Literature-based discovery of new candidates for drug repurposing

被引:59
|
作者
Yang, Hsih-Te [2 ,3 ]
Ju, Jiun-Huang [1 ]
Wong, Yue-Ting [1 ]
Shmulevich, Ilya [4 ,5 ]
Chiang, Jung-Hsien [2 ]
机构
[1] Natl Cheng Kung Univ, Dept Comp Sci & Informat Engn, Tainan, Taiwan
[2] Natl Cheng Kung Univ, Dept Comp Sci & Informat Engn, Inst Med Informat, Tainan, Taiwan
[3] Natl Cheng Kung Univ, Inst Oral Med, Tainan, Taiwan
[4] Inst Syst Biol, Seattle, WA USA
[5] Genome Data Anal Ctr, Seattle, WA USA
关键词
text-mining; ABC model; drug repurposing; information extraction; natural language processing; drug target discovery; UPDATE; NORMALIZATION; THALIDOMIDE; INTEGRATION; CARCINOMA; TAMOXIFEN; KNOWLEDGE; ASPIRIN;
D O I
10.1093/bib/bbw030
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Drug development is an expensive and time-consuming process; these could be reduced if the existing resources could be used to identify candidates for drug repurposing. This study sought to do this by text mining a large-scale literature repository to curate repurposed drug lists for different cancers. We devised a pattern-based relationship extraction method to extract disease-gene and gene-drug direct relationships from the literature. These direct relationships are used to infer indirect relationships using the ABC model. A gene-shared ranking method based on drug target similarity was then proposed to prioritize the indirect relationships. Our method of assessing drug target similarity correlated to existing anatomical therapeutic chemical code-based methods with a Pearson correlation coefficient of 0.9311. The indirect relationships ranking method achieved a significant mean average precision score of top 100 most common diseases. We also confirmed the suitability of candidates identified for repurposing as anticancer drugs by conducting a manual review of the literature and the clinical trials. Eventually, for visualization and enrichment of huge amount of repurposed drug information, a chord diagram was demonstrated to rapidly identify two novel indications for further biological evaluations.
引用
收藏
页码:488 / 497
页数:10
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