A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text.

Journal of Biomedical Informatics
Rong Xu, Quanqiu Wang

Abstract

An important task in pharmacogenomics (PGx) studies is to identify genetic variants that may impact drug response. The success of many systematic and integrative computational approaches for PGx studies depends on the availability of accurate, comprehensive and machine understandable drug-gene relationship knowledge bases. Scientific literature is one of the most comprehensive knowledge sources for PGx-specific drug-gene relationships. However, the major barrier in accessing this information is that the knowledge is buried in a large amount of free text with limited machine understandability. Therefore there is a need to develop automatic approaches to extract structured PGx-specific drug-gene relationships from unstructured free text literature. In this study, we have developed a conditional relationship extraction approach to extract PGx-specific drug-gene pairs from 20 million MEDLINE abstracts using known drug-gene pairs as prior knowledge. We have demonstrated that the conditional drug-gene relationship extraction approach significantly improves the precision and F1 measure compared to the unconditioned approach (precision: 0.345 vs. 0.11; recall: 0.481 vs. 1.00; F1: 0.402 vs. 0.201). In this study, a method based on co-oc...Continue Reading

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Citations

Feb 14, 2013·BMC Bioinformatics·Carlo A TrugenbergerSvetlana Bureeva
Feb 28, 2013·Therapeutic Delivery·Craig RussellAfzal R Mohammed
May 21, 2013·Journal of the American Medical Informatics Association : JAMIA·Rong Xu, QuanQiu Wang
May 20, 2014·BioMed Research International·À BravoL I Furlong
Jul 29, 2015·PLoS Computational Biology·Bethany Percha, Russ B Altman
Dec 21, 2017·PloS One·A S M Ashique MahmoodK Vijay-Shanker
Apr 28, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yuting XingJianping Yin
Jan 4, 2020·Scientific Data·Joël LegrandAdrien Coulet
May 6, 2017·Chemical Reviews·Martin KrallingerAlfonso Valencia

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