Table 2 An overview of computational drug repositioning studies, their adopted strategies, computational approaches, main techniques, data sources, key findings, and evaluation metrics
Study | Strateg(ies) | Computational approach(es) | Main technique(s) | Data source(s) | Evaluation criteria | Key finding(s) | ||||
|---|---|---|---|---|---|---|---|---|---|---|
Genome | Chemical structures | Phenome | Data mining | Machine learning | Network analysis | |||||
Hu et al. [123] | \(\checkmark\) | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | CNN | KEGG and DrugBank | CV, ROC and Comp(Acc, Sen, F1, and AUC) | R-TIs |
Han et al. [99] | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | TM, GCN, and MF | OMIM | CV and Comp(MAP, AUC, and NDCG) | D-GAs |
Zeng et al. [106] | \(\checkmark\) | Â | \(\checkmark\) | Â | \(\checkmark\) | Â | MM-AE and V-AE | DrugBank, repoDB, and ClinicalTrials.gov | CV, AUC, AUC-PR, and Comp(Rec-TK) | R-DIs |
Yang et al. [127] | \(\checkmark\) | Â | \(\checkmark\) | Â | Â | \(\checkmark\) | ARM and LP | PharmGKB, SIDER, and MedHelp [128] | CV, AUC, AUC-PR, and Comp(Send, Spc, and F1) | R-DIs |
Ozsoy et al. [119] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | Â | SM, PDo, and CF | PubChem, UniProt, SIDER, and TIRs [35] | CV and Comp(Prec, Rec, F1, Spc, and AUC) | R-DIs |
Segler et al. [124] | Â | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | RNN | SMILES | EOR | R-DIs |
Altae-Tran et al. [122] | Â | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | Â | CCN and LSTM | SIDER and Tox21 [129] | Acc and AUC | R-DIs |
Papanikolaou et al. [105] |  | \(\checkmark\) |  | \(\checkmark\) |  |  | NER | DrugBank | — | R-RAs |
Brown et al. [104] | Â | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | Â | SM and Clust | MEDLINE and DrugBank | CSs | R-DIs |
Nugent et al. [59] | Â | Â | \(\checkmark\) | \(\checkmark\) | Â | Â | SCM | Comp(Acc) | R-DIs | |
Aliper et al. [121] | \(\checkmark\) | Â | Â | Â | \(\checkmark\) | Â | DNN | LINCS | CV, F1, NNCM, Spr, and Comp(Acc) | R-RAs |
Lim et al. [118] | \(\checkmark\) | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | SM and CF | ZINC [130] | CV and Comp(Acc,and Rec) | R-TIs |
Sridhar et al. [60] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | Â | SM and PSL | DrugBank | Comp(AUC, AUC-PR, F1) and CSs | R-RIs |
Zheng et al. [39] | Â | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | Â | SM | BindingDB [131] | CV, Acc, Spc, Sen, AUC, Prec, F1, Comp(AUC, Sen, and Spc), and CSs | R-TIs |
Rastegar-Mojarad et al. [103] | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | \(\checkmark\) | TM and SM | Comp(CoS) | R-DIs | |
Rakshit et al. [126] | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | \(\checkmark\) | TM and Genotator [135], PolySearch [95], Pescador [136], and DrugBank | Comp(Acc) | R-TIs | Â |
Huang et al. [27] | \(\checkmark\) | Â | Â | Â | \(\checkmark\) | \(\checkmark\) | SM and BGL | CMap | CV, AUC, Comp(AUC), and CSs | R-TIs |
Zhu et al. [108] | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | Â | Â | SM and WOL | PharmGKB | CSs | R-DIs |
Tari et al. [102] | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | Â | Â | TM and LFRs | Medline, GO, UniProt, NCBI, CancerQuest [137], and DrugBank | Comp(Rec) and CSs | R-DIs |
Okada et al. [23] | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | Â | Â | GWAS | GWASs | P and CSs | R-DIs |
Yang et al. [117] | \(\checkmark\) | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | CI-PMF | Comp(AUC and Prec) and CSs | R-DIs | |
