{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T01:39:10Z","timestamp":1784165950249,"version":"3.55.0"},"reference-count":161,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T00:00:00Z","timestamp":1595376000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T00:00:00Z","timestamp":1595376000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Drug repositioning is the process of identifying novel therapeutic potentials for existing drugs and discovering therapies for untreated diseases. Drug repositioning, therefore, plays an important role in optimizing the pre-clinical process of developing novel drugs by saving time and cost compared to the traditional de novo drug discovery processes. Since drug repositioning relies on data for existing drugs and diseases the enormous growth of publicly available large-scale biological, biomedical, and electronic health-related data along with the high-performance computing capabilities have accelerated the development of computational drug repositioning approaches. Multidisciplinary researchers and scientists have carried out numerous attempts, with different degrees of efficiency and success, to computationally study the potential of repositioning drugs to identify alternative drug indications. This study reviews recent advancements in the field of computational drug repositioning. First, we highlight different drug repositioning strategies and provide an overview of frequently used resources. Second, we summarize computational approaches that are extensively used in drug repositioning studies. Third, we present different computing and experimental models to validate computational methods. Fourth, we address prospective opportunities, including a few target areas. Finally, we discuss challenges and limitations encountered in computational drug repositioning and conclude with an outline of further research directions.<\/jats:p>","DOI":"10.1186\/s13321-020-00450-7","type":"journal-article","created":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T12:03:38Z","timestamp":1595419418000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":332,"title":["A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions"],"prefix":"10.1186","volume":"12","author":[{"given":"Tamer N.","family":"Jarada","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jon G.","family":"Rokne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6657-9738","authenticated-orcid":false,"given":"Reda","family":"Alhajj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,7,22]]},"reference":[{"issue":"8","key":"450_CR1","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/nrd1468","volume":"3","author":"TT Ashburn","year":"2004","unstructured":"Ashburn TT, Thor KB (2004) Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3(8):673\u2013683","journal-title":"Nat Rev Drug Discov"},{"issue":"1","key":"450_CR2","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/nrd.2018.168","volume":"18","author":"S Pushpakom","year":"2019","unstructured":"Pushpakom S, Iorio F, Eyers PA, Escott KJ, Hopper S, Wells A, Doig A, Guilliams T, Latimer J, McNamee C et al (2019) Drug repurposing: progress, challenges and recommendations. Nat Rev Drug Discov 18(1):41\u201358","journal-title":"Nat Rev Drug Discov"},{"key":"450_CR3","doi-asserted-by":"crossref","unstructured":"Ledford\u00a0H (2020) Dozens of coronavirus drugs are in development\u2014what happens next? Nature","DOI":"10.1038\/d41586-020-01367-9"},{"key":"450_CR4","first-page":"969","volume":"105","author":"MB Serafin","year":"2020","unstructured":"Serafin MB, Bottega A, Foletto VS, da Rosa TF, H\u00f6rner A, H\u00f6rner R (2020) Drug repositioning an alternative for the treatment of coronavirus COVID-19. Int J Antimicrob Agents 105:969","journal-title":"Int J Antimicrob Agents"},{"key":"450_CR5","first-page":"4","volume":"1","author":"M Harris","year":"2020","unstructured":"Harris M, Bhatti Y, Buckley J, Sharma D (2020) Fast and frugal innovations in response to the COVID-19 pandemic. Nat Med 1:4","journal-title":"Nat Med"},{"issue":"6493","key":"450_CR6","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1126\/science.abb9332","volume":"368","author":"RK Guy","year":"2020","unstructured":"Guy RK, DiPaola RS, Romanelli F, Dutch RE (2020) Rapid repurposing of drugs for COVID-19. Science 368(6493):829\u2013830","journal-title":"Science"},{"issue":"33","key":"450_CR7","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1073\/pnas.1000138107","volume":"107","author":"F Iorio","year":"2010","unstructured":"Iorio F, Bosotti R, Scacheri E, Belcastro V, Mithbaokar P, Ferriero R, Murino L, Tagliaferri R, Brunetti-Pierri N, Isacchi A et al (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci 107(33):621\u2013626","journal-title":"Proc Natl Acad Sci"},{"issue":"8","key":"450_CR8","doi-asserted-by":"crossref","first-page":"3424","DOI":"10.1073\/pnas.0915125107","volume":"107","author":"C Gloeckner","year":"2010","unstructured":"Gloeckner C, Garner AL, Mersha F, Oksov Y, Tricoche N, Eubanks LM, Lustigman S, Kaufmann GF, Janda KD (2010) Repositioning of an existing drug for the neglected tropical disease onchocerciasis. Proc Natl Acad Sci 107(8):3424\u20133429","journal-title":"Proc Natl Acad Sci"},{"issue":"7270","key":"450_CR9","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1038\/nature08506","volume":"462","author":"MJ Keiser","year":"2009","unstructured":"Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB et al (2009) Predicting new molecular targets for known drugs. Nature 462(7270):175","journal-title":"Nature"},{"issue":"4","key":"450_CR10","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1093\/bib\/bbr013","volume":"12","author":"JT Dudley","year":"2011","unstructured":"Dudley JT, Deshpande T, Butte AJ (2011) Exploiting drug\u2013disease relationships for computational drug repositioning. Brief Bioinf 12(4):303\u2013311","journal-title":"Brief Bioinf"},{"issue":"1","key":"450_CR11","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1093\/bib\/bbv020","volume":"17","author":"J Li","year":"2015","unstructured":"Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z (2015) A survey of current trends in computational drug repositioning. Brief Bioinf 17(1):2\u201312","journal-title":"Brief Bioinf"},{"issue":"5795","key":"450_CR12","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1126\/science.1132939","volume":"313","author":"J Lamb","year":"2006","unstructured":"Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet J-P, Subramanian A, Ross KN et al (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313(5795):1929\u20131935","journal-title":"Science"},{"issue":"8","key":"450_CR13","doi-asserted-by":"crossref","first-page":"e6536","DOI":"10.1371\/journal.pone.0006536","volume":"4","author":"G Hu","year":"2009","unstructured":"Hu G, Agarwal P (2009) Human disease\u2013drug network based on genomic expression profiles. PLoS ONE 4(8):e6536","journal-title":"PLoS ONE"},{"issue":"96","key":"450_CR14","doi-asserted-by":"crossref","first-page":"96ra77","DOI":"10.1126\/scitranslmed.3001318","volume":"3","author":"M