Assisting document triage for human kinome curation via machine learning

Database : the Journal of Biological Databases and Curation
Yi-Yu HsuZhiyong Lu

Abstract

In the era of data explosion, the increasing frequency of published articles presents unorthodox challenges to fulfill specific curation requirements for bio-literature databases. Recognizing these demands, we designed a document triage system with automatic methods that can improve efficiency to retrieve the most relevant articles in curation workflows and reduce workloads for biocurators. Since the BioCreative VI (2017), we have implemented texting mining processing in our system in hopes of providing higher effectiveness for curating articles related to human kinase proteins. We tested several machine learning methods together with state-of-the-art concept extraction tools. For features, we extracted rich co-occurrence and linguistic information to model the curation process of human kinome articles by the neXtProt database. As shown in the official evaluation on the human kinome curation task in BioCreative VI, our system can effectively retrieve 5.2 and 6.5 kinase articles with the relevant disease (DIS) and biological process (BP) information, respectively, among the top 100 returned results. Comparing to neXtA5, our system demonstrates significant improvements in prioritizing kinome-related articles as follows: our syste...Continue Reading

References

Nov 20, 2012·Database : the Journal of Biological Databases and Curation·Sun KimW John Wilbur
Nov 20, 2012·Database : the Journal of Biological Databases and Curation·Zhiyong Lu, Lynette Hirschman
Nov 28, 2012·Database : the Journal of Biological Databases and Curation·Thomas C WiegersCarolyn J Mattingly
Dec 5, 2012·Journal of Proteome Research·Pascale GaudetLydie Lane
Sep 18, 2015·BioMed Research International·Chih-Hsuan WeiZhiyong Lu
Jul 5, 2016·Database : the Journal of Biological Databases and Curation·Luc MottinPatrick Ruch
Oct 17, 2017·Bioinformatics·Sylvain PouxThe UniProt Consortium
Dec 9, 2017·Database : the Journal of Biological Databases and Curation·Ruoyao DingCecilia N Arighi

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Citations

Apr 16, 2020·Database : the Journal of Biological Databases and Curation·Xiangying JiangHagit Shatkay
Feb 13, 2019·Database : the Journal of Biological Databases and Curation·Yi-Yu HsuