2012. pp. 1\u20134.","DOI":"10.1109\/BIBM.2012.6392722"},{"issue":"18","key":"6237_CR25","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.4155\/fmc-2022-0074","volume":"14","author":"D Shyam Sundar","year":"2022","unstructured":"Shyam Sundar D, Pritish R, Ibrahim Roshan K. Literature-based drug\u2013drug similarity for drug repurposing: Impact of medical subject headings term refinement and hierarchical clustering. Future Med Chem. 2022;14(18):1309\u201323.","journal-title":"Future Med Chem"},{"issue":"1","key":"6237_CR26","doi-asserted-by":"publisher","first-page":"1197","DOI":"10.1038\/s41467-019-09186-x","volume":"10","author":"F Cheng","year":"2021","unstructured":"Cheng F, Kov\u00e1cs IA, Barab\u00e1si A-L. Network-based prediction of drug combinations. Nat Commun. 2021;10(1):1197.","journal-title":"Nat Commun"},{"issue":"1","key":"6237_CR27","doi-asserted-by":"publisher","first-page":"170029","DOI":"10.1038\/sdata.2017.29","volume":"4","author":"AS Brown","year":"2017","unstructured":"Brown AS, Patel CJ. A standard database for drug repositioning. Sci Data. 2017;4(1):170029.","journal-title":"Sci Data"},{"key":"6237_CR28","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-60761-244-5_1","volume-title":"An historical overview of drug discovery","author":"AS Pina","year":"2010","unstructured":"Pina AS, Hussain A, Roque ACA. An historical overview of drug discovery. Totowa, NJ: Humana Press; 2010."},{"issue":"9","key":"6237_CR29","doi-asserted-by":"publisher","first-page":"2006643","DOI":"10.1371\/journal.pbio.2006643","volume":"16","author":"T Stoeger","year":"2018","unstructured":"Stoeger T, Gerlach M, Morimoto RI, Nunes Amaral LA. Large-scale investigation of the reasons why potentially important genes are ignored. PLoS Biol. 2018;16(9):2006643.","journal-title":"PLoS Biol"},{"issue":"3","key":"6237_CR30","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1021\/jm401144z","volume":"57","author":"H Li","year":"2014","unstructured":"Li H, Xiao H, Lin L, Jou D, Kumari V, Lin J, Li C. Drug design targeting protein\u2013protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning: Discovery of raloxifene and bazedoxifene as novel inhibitors of il-6\/gp130 interface. J Med Chem. 2014;57(3):632\u201341.","journal-title":"J Med Chem"},{"issue":"19","key":"6237_CR31","doi-asserted-by":"publisher","first-page":"109","DOI":"10.3389\/fphar.2019.00109","volume":"10","author":"J Ma","year":"2019","unstructured":"Ma J, Wang J, Ghoraie LS, Men X, Haibe-Kains B, Penggao D. A comparative study of cluster detection algorithms in protein\u2013protein interaction for drug target discovery and drug repurposing. Front Pharmacol. 2019;10(19):109.","journal-title":"Front Pharmacol"},{"issue":"1","key":"6237_CR32","doi-asserted-by":"publisher","first-page":"1280237","DOI":"10.1155\/2021\/1280237","volume":"2021","author":"NS Soleimani Zakeri","year":"2021","unstructured":"Soleimani Zakeri NS, Pashazadeh S, MotieGhader H. Drug repurposing for Alzheimer\u2019s disease based on protein\u2013protein interaction network. Biomed Res Int. 2021;2021(1):1280237.","journal-title":"Biomed Res Int"},{"issue":"1","key":"6237_CR33","doi-asserted-by":"publisher","first-page":"170029","DOI":"10.1038\/sdata.2017.29","volume":"4","author":"AS Brown","year":"2017","unstructured":"Brown AS, Patel CJ. A standard database for drug repositioning. Sci Data. 2017;4(1):170029.","journal-title":"Sci Data"},{"issue":"7","key":"6237_CR34","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1093\/bioinformatics\/btq064","volume":"26","author":"G Yu","year":"2010","unstructured":"Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S. Gosemsim: an r package for measuring semantic similarity among go terms and gene products. Bioinformatics. 2010;26(7):976\u20138.","journal-title":"Bioinformatics"},{"issue":"1","key":"6237_CR35","doi-asserted-by":"publisher","first-page":"1197","DOI":"10.1038\/s41467-019-09186-x","volume":"10","author":"F Cheng","year":"2019","unstructured":"Cheng F, Kov\u00e1cs IA, Barab\u00e1si A-L. Network-based prediction of drug combinations. Nat Commun. 2019;10(1):1197.","journal-title":"Nat Commun"},{"issue":"1","key":"6237_CR36","first-page":"195","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith TF, Waterman MS. Identification of common molecular subsequences. J Chem Inf Model. 1981;147(1):195\u20137.","journal-title":"J Chem Inf Model"},{"issue":"4","key":"6237_CR37","first-page":"753","volume":"53","author":"F Cheng","year":"2013","unstructured":"Cheng F, Li W, Wu Z, Wang X, Zhang C, Li J, Liu G, Tang Y. Prediction of polypharmacological profiles of drugs by the integration of chemical, side effect, and therapeutic space. J Mol Biol. 2013;53(4):753\u201362.","journal-title":"J Mol Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06237-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-025-06237-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06237-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T11:26:26Z","timestamp":1757330786000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-025-06237-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,1]]},"references-count":37,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["6237"],"URL":"https:\/\/doi.org\/10.1186\/s12859-025-06237-7","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2025,8,1]]},"assertion":[{"value":"5 April 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 July 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 August 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"203"}}