Sirota","year":"2011","unstructured":"Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ (2011) Discovery and peclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med 3(96):96ra77\u201396ra77","journal-title":"Sci Transl Med"},{"issue":"3","key":"450_CR15","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1093\/bioinformatics\/bts698","volume":"29","author":"X Liu","year":"2012","unstructured":"Liu X, Wang S, Meng F, Wang J, Zhang Y, Dai E, Yu X, Li X, Jiang W (2012) SM2miR: a database of the experimentally validated small molecules\u2019 effects on microrna expression. Bioinformatics 29(3):409\u2013411","journal-title":"Bioinformatics"},{"key":"450_CR16","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1038\/srep00282","volume":"2","author":"W Jiang","year":"2012","unstructured":"Jiang W, Chen X, Liao M, Li W, Lian B, Wang L, Meng F, Liu X, Chen X, Jin Y et al (2012) Identification of links between small molecules and mirnas in human cancers based on transcriptional Responses. Sci Rep 2:282","journal-title":"Sci Rep"},{"issue":"4","key":"450_CR17","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/nbt.2151","volume":"30","author":"P Sanseau","year":"2012","unstructured":"Sanseau P, Agarwal P, Barnes MR, Pastinen T, Richards JB, Cardon LR, Mooser V (2012) Use of genome-wide association studies for drug repositioning. Nat Biotechnol 30(4):317","journal-title":"Nat Biotechnol"},{"issue":"7391","key":"450_CR18","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1038\/nature11005","volume":"483","author":"MJ Garnett","year":"2012","unstructured":"Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J et al (2012) Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483(7391):570","journal-title":"Nature"},{"issue":"4","key":"450_CR19","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1093\/bib\/bbs082","volume":"15","author":"JL Rukov","year":"2013","unstructured":"Rukov JL, Wilentzik R, Jaffe I, Vinther J, Shomron N (2013) Pharmaco-miR: linking microRNAs and drug effects. Brief Bioinf 15(4):648\u2013659","journal-title":"Brief Bioinf"},{"issue":"7\u20138","key":"450_CR20","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1016\/j.drudis.2012.07.014","volume":"18","author":"F Iorio","year":"2013","unstructured":"Iorio F, Rittman T, Ge H, Menden M, Saez-Rodriguez J (2013) Transcriptional data: a new gateway to drug repositioning? Drug Discov Today 18(7\u20138):350\u2013357","journal-title":"Drug Discov Today"},{"issue":"12","key":"450_CR21","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1158\/2159-8290.CD-13-0183","volume":"3","author":"NS Jahchan","year":"2013","unstructured":"Jahchan NS, Dudley JT, Mazur PK, Flores N, Yang D, Palmerton A, Zmoos A-F, Vaka D, Tran KQ, Zhou M et al (2013) A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer A Drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discov 3(12):1364\u20131377","journal-title":"Cancer Discov"},{"issue":"D1","key":"450_CR22","doi-asserted-by":"crossref","first-page":"D1070","DOI":"10.1093\/nar\/gkt1023","volume":"42","author":"Y Li","year":"2013","unstructured":"Li Y, Qiu C, Tu J, Geng B, Yang J, Jiang T, Cui Q (2013) HMDD v2.0: a database for experimentally supported human microrna and disease associations. Nucleic Acids Res 42(D1):D1070\u2013D1074","journal-title":"Nucleic Acids Res"},{"issue":"7488","key":"450_CR23","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature12873","volume":"506","author":"Y Okada","year":"2014","unstructured":"Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Yoshida S et al (2014) Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506(7488):376","journal-title":"Nature"},{"key":"450_CR24","first-page":"342","volume":"5","author":"D Vidovi\u0107","year":"2014","unstructured":"Vidovi\u0107 D, Koleti A, Sch\u00fcrer SC (2014) Large-scale integration of small molecule-induced genome-wide transcriptional responses, kinome-wide Binding Affinities and Cell-growth Inhibition Profiles Reveal Global Trends Characterizing Systems-level Drug Action. Front Genet 5:342","journal-title":"Front Genet"},{"issue":"3","key":"450_CR25","doi-asserted-by":"crossref","first-page":"140","DOI":"10.5732\/cjc.013.10094","volume":"33","author":"X-M Ding","year":"2014","unstructured":"Ding X-M (2014) MicroRNAs: regulators of cancer metastasis and epithelial\u2013mesenchymal transition (EMT). Chin J Cancer 33(3):140","journal-title":"Chin J Cancer"},{"issue":"3","key":"450_CR26","first-page":"219","volume":"2","author":"X Wen","year":"2014","unstructured":"Wen X, Deng F-M, Wang J (2014) MicroRNAs as predictive biomarkers and therapeutic targets in prostate cancer. Am J Clin Exp Urol 2(3):219","journal-title":"Am J Clin Exp Urol"},{"issue":"13","key":"450_CR27","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-16-S13-S4","volume":"16","author":"H Huang","year":"2015","unstructured":"Huang H, Nguyen T, Ibrahim S, Shantharam S, Yue Z, Chen JY (2015) DMAP: a connectivity map database to enable identification of novel drug repositioning candidates. BMC Bioinf 16(13):S4","journal-title":"BMC Bioinf"},{"issue":"6","key":"450_CR28","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1016\/j.cell.2017.10.049","volume":"171","author":"A Subramanian","year":"2017","unstructured":"Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK et al (2017) A next generation connectivity map: L1000 platform and the first 1,000,000 profiles. Cell 171(6):1437\u20131452","journal-title":"Cell"},{"issue":"D1","key":"450_CR29","doi-asserted-by":"crossref","first-page":"D1013","DOI":"10.1093\/nar\/gky1010","volume":"47","author":"Z Huang","year":"2018","unstructured":"Huang Z, Shi J, Gao Y, Cui C, Zhang S, Li J, Zhou Y, Cui Q (2018) HMDD v3. 0: a database for experimentally supported human microrna-disease associations. Nucleic Acids Res 47(D1):D1013\u2013D1017","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"450_CR30","doi-asserted-by":"crossref","first-page":"i232","DOI":"10.1093\/bioinformatics\/btn162","volume":"24","author":"Y Yamanishi","year":"2008","unstructured":"Yamanishi Y, Araki M, Gutteridge A, Honda W, Kanehisa M (2008) Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics 24(13):i232\u2013i240","journal-title":"Bioinformatics"},{"issue":"7","key":"450_CR31","doi-asserted-by":"crossref","first-page":"e1000423","DOI":"10.1371\/journal.pcbi.1000423","volume":"5","author":"SL Kinnings","year":"2009","unstructured":"Kinnings SL, Liu N, Buchmeier N, Tonge PJ, Xie L, Bourne PE (2009) Drug discovery using chemical systems biology: repositioning the safe medicine comtan to treat multi-drug and Extensively Drug Resistant Tuberculosis. PLOS Comput Biol 5(7):e1000423","journal-title":"PLOS Comput Biol"},{"issue":"18","key":"450_CR32","doi-asserted-by":"crossref","first-page":"2397","DOI":"10.1093\/bioinformatics\/btp433","volume":"25","author":"K Bleakley","year":"2009","unstructured":"Bleakley K, Yamanishi Y (2009) Supervised prediction of drug-target interactions using bipartite local models. Bioinformatics 25(18):2397\u20132403","journal-title":"Bioinformatics"},{"issue":"4","key":"450_CR33","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1093\/bib\/bbr028","volume":"12","author":"SJ Swamidass","year":"2011","unstructured":"Swamidass SJ (2011) Mining small-molecule screens to repurpose drugs. Brief Bioinf 12(4):327\u2013335","journal-title":"Brief Bioinf"},{"issue":"11","key":"450_CR34","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1093\/bioinformatics\/bts186","volume":"28","author":"E Pihan","year":"2012","unstructured":"Pihan E, Colliandre L, Guichou J-F, Douguet D (2012) e-Drug 3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design. Bioinformatics 28(11):1540\u20131541","journal-title":"Bioinformatics"},{"key":"450_CR35","doi-asserted-by":"crossref","unstructured":"Li\u00a0J, Lu\u00a0Z (2012) A new method for computational drug repositioning using drug pairwise similarity. In: 2012 IEEE international conference on bioinformatics and biomedicine. IEEE, pp. 1\u20134","DOI":"10.1109\/BIBM.2012.6392722"},{"issue":"11","key":"450_CR36","doi-asserted-by":"crossref","first-page":"e79568","DOI":"10.1371\/journal.pone.0079568","volume":"8","author":"PA Novick","year":"2013","unstructured":"Novick PA, Ortiz OF, Poelman J, Abdulhay AY, Pande VS (2013) SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery. PLoS ONE 8(11):e79568","journal-title":"PLoS ONE"},{"issue":"11","key":"450_CR37","doi-asserted-by":"crossref","first-page":"e78518","DOI":"10.1371\/journal.pone.0078518","volume":"8","author":"Y Wang","year":"2013","unstructured":"Wang Y, Chen S, Deng N, Wang Y (2013) Drug repositioning by Kernel-based integration of molecular structure, molecular activity, and phenotype data. PLoS ONE 8(11):e78518","journal-title":"PLoS ONE"},{"issue":"5","key":"450_CR38","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1039\/c3mb70554d","volume":"10","author":"F Tan","year":"2014","unstructured":"Tan F, Yang R, Xu X, Chen X, Wang Y, Ma H, Liu X, Wu X, Chen Y, Liu L et al (2014) Drug repositioning by applying \u2018expression profiles\u2019 generated by integrating chemical structure similarity and gene semantic similarity. Mol BioSyst 10(5):1126\u20131138","journal-title":"Mol BioSyst"},{"key":"450_CR39","doi-asserted-by":"crossref","first-page":"11970","DOI":"10.1038\/srep11970","volume":"5","author":"C Zheng","year":"2015","unstructured":"Zheng C, Guo Z, Huang C, Wu Z, Li Y, Chen X, Fu Y, Ru J, Shar PA, Wang Y et al (2015) Large-scale direct targeting for drug repositioning and discovery. Sci Rep 5:11970","journal-title":"Sci Rep"},{"key":"450_CR40","first-page":"4","volume-title":"Genes VIII","author":"B Lewin","year":"2004","unstructured":"Lewin B (2004) Genes VIII. Pearson Prentice Hall, Upper Saddle River, p 4"},{"issue":"5507","key":"450_CR41","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1126\/science.1058040","volume":"291","author":"JC Venter","year":"2001","unstructured":"Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al (2001) The sequence of the human genome. Science 291(5507):1304\u20131351","journal-title":"Science"},{"issue":"10","key":"450_CR42","doi-asserted-by":"crossref","first-page":"e1000543","DOI":"10.1371\/journal.pcbi.1000543","volume":"5","author":"DK Slonim","year":"2009","unstructured":"Slonim DK, Yanai I (2009) Getting started in gene expression microarray analysis. PLOS Comput Biol 5(10):e1000543","journal-title":"PLOS Comput Biol"},{"issue":"1","key":"450_CR43","first-page":"39","volume":"1","author":"I Lobo","year":"2008","unstructured":"Lobo I (2008) Environmental influences on gene expression. Nat Educ 1(1):39","journal-title":"Nat Educ"},{"key":"450_CR44","series-title":"A practical approach to microarray data analysis","first-page":"91","volume-title":"Singular value decomposition and principal component analysis","author":"ME Wall","year":"2003","unstructured":"Wall ME, Rechtsteiner A, Rocha LM (2003) Singular value decomposition and principal component analysis. A practical approach to microarray data analysis. Springer, Berlin, pp 91\u2013109"},{"issue":"1","key":"450_CR45","doi-asserted-by":"crossref","first-page":"S115","DOI":"10.1093\/bioinformatics\/17.suppl_1.S115","volume":"17","author":"L Hunter","year":"2001","unstructured":"Hunter L, Taylor RC, Leach SM, Simon R (2001) GEST: a gene expression search tool based on a novel Bayesian similarity metric. Bioinformatics 17(1):S115\u2013S122","journal-title":"Bioinformatics"},{"issue":"1","key":"450_CR46","first-page":"D562","volume":"33","author":"T Barrett","year":"2005","unstructured":"Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau W-C, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R (2005) NCBI GEO: mining millions of expression profiles\u2013database and tools. Nucleic Acids Res 33(1):D562\u2013D566","journal-title":"Nucleic Acids Res"},{"issue":"5643","key":"450_CR47","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1126\/science.1090887","volume":"302","author":"J Quackenbush","year":"2003","unstructured":"Quackenbush J (2003) Microarrays-guilt by association. Science 302(5643):240\u2013241","journal-title":"Science"},{"issue":"3","key":"450_CR48","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1093\/abbs\/gmu003","volume":"46","author":"Z Xing","year":"2014","unstructured":"Xing Z, Li D, Yang L, Xi Y, Su X (2014) MicroRNAs and anticancer drugs. Acta Biochim Biophys Sin 46(3):233\u2013239","journal-title":"Acta Biochim Biophys Sin"},{"issue":"2","key":"450_CR49","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1111\/imm.12195","volume":"141","author":"SJ Hebbring","year":"2014","unstructured":"Hebbring SJ (2014) The challenges, advantages and future of phenome-wide association studies. Immunology 141(2):157\u2013165","journal-title":"Immunology"},{"issue":"1","key":"450_CR50","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/sj.bjp.0707307","volume":"152","author":"D Rognan","year":"2007","unstructured":"Rognan D (2007) Chemogenomic approaches to rational drug design. Br J Pharmacol 152(1):38\u201352","journal-title":"Br J Pharmacol"},{"issue":"1","key":"450_CR51","doi-asserted-by":"crossref","first-page":"167","DOI":"10.3390\/molecules24010167","volume":"24","author":"W Mangione","year":"2019","unstructured":"Mangione W, Samudrala R (2019) Identifying protein features responsible for improved drug repurposing accuracies using the CANDO platform: implications for drug design. Molecules 24(1):167","journal-title":"Molecules"},{"issue":"25","key":"450_CR52","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1186\/s12859-019-3270-y","volume":"20","author":"Y Yan","year":"2019","unstructured":"Yan Y, Huang S-Y (2019) Pushing the accuracy limit of shape complementarity for protein\u2013protein docking. BMC Bioinf 20(25):696","journal-title":"BMC Bioinf"},{"issue":"5886","key":"450_CR53","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1126\/science.1158140","volume":"321","author":"M Campillos","year":"2008","unstructured":"Campillos M, Kuhn M, Gavin A-C, Jensen LJ, Bork P (2008) Drug target identification using side-effect similarity. Science 