Zhang et al. [116] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | Â | SM and BCD | CV, Comp(AUC), and CSs | R-DIs | |
Bisgin et al. [58] | Â | Â | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | SM and LDA | SIDER | Acc and CSs | R-TIs |
Tan et al. [38] | \(\checkmark\) | \(\checkmark\) | Â | Â | Â | \(\checkmark\) | SM and Clust | PubChem and DrugBank | Comp(Acc) | R-TIs |
Ye et al. [57] | Â | Â | \(\checkmark\) | Â | Â | \(\checkmark\) | SM | SIDER | CV, Acc, and CSs | R-TIs |
Menden et al. [114] | \(\checkmark\) | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | FF-PNN and RF | CCL [18] | CV, Acc, \(R_{p}\), \(R^{2}\), RMSE, and CSs | R-TIs |
Napolitano et al. [115] | \(\checkmark\) | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | SVM and CF | CMap, NCBI, DrugBank, and ATC [141] | CV, Acc, Comp(AUC) | R-DIs |
Wang et al. [37] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | SM, KF, and SVM | PubChem, KEGG, BRENDA [142], SuperTarget [143], DrugBank, and SIDER | CV, Comp(AUC, Acc, Sens, Spc, Prec, and F1), $ CSs | R-DIs |
Gottlieb et al. [56] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | SM | DrugBank, Drugs.com, and SIDER | CV, Acc, AUC, and CSs | R-TIs |
Wu et al. [125] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | SM and Clust | KEGG | CV, Comp(Acc), and CSs | R-DIs |
Chen et al. [107] | \(\checkmark\) | Â | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | SM and LP | Acc, AUC, Copm(Acc and AUC), and CSs | R-TIs | |
Li and Lu [96] | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | \(\checkmark\) | TM | ClinicalTrials.gov and PharmGKB | Acc, Comp(Acc), and CSs | PGx |
Li and Lu [35] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | SM and BGL | CV (Sen, Spc, and AUC), Comp(Spc, Sen, and AUC), and CSs | R-TIs | |
Hoehndorf et al. [55] | \(\checkmark\) | Â | \(\checkmark\) | Â | \(\checkmark\) | Â | SM | PhenomeNET [145] and PharmGKB | AUC and CSs | R-TIs |
Gottlieb et al. [113] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | Â | SM and LR | DrugBank, SMILES, Matador [143], DCDB [146], KEGG, DailyMed [147], SIDER, GO, UniPort, and ClinicalTrials.gov | CV, Acc, P, AUC, and Comp(Acc and AUC) | R-DIs |
Sirota et al. [14] | \(\checkmark\) | Â | Â | Â | \(\checkmark\) | Â | Clust and SM | GEO and CMap | CSs | R-DIs |
Hu and Agarwal [13] | \(\checkmark\) | Â | Â | Â | Â | \(\checkmark\) | SM | GEO, CMap, and DrugBank | Acc, Comp(Rec and Sens), and CSs | R-DIs |
Li et al. [101] | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | Â | TM, SM and CMap | OPHID [148], PubMed | CV, Comp(Sen, Spc, PPV, F1, and Acc), and CSs | R-DIs |
Bleakley et al. [32] | \(\checkmark\) | \(\checkmark\) | Â | Â | \(\checkmark\) | \(\checkmark\) | SM, BGL, and SVM | CV, Comp(AYC and AUC-PR), and CSs | R-TIs | |
Kinnings et al. [31] | \(\checkmark\) | \(\checkmark\) | Â | Â | Â | \(\checkmark\) | SM | MDDR [149] | Comp(Acc) and CSs | R-TIs |
Keiser et al. [9] | Â | \(\checkmark\) | Â | Â | \(\checkmark\) | \(\checkmark\) | SM and BGL | CV, Comp(AUC, Sens, Spc, and PPV), and CSs | R-TIs | |
Yamanishi et al. [30] | \(\checkmark\) | \(\checkmark\) | Â | Â | \(\checkmark\) | \(\checkmark\) | SM and BGL | CV, Comp(AUC, Sens, Spc, and PPV), and CSs | R-TIs | |
Cheng et al. [95] | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | \(\checkmark\) | TM | Comp(F1) and CSs | BER | |
Campillos et al. [53] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | Â | SM | Comp(Spc and Sen) and CSs | R-DIs | |
Lamb et al. [12] | \(\checkmark\) | Â | Â | Â | \(\checkmark\) | Â | Clust and CMap | CHC | CSs | R-DIs |