GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique.

BMC Bioinformatics
Wei YuMarta Gwinn

Abstract

Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts req...Continue Reading

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Citations

Apr 14, 2011·European Journal of Human Genetics : EJHG·Sheri D SchullyMuin J Khoury
Apr 7, 2012·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Byron C WallaceThomas A Trikalinos
May 25, 2013·Nucleic Acids Research·Chih-Hsuan WeiZhiyong Lu
Jan 28, 2010·BMC Bioinformatics·Byron C WallaceChristopher H Schmid
Feb 3, 2012·BioData Mining·Theodoros G SoldatosReinhard Schneider
May 31, 2014·PLoS Computational Biology·Jisoo ParkDonna K Slonim
Feb 22, 2012·PloS One·Jessica L RowellMarta Gwinn
Nov 19, 2013·Journal of Comparative Effectiveness Research·Byron C WallaceThomas A Trikalinos
Oct 18, 2014·Nucleic Acids Research·Xia RanJinyu Wu
Jun 10, 2016·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Wei YuMuin J Khoury
Jun 14, 2016·Journal of Biomedical Informatics·Kazuma HashimotoSophia Ananiadou
Aug 17, 2010·Journal of Biomedical Informatics·Shashank Agarwal, Hong Yu
Nov 30, 2011·Genetic Epidemiology·Muin J KhouryWei Yu
May 6, 2017·Chemical Reviews·Martin KrallingerAlfonso Valencia
Nov 19, 2021·Health Information and Libraries Journal·Joseph K BurnsSylvain Boet

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Software Mentioned

EzInstall
SVM
Java Runtime Environment ( JRE )
J2EE
grid
LibSVM
- utility
HuGE Navigator
EMBASE
MetaMap Transfer ( MMTx )

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