321(5886):263\u2013266","journal-title":"Science"},{"issue":"12","key":"450_CR54","doi-asserted-by":"crossref","first-page":"e28025","DOI":"10.1371\/journal.pone.0028025","volume":"6","author":"L Yang","year":"2011","unstructured":"Yang L, Agarwal P (2011) Systematic drug repositioning based on clinical side-effects. PLoS ONE 6(12):e28025","journal-title":"PLoS ONE"},{"key":"450_CR55","first-page":"388","volume-title":"Linking pharmGKB to phenotype studies and animal models of disease for drug repurposing Biocomputing 2012","author":"R Hoehndorf","year":"2012","unstructured":"Hoehndorf R, Oellrich A, Rebholz-Schuhmann D, Schofield PN, Gkoutos GV (2012) Linking pharmGKB to phenotype studies and animal models of disease for drug repurposing Biocomputing 2012. World Scientific, Singapore, pp 388\u2013399"},{"key":"450_CR56","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/msb.2012.26","volume":"8","author":"A Gottlieb","year":"2012","unstructured":"Gottlieb A, Stein GY, Oron Y, Ruppin E, Sharan R (2012) INDI: a computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol 8:1","journal-title":"Mol Syst Biol"},{"issue":"2","key":"450_CR57","doi-asserted-by":"crossref","first-page":"e87864","DOI":"10.1371\/journal.pone.0087864","volume":"9","author":"H Ye","year":"2014","unstructured":"Ye H, Liu Q, Wei J (2014) Construction of drug network based on side effects and its application for drug repositioning. PLoS ONE 9(2):e87864","journal-title":"PLoS ONE"},{"issue":"1","key":"450_CR58","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1186\/1471-2105-15-267","volume":"15","author":"H Bisgin","year":"2014","unstructured":"Bisgin H, Liu Z, Fang H, Kelly R, Xu X, Tong W (2014) A phenome-guided drug repositioning through a latent variable model. BMC Bioinf 15(1):267","journal-title":"BMC Bioinf"},{"key":"450_CR59","doi-asserted-by":"crossref","first-page":"e46","DOI":"10.7717\/peerj-cs.46","volume":"2","author":"T Nugent","year":"2016","unstructured":"Nugent T, Plachouras V, Leidner JL (2016) Computational drug repositioning based on side-effects mined from social media. PeerJ Comput Sci 2:e46","journal-title":"PeerJ Comput Sci"},{"issue":"20","key":"450_CR60","doi-asserted-by":"crossref","first-page":"3175","DOI":"10.1093\/bioinformatics\/btw342","volume":"32","author":"D Sridhar","year":"2016","unstructured":"Sridhar D, Fakhraei S, Getoor L (2016) A probabilistic approach for collective similarity-based drug\u2013drug interaction prediction. Bioinformatics 32(20):3175\u20133182","journal-title":"Bioinformatics"},{"issue":"D1","key":"450_CR61","doi-asserted-by":"crossref","first-page":"D711","DOI":"10.1093\/nar\/gky964","volume":"47","author":"A Athar","year":"2018","unstructured":"Athar A, F\u00fcllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I et al (2018) ArrayExpress update-from bulk to single-cell expression data. Nucleic Acids Res 47(D1):D711\u2013D715","journal-title":"Nucleic Acids Res"},{"issue":"7391","key":"450_CR62","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","volume":"483","author":"J Barretina","year":"2012","unstructured":"Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Leh\u00e1r J, Kryukov GV, Sonkin D et al (2012) The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483(7391):603","journal-title":"Nature"},{"issue":"9","key":"450_CR63","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2003-4-9-r60","volume":"4","author":"G Dennis","year":"2003","unstructured":"Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 4(9):R60","journal-title":"Genome Biol"},{"issue":"1","key":"450_CR64","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1093\/bioinformatics\/bts656","volume":"29","author":"C Pacini","year":"2012","unstructured":"Pacini C, Iorio F, Gon\u00e7alves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J (2012) DvD: an R\/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Bioinformatics 29(1):132\u2013134","journal-title":"Bioinformatics"},{"issue":"D1","key":"450_CR65","doi-asserted-by":"crossref","first-page":"D246","DOI":"10.1093\/nar\/gkx1158","volume":"46","author":"I Papatheodorou","year":"2017","unstructured":"Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, F\u00fcllgrabe A, Fuentes AM-P, George N et al (2017) Expression atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Res 46(D1):D246\u2013D251","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"450_CR66","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","volume":"30","author":"R Edgar","year":"2002","unstructured":"Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30(1):207\u2013210","journal-title":"Nucleic Acids Res"},{"issue":"43","key":"450_CR67","doi-asserted-by":"crossref","first-page":"15 545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression Profiles. Proc Natl Acad Sci 102(43):15 545\u201315 550","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"450_CR68","first-page":"D716","volume":"38","author":"AC Culhane","year":"2009","unstructured":"Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M et al (2009) GeneSigDB\u2013a curated database of gene expression signatures. Nucleic Acids Res 38(1):D716\u2013D725","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"450_CR69","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25(1):25","journal-title":"Nat Genet"},{"key":"450_CR70","first-page":"1","volume":"2011","author":"J Zhang","year":"2011","unstructured":"Zhang J, Baran J, Cros A, Guberman JM, Haider S, Hsu J, Liang Y, Rivkin E, Wang J, Whitty B et al (2011) International cancer genome consortium data portal-a one-stop shop for cancer genomics data. Database 2011:1","journal-title":"Database"},{"issue":"1","key":"450_CR71","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27\u201330","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"450_CR72","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.cels.2017.11.001","volume":"6","author":"AB Keenan","year":"2018","unstructured":"Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A et al (2018) The library of integrated network-based cellular signatures NIH program: system-level cataloging of human cells response to perturbations. Cell Syst 6(1):13\u201324","journal-title":"Cell Syst"},{"issue":"12","key":"450_CR73","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","volume":"27","author":"A Liberzon","year":"2011","unstructured":"Liberzon A, Subramanian A, Pinchback R, Thorvaldsd\u00f3ttir H, Tamayo P, Mesirov JP (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics 27(12):1739\u20131740","journal-title":"Bioinformatics"},{"issue":"2","key":"450_CR74","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.cell.2018.03.042","volume":"173","author":"C Hutter","year":"2018","unstructured":"Hutter C, Zenklusen JC (2018) The cancer genome atlas: creating lasting value beyond its data. Cell 173(2):283\u2013285","journal-title":"Cell"},{"issue":"1","key":"450_CR75","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/nrc2044","volume":"7","author":"J Lamb","year":"2007","unstructured":"Lamb J (2007) The connectivity map: a new