SemaTyP: a knowledge graph based literature mining method for drug discovery

BMC Bioinformatics
Shengtian SangJian Wang

Abstract

Drug discovery is the process through which potential new medicines are identified. High-throughput screening and computer-aided drug discovery/design are the two main drug discovery methods for now, which have successfully discovered a series of drugs. However, development of new drugs is still an extremely time-consuming and expensive process. Biomedical literature contains important clues for the identification of potential treatments. It could support experts in biomedicine on their way towards new discoveries. Here, we propose a biomedical knowledge graph-based drug discovery method called SemaTyP, which discovers candidate drugs for diseases by mining published biomedical literature. We first construct a biomedical knowledge graph with the relations extracted from biomedical abstracts, then a logistic regression model is trained by learning the semantic types of paths of known drug therapies' existing in the biomedical knowledge graph, finally the learned model is used to discover drug therapies for new diseases. The experimental results show that our method could not only effectively discover new drug therapies for new diseases, but also could provide the potential mechanism of action of the candidate drugs. In this pape...Continue Reading

References

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Citations

May 19, 2020·Briefings in Bioinformatics·Sendong ZhaoFei Wang
Nov 20, 2018·Expert Opinion on Drug Discovery·Yinqiu XuKejiang Lin
Mar 20, 2019·Expert Opinion on Drug Discovery·Samantha Kanza, Jeremy Graham Frey
Apr 10, 2019·BMC Medical Informatics and Decision Making·Di ZhaoChunmei Yang
Jul 25, 2019·Frontiers in Bioengineering and Biotechnology·Andrew R Sedler, Cassie S Mitchell
Mar 13, 2019·Journal of Biomedical Informatics·Vishrawas GopalakrishnanAidong Zhang
May 7, 2021·Annual Review of Biomedical Data Science·Tiffany J CallahanLawrence E Hunter
Jul 31, 2021·BMC Bioinformatics·Xi YangKai Lu
Nov 1, 2021·Drug Discovery Today·Vinicius M AlvesAlexander Tropsha
Dec 2, 2021·Briefings in Bioinformatics·Margaret G GuoRuss B Altman
Jun 23, 2020··Lili WuJie Tang

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Software Mentioned

Nell
SemaTyP
RWA
SemKG
YAGO
DBpedia
Freebase
SemRep
MetaMap

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