tool for biomedical research. Nat Rev Cancer 7(1):54","journal-title":"Nat Rev Cancer"},{"issue":"D1","key":"450_CR76","first-page":"D158","volume":"45","author":"TU Consortium","year":"2016","unstructured":"Consortium TU (2016) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45(D1):D158\u2013D169","journal-title":"Nucleic Acids Res"},{"key":"450_CR77","unstructured":"Gillen J\u00a0E, Tse\u00a0T, Ide N\u00a0C, McCray A\u00a0T (2004) Design, Implementation and Management of a Web\u2013based data entry system for Clinicaltrials.gov. In: Medinfo, pp. 1466\u20131470"},{"issue":"D1","key":"450_CR78","doi-asserted-by":"crossref","first-page":"D1075","DOI":"10.1093\/nar\/gkv1075","volume":"44","author":"M Kuhn","year":"2015","unstructured":"Kuhn M, Letunic I, Jensen LJ, Bork P (2015) The SIDER database of drugs and side effects. Nucleic Acids Res 44(D1):D1075\u2013D1079","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"450_CR79","doi-asserted-by":"crossref","first-page":"D945","DOI":"10.1093\/nar\/gkw1074","volume":"45","author":"A Gaulton","year":"2016","unstructured":"Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibri\u00e1n-Uhalte E et al (2016) The ChEMBL database in 2017. Nucleic Acids Res 45(D1):D945\u2013D954","journal-title":"Nucleic Acids Res"},{"key":"450_CR80","doi-asserted-by":"crossref","unstructured":"Swain\u00a0M (2012) Chemicalize.org","DOI":"10.1021\/ci300046g"},{"key":"450_CR81","doi-asserted-by":"crossref","unstructured":"Pence H\u00a0E, Williams\u00a0A (2010) ChemSpider: an Online Chemical Information Resource","DOI":"10.1021\/ed100697w"},{"issue":"D1","key":"450_CR82","doi-asserted-by":"crossref","first-page":"D1074","DOI":"10.1093\/nar\/gkx1037","volume":"46","author":"DS Wishart","year":"2017","unstructured":"Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D, Li C, Sayeeda Z et al (2017) Drugbank 5.0: a major update to the drugbank database for 2018. Nucleic Acids Res 46(D1):D1074\u2013D1082","journal-title":"Nucleic Acids Res"},{"key":"450_CR83","first-page":"993","volume":"26","author":"O Ursu","year":"2016","unstructured":"Ursu O, Holmes J, Knockel J, Bologa CG, Yang JJ, Mathias SL, Nelson SJ, Oprea TI (2016) DrugCentral: online drug compendium. Nucleic Acids Res 26:993","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"450_CR84","doi-asserted-by":"crossref","first-page":"D1202","DOI":"10.1093\/nar\/gkv951","volume":"44","author":"S Kim","year":"2015","unstructured":"Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA et al (2015) Pubchem substance and compound databases. Nucleic Acids Res 44(D1):D1202\u2013D1213","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"450_CR85","doi-asserted-by":"crossref","first-page":"D302","DOI":"10.1093\/nar\/gkj120","volume":"34","author":"A Kouranov","year":"2006","unstructured":"Kouranov A, Xie L, de la Cruz J, Chen L, Westbrook J, Bourne PE, Berman HM (2006) The RCSB PDB information portal for structural genomics. Nucleic Acids Res 34(1):D302\u2013D305","journal-title":"Nucleic Acids Res"},{"issue":"80","key":"450_CR86","first-page":"80ps16","volume":"3","author":"R Huang","year":"2001","unstructured":"Huang R, Southall N, Wang Y, Yasgar A, Shinn P, Jadhav A, Nguyen D-T, Austin CP (2001) The NCGC pharmaceutical collection: a comprehensive resource of clinically approved drugs enabling Repurposing and Chemical Genomics. Sci Transl Med 3(80):80ps16","journal-title":"Sci Transl Med"},{"key":"450_CR87","first-page":"31","volume":"48","author":"Y Wang","year":"2019","unstructured":"Wang Y, Zhang S, Li F, Zhou Y, Zhang Y, Wang Z, Zhang R, Zhu J, Ren Y, Tan Y et al (2019) Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. Nucleic Acids Res 48:31\u201341","journal-title":"Nucleic Acids Res"},{"key":"450_CR88","doi-asserted-by":"crossref","first-page":"170029","DOI":"10.1038\/sdata.2017.29","volume":"4","author":"AS Brown","year":"2017","unstructured":"Brown AS, Patel CJ (2017) A standard database for drug repositioning. Sci Data 4:170029","journal-title":"Sci Data"},{"issue":"1","key":"450_CR89","first-page":"D514","volume":"33","author":"A Hamosh","year":"2005","unstructured":"Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic gisorders. Nucleic Acids Res 33(1):D514\u2013D517","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"450_CR90","doi-asserted-by":"crossref","first-page":"D913","DOI":"10.1093\/nar\/gkm1009","volume":"36","author":"T Hernandez-Boussard","year":"2007","unstructured":"Hernandez-Boussard T, Whirl-Carrillo M, Hebert JM, Gong L, Owen R, Gong M, Gor W, Liu F, Truong C, Whaley R et al (2007) The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Nucleic Acids Res 36(1):D913\u2013D918","journal-title":"Nucleic Acids Res"},{"key":"450_CR91","unstructured":"FDA. (2020, January) Drugs@FDA. http:\/\/www.fda.gov\/drugsatfda"},{"issue":"9","key":"450_CR92","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","volume":"98","author":"VG Tusher","year":"2001","unstructured":"Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci 98(9):5116\u20135121","journal-title":"Proc Natl Acad Sci"},{"key":"450_CR93","doi-asserted-by":"crossref","unstructured":"Lu\u00a0Z (2011) PubMed and Beyond: a Survey of Web Tools for Searching Biomedical Literature. Database, vol. 2011","DOI":"10.1093\/database\/baq036"},{"issue":"2","key":"450_CR94","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.jbi.2012.10.007","volume":"46","author":"F Zhu","year":"2013","unstructured":"Zhu F, Patumcharoenpol P, Zhang C, Yang Y, Chan J, Meechai A, Vongsangnak W, Shen B (2013) Biomedical text mining and its applications in cancer research. J Biomed Inf 46(2):200\u2013211","journal-title":"J Biomed Inf"},{"issue":"2","key":"450_CR95","doi-asserted-by":"crossref","first-page":"W399","DOI":"10.1093\/nar\/gkn296","volume":"36","author":"D Cheng","year":"2008","unstructured":"Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS (2008) PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res 36(2):W399\u2013W405","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"450_CR96","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1016\/j.jbi.2012.04.005","volume":"45","author":"J Li","year":"2012","unstructured":"Li J, Lu Z (2012) Systematic identification of pharmacogenomics information from clinical trials. J Biomed Inf 45(5):870\u2013878","journal-title":"J Biomed Inf"},{"issue":"22","key":"450_CR97","doi-asserted-by":"crossref","first-page":"2909","DOI":"10.1093\/bioinformatics\/btt474","volume":"29","author":"R Leaman","year":"2013","unstructured":"Leaman R, Islamaj Do\u011fan R, Lu Z (2013) DNorm: disease name normalization with pairwise learning to rank. Bioinformatics 29(22):2909\u20132917","journal-title":"Bioinformatics"},{"key":"450_CR98","first-page":"1","volume":"2012","author":"AP Davis","year":"2012","unstructured":"Davis AP, Wiegers TC, Rosenstein MC, Mattingly CJ (2012) MEDIC: a practical disease vocabulary used at the comparative toxicogenomics database. Database 2012:1","journal-title":"Database"},{"key":"450_CR99","doi-asserted-by":"crossref","unstructured":"Han\u00a0P, Yang\u00a0P, Zhao\u00a0P, Shang\u00a0S, Liu\u00a0Y, Zhou\u00a0J, Gao\u00a0X, Kalnis\u00a0P (2019) GCN\u2013MF: Disease\u2013gene Association Identification by Graph Convolutional Networks and Matrix Factorization. In: Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. ACM, pp. 705\u2013713","DOI":"10.1145\/3292500.3330912"},{"key":"450_CR100","doi-asserted-by":"crossref","unstructured":"Gong\u00a0L, Huang\u00a0D, Sun\u00a0S, Gao\u00a0Z, Pan\u00a0C, Yang\u00a0R, Li\u00a0Y, Yang\u00a0G (2018) Extraction of interactions of Genes2Genes related to breast cancer. In: 2018 IEEE 16th international conference on software engineering research, management and applications (SERA). IEEE, pp. 108\u2013112","DOI":"10.1109\/SERA.2018.8477190"},{"issue":"7","key":"450_CR101","doi-asserted-by":"crossref","first-page":"e1000450","DOI":"10.1371\/journal.pcbi.1000450","volume":"5","author":"J Li","year":"2009","unstructured":"Li J, Zhu X, Chen JY (2009) Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLOS Comput Biol 5(7):e1000450","journal-title":"PLOS Comput Biol"},{"key":"450_CR102","series-title":"Systematic drug repurposing through text mining","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/978-1-4939-0709-0_14","volume-title":"Biomedical literature mining","author":"LB Tari","year":"2014","unstructured":"Tari LB, Patel JH (2014) Biomedical literature mining. Systematic drug repurposing through text mining. Springer, Berlin, pp 253\u2013267"},{"key":"450_CR103","doi-asserted-by":"crossref","unstructured":"Rastegar-Mojarad M, Elayavilli R\u00a0K, Li\u00a0D, Prasad\u00a0R, Liu\u00a0H (2015) A new method for prioritizing drug repositioning candidates extracted by literature\u2013based discovery. In: 2015 IEEE international conference on bioinformatics and biomedicine (BIBM). IEEE, pp. 669\u2013674","DOI":"10.1109\/BIBM.2015.7359766"},{"issue":"3","key":"450_CR104","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/jamia\/ocw142","volume":"24","author":"AS Brown","year":"2016","unstructured":"Brown AS, Patel CJ (2016) MeSHDD: literature-based drug\u2013drug similarity for drug repositioning. J Am Med Inf Assoc 24(3):614\u2013618","journal-title":"J Am Med Inf Assoc"},{"issue":"5","key":"450_CR105","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/s12859-016-1041-6","volume":"17","author":"N Papanikolaou","year":"2016","unstructured":"Papanikolaou N, Pavlopoulos GA, Theodosiou T, Vizirianakis IS, Iliopoulos I (2016) DrugQuest\u2014a text mining workflow for drug association discovery. BMC Bioinf 17(5):182","journal-title":"BMC Bioinf"},{"issue":"24","key":"450_CR106","doi-asserted-by":"crossref","first-page":"5191","DOI":"10.1093\/bioinformatics\/btz418","volume":"35","author":"X Zeng","year":"2019","unstructured":"Zeng X, Zhu S, Liu X, Zhou Y, Nussinov R, Cheng F (2019) deepDR: a network-based deep learning approach to in silico drug repositioning. Bioinformatics 35(24):5191\u20138","journal-title":"Bioinformatics"},{"issue":"7","key":"450_CR107","doi-asserted-by":"crossref","first-page":"e1002574","DOI":"10.1371\/journal.pcbi.1002574","volume":"8","author":"B Chen","year":"2012","unstructured":"Chen B, Ding Y, Wild DJ (2012) Assessing drug target association using semantic linked data. PLOS Comput Biol 8(7):e1002574","journal-title":"PLOS Comput Biol"},{"key":"450_CR108","first-page":"172","volume-title":"Biocomputing 2014","author":"Q Zhu","year":"2014","unstructured":"Zhu Q, Tao C, Shen F, Chute CG (2014) Exploring the pharmacogenomics knowledge base (PharmGKB) for repositioning breast cancer drugs by leveraging web ontology language (OWL) and cheminformatics approaches. Biocomputing 2014. World Scientific, Singapore, pp 172\u2013182"},{"issue":"14","key":"450_CR109","doi-asserted-by":"crossref","first-page":"3013","DOI":"10.1021\/jm020491t","volume":"46","author":"M Shen","year":"2003","unstructured":"Shen M, Xiao Y, Golbraikh A, Gombar VK, Tropsha A (2003) Development and validation of K-nearest-neighbor QSPR models of metabolic stability of drug candidates. J Med Chem 46(14):3013\u20133020","journal-title":"J Med Chem"},{"issue":"4","key":"450_CR110","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1021\/ci030283p","volume":"43","author":"RG Susnow","year":"2003","unstructured":"Susnow RG, Dixon SL (2003) Use of Robust Classification Techniques for the Prediction of Human Cytochrome P450 2D6 Inhibition. J Chem Inf Comput Sci 43(4):1308\u20131315","journal-title":"J Chem Inf Comput Sci"},{"key":"450_CR111","unstructured":"Cristianini N, Shawe-Taylor J (2004) Support vector machines and other Kernel-based learning methods. Cambridge"},{"issue":"6","key":"450_CR112","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1016\/j.drudis.2018.01.039","volume":"23","author":"H Chen","year":"2018","unstructured":"Chen H, Engkvist O, Wang Y, Olivecrona M, Blaschke T (2018) The rise of deep learning in drug discovery. Drug Discov Today 23(6):1241\u20131250","journal-title":"Drug Discov Today"},{"key":"450_CR113","first-page":"1","volume":"7","author":"A Gottlieb","year":"2011","unstructured":"Gottlieb A, Stein GY, Ruppin E, Sharan R (2011) PREDICT: a method for inferring novel drug indications with application to personalized medicine. Mole Syst Biol 7:1","journal-title":"Mole Syst Biol"},{"issue":"4","key":"450_CR114","doi-asserted-by":"crossref","first-page":"e61318","DOI":"10.1371\/journal.pone.0061318","volume":"8","author":"MP Menden","year":"2013","unstructured":"Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J (2013) Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties. PLoS ONE 8(4):e61318","journal-title":"PLoS ONE"},{"issue":"1","key":"450_CR115","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1758-2946-5-30","volume":"5","author":"F Napolitano","year":"2013","unstructured":"Napolitano F, Zhao Y, Moreira VM, Tagliaferri R, Kere J, D\u2019Amato M, Greco D (2013) Drug repositioning: a machine-learning approach through data integration. J Cheminf 5(1):30","journal-title":"J Cheminf"},{"key":"450_CR116","unstructured":"Zhang\u00a0P, Wang\u00a0F, Hu\u00a0J (2014) Towards drug repositioning: a unified computational framework for integrating multiple aspects of drug similarity and disease similarity. In: AMIA annual symposium proceedings, vol. 2014. American Medical Informatics Association, p. 1258"},{"issue":"9","key":"450_CR117","doi-asserted-by":"crossref","first-page":"2562","DOI":"10.1021\/ci500340n","volume":"54","author":"J Yang","year":"2014","unstructured":"Yang J, Li Z, Fan X, Cheng Y (2014) Drug-disease association and drug-repositioning predictions in complex diseases using causal inference-probabilistic matrix factorization. J Chem Inf Model 54(9):2562\u20132569","journal-title":"J Chem Inf Model"},{"issue":"10","key":"450_CR118","doi-asserted-by":"crossref","first-page":"e1005135","DOI":"10.1371\/journal.pcbi.1005135","volume":"12","author":"H Lim","year":"2016","unstructured":"Lim H, Poleksic A, Yao Y, Tong H, He D, Zhuang L, Meng P, Xie L (2016) Large-scale off-target identification using fast and accurate dual regularized one-class collaborative filtering and its application to drug repurposing. PLOS Comput Biol 12(10):e1005135","journal-title":"PLOS Comput Biol"},{"issue":"1","key":"450_CR119","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1186\/s12859-018-2142-1","volume":"19","author":"MG Ozsoy","year":"2018","unstructured":"Ozsoy MG, \u00d6zyer T, Polat F, Alhajj R (2018) Realizing drug repositioning by adapting a recommendation system to handle the process. BMC Bioinf 19(1):136","journal-title":"BMC Bioinf"},{"issue":"12","key":"450_CR120","doi-asserted-by":"crossref","first-page":"4462","DOI":"10.1021\/acs.molpharmaceut.7b00578","volume":"14","author":"A Korotcov","year":"2017","unstructured":"Korotcov A, Tkachenko V, Russo DP, Ekins S (2017) Comparison of deep learning with multiple machine learning methods and metrics using diverse drug Discovery Data Sets. Mol Pharm 14(12):4462\u20134475","journal-title":"Mol Pharm"},{"issue":"7","key":"450_CR121","doi-asserted-by":"crossref","first-page":"2524","DOI":"10.1021\/acs.molpharmaceut.6b00248","volume":"13","author":"A Aliper","year":"2016","unstructured":"Aliper A, Plis S, Artemov A, Ulloa A, Mamoshina P, Zhavoronkov A (2016) Deep learning applications for predicting pharmacological properties of drugs and drug repurposing using transcriptomic data. Mol Pharm 13(7):2524\u20132530","journal-title":"Mol Pharm"},{"issue":"4","key":"450_CR122","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1021\/acscentsci.6b00367","volume":"3","author":"H Altae-Tran","year":"2017","unstructured":"Altae-Tran H, Ramsundar B, Pappu AS, Pande V (2017) Low data drug discovery with one-shot learning. ACS Central Sci 3(4):283\u2013293","journal-title":"ACS Central Sci"},{"issue":"25","key":"450_CR123","first-page":"1","volume":"20","author":"S Hu","year":"2019","unstructured":"Hu S, Zhang C, Chen P, Gu P, Zhang J, Wang B (2019) Predicting drug-target interactions from drug structure and protein sequence using novel convolutional Neural Networks. BMC Bioinf 20(25):1\u201312","journal-title":"BMC Bioinf"},{"issue":"1","key":"450_CR124","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1021\/acscentsci.7b00512","volume":"4","author":"MH Segler","year":"2017","unstructured":"Segler MH, Kogej T, Tyrchan C, Waller MP (2017) Generating focused molecule libraries for drug discovery with recurrent neural networks. ACS Central Sci 4(1):120\u2013131","journal-title":"ACS Central Sci"},{"issue":"5","key":"450_CR125","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1186\/1752-0509-7-S5-S6","volume":"7","author":"C Wu","year":"2013","unstructured":"Wu C, Gudivada RC, Aronow BJ, Jegga AG (2013) Computational drug repositioning through heterogeneous network clustering. BMC Syst Biol 7(5):S6","journal-title":"BMC Syst Biol"},{"issue":"3","key":"450_CR126","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1016\/j.bbrc.2014.12.101","volume":"457","author":"H Rakshit","year":"2015","unstructured":"Rakshit H, Chatterjee P, Roy D (2015) A bidirectional drug repositioning approach for Parkinson\u2019s disease through network-based inference. Biochem Biophys Res Commun 457(3):280\u2013287","journal-title":"Biochem Biophys Res Commun"},{"key":"450_CR127","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.artmed.2019.03.003","volume":"96","author":"CC Yang","year":"2019","unstructured":"Yang CC, Zhao M (2019) Mining heterogeneous network for drug repositioning using phenotypic information extracted from social media and pharmaceutical databases. Artif Intell Med 96:80\u201392","journal-title":"Artif Intell Med"},{"key":"450_CR128","unstructured":"MedHelp. (2020, January) MedHelp. https:\/\/www.medhelp.org\/"},{"key":"450_CR129","unstructured":"NIEHS. (2020, January) Tox21. [Online]. Available: https:\/\/ntp.niehs.nih.gov\/whatwestudy\/tox21\/index.html?utm_source=direct&utm_medium=prod&utm_campaign=ntpgolinks&utm_term=tox2"},{"key":"450_CR130","unstructured":"Irwin and Shoichet Laboratories. (2020, January) ZINC. https:\/\/zinc.docking.org\/"},{"key":"450_CR131","unstructured":"Chemaxon. (2020, January) BindingDB. https:\/\/www.bindingdb.org\/bind\/index.jsp"},{"issue":"23","key":"450_CR132","doi-asserted-by":"crossref","first-page":"3158","DOI":"10.1093\/bioinformatics\/bts591","volume":"28","author":"H Kilicoglu","year":"2012","unstructured":"Kilicoglu H, Shin D, Fiszman M, Rosemblat G, Rindflesch TC (2012) SemMedDB: a PubMed-scale repository of biomedical semantic predications. Bioinformatics 28(23):3158\u20133160","journal-title":"Bioinformatics"},{"issue":"1","key":"450_CR133","doi-asserted-by":"crossref","first-page":"D267","DOI":"10.1093\/nar\/gkh061","volume":"32","author":"O Bodenreider","year":"2004","unstructured":"Bodenreider O (2004) The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Res 32(1):D267\u2013D270","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"450_CR134","doi-asserted-by":"crossref","first-page":"D914","DOI":"10.1093\/nar\/gku935","volume":"43","author":"AP Davis","year":"2014","unstructured":"Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ (2014) The comparative toxicogenomics database\u2019s 10th year anniversary: update 2015. Nucleic Acids Res 43(D1):D914\u2013D920","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"450_CR135","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/1755-8794-3-50","volume":"3","author":"DP Wall","year":"2010","unstructured":"Wall DP, Pivovarov R, Tong M, Jung J-Y, Fusaro VA, DeLuca TF, Tonellato PJ (2010) Genotator: a disease-agnostic tool for genetic annotation of disease. BMC Med Genom 3(1):50","journal-title":"BMC Med Genom"},{"issue":"1","key":"450_CR136","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1186\/1471-2105-12-435","volume":"12","author":"A Barbosa-Silva","year":"2011","unstructured":"Barbosa-Silva A, Fontaine J-F, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA (2011) PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinf 12(1):435","journal-title":"BMC Bioinf"},{"key":"450_CR137","unstructured":"Emory University. (2020, January) CancerQuest. https:\/\/www.cancerquest.org\/"},{"key":"450_CR138","unstructured":"Darryl Nishimura. (2020, January) BioCarta. https:\/\/omictools.com\/biocarta--tool"},{"key":"450_CR139","unstructured":"NDF-RT. (2020, January) National drug file\u2014reference terminology (NDF\u2013RT). https:\/\/www.nlm.nih.gov\/research\/umls\/sourcereleasedocs\/current\/NDFRT\/index.html"},{"issue":"1","key":"450_CR140","first-page":"D767","volume":"37","author":"T Keshava Prasad","year":"2008","unstructured":"Keshava Prasad T, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A et al (2008) Human protein reference database\u20132009 Update. Nucleic Acids Res 37(1):D767\u2013D772","journal-title":"Nucleic Acids Res"},{"key":"450_CR141","unstructured":"Darryl Nishimura. (2020, January) WHO. https:\/\/www.whocc.no\/atc_ddd_index\/"},{"issue":"1","key":"450_CR142","doi-asserted-by":"crossref","first-page":"D431","DOI":"10.1093\/nar\/gkh081","volume":"32","author":"I Schomburg","year":"2004","unstructured":"Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D (2004) BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 32(1):D431\u2013D433","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"450_CR143","doi-asserted-by":"crossref","first-page":"D919","DOI":"10.1093\/nar\/gkm862","volume":"36","author":"S G\u00fcnther","year":"2007","unstructured":"G\u00fcnther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ et al (2007) SuperTarget and matador: resources for exploring drug-target relationships. Nucleic Acids Res 36(1):D919\u2013D922","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"450_CR144","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1186\/1471-2105-11-255","volume":"11","author":"B Chen","year":"2010","unstructured":"Chen B, Dong X, Jiao D, Wang H, Zhu Q, Ding Y, Wild DJ (2010) Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinf 11(1):255","journal-title":"BMC Bioinf"},{"issue":"18","key":"450_CR145","doi-asserted-by":"crossref","first-page":"e119","DOI":"10.1093\/nar\/gkr538","volume":"39","author":"R Hoehndorf","year":"2011","unstructured":"Hoehndorf R, Schofield PN, Gkoutos GV (2011) PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res 39(18):e119\u2013e119","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"450_CR146","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1093\/bioinformatics\/btp697","volume":"26","author":"Y Liu","year":"2009","unstructured":"Liu Y, Hu B, Fu C, Chen X (2009) DCDB: drug combination database. Bioinformatics 26(4):587\u2013588","journal-title":"Bioinformatics"},{"key":"450_CR147","unstructured":"NIH. (2020, January) DailyMed. http:\/\/dailymed.nlm.nih.gov"},{"issue":"9","key":"450_CR148","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1093\/bioinformatics\/bti273","volume":"21","author":"KR Brown","year":"2005","unstructured":"Brown KR, Jurisica I (2005) Online predicted human interaction database. Bioinformatics 21(9):2076\u20132082","journal-title":"Bioinformatics"},{"issue":"4","key":"450_CR149","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1021\/ci010385k","volume":"42","author":"A Schuffenhauer","year":"2002","unstructured":"Schuffenhauer A, Zimmermann J, Stoop R, van der Vyver J-J, Lecchini S, Jacoby E (2002) An ontology for pharmaceutical ligands and its application for in silico screening and library design. J Chem Inf Comput Sci 42(4):947\u2013955","journal-title":"J Chem Inf Comput Sci"},{"issue":"6","key":"450_CR150","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1002\/humu.10212","volume":"21","author":"PD Stenson","year":"2003","unstructured":"Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN (2003) Human gene mutation database (HGMD\u00ae): 2003 update. Hum Mutat 21(6):577\u2013581","journal-title":"Hum Mutat"},{"issue":"1","key":"450_CR151","doi-asserted-by":"crossref","first-page":"D521","DOI":"10.1093\/nar\/gkl923","volume":"35","author":"DS Wishart","year":"2007","unstructured":"Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S et al (2007) HMDB: the human metabolome database. Nucleic Acids Res 35(1):D521\u2013D526","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"450_CR152","first-page":"252","volume":"6","author":"BL Roth","year":"2000","unstructured":"Roth BL, Lopez E, Patel S, Kroeze WK (2000) The multiplicity of serotonin receptors: uselessly diverse molecules or an embarrassment of riches? The Neurosci 6(4):252\u2013262","journal-title":"The Neurosci"},{"issue":"1","key":"450_CR153","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1093\/nar\/gkg034","volume":"31","author":"Cv Mering","year":"2003","unstructured":"Mering Cv, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 31(1):258\u2013261","journal-title":"Nucleic Acids Res"},{"key":"450_CR154","unstructured":"W.\u00a0H. Organization. (2020, June) Obesity and Overweight. https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/obesity-and-overweight"},{"key":"450_CR155","unstructured":"W.\u00a0H. Organization. (2020, June) Obesity. https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/cancer"},{"issue":"7","key":"450_CR156","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1158\/1535-7163.MCT-12-0968","volume":"12","author":"ZY Pessetto","year":"2013","unstructured":"Pessetto ZY, Weir SJ, Sethi G, Broward MA, Godwin AK (2013) Drug repurposing for gastrointestinal stromal tumor. Mol Cancer Ther 12(7):1299\u20131309","journal-title":"Mol Cancer Ther"},{"key":"450_CR157","doi-asserted-by":"crossref","first-page":"313","DOI":"10.3389\/fonc.2013.00313","volume":"3","author":"J Stenvang","year":"2013","unstructured":"Stenvang J, K\u00fcmler I, Nyg\u00e5rd SB, Smith DH, Nielsen D, Br\u00fcnner N, Moreira JMA (2013) Biomarker-guided repurposing of chemotherapeutic drugs for cancer therapy: a novel strategy in drug development. Front Oncol 3:313","journal-title":"Front Oncol"},{"key":"450_CR158","series-title":"Biocomputing 2014","first-page":"136","volume-title":"Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach","author":"C Ng","year":"2014","unstructured":"Ng C, Hauptman R, Zhang Y, Bourne PE, Xie L (2014) Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach. Biocomputing 2014. World Scientific, Singapore, pp 136\u2013147"},{"issue":"1","key":"450_CR159","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1186\/1471-2105-14-288","volume":"14","author":"I Molineris","year":"2013","unstructured":"Molineris I, Ala U, Provero P, Di Cunto F (2013) Drug repositioning for orphan genetic diseases through conserved anticoexpressed gene clusters (CAGCs). BMC Bioinf 14(1):288","journal-title":"BMC Bioinf"},{"issue":"4","key":"450_CR160","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1093\/bib\/bbr006","volume":"12","author":"K Xu","year":"2011","unstructured":"Xu K, Cote TR (2011) Database Identifies FDA-approved Drugs with Potential to be Repurposed for Treatment of Orphan Diseases. Briefings in bioinformatics 12(4):341\u2013345","journal-title":"Briefings in bioinformatics"},{"key":"450_CR161","doi-asserted-by":"crossref","unstructured":"Carvalho T (2020) COVID-19 Research in Brief: 30 May to 5 June, 2020. Nature Medicine","DOI":"10.1038\/d41591-020-00023-z"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-020-00450-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13321-020-00450-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-020-00450-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,3]],"date-time":"2022-11-03T23:41:03Z","timestamp":1667518863000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-020-00450-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,22]]},"references-count":161,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["450"],"URL":"https:\/\/doi.org\/10.1186\/s13321-020-00450-7","relation":{},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,22]]},"assertion":[{"value":"19 February 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 July 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 July 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"No competing interest to declare","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"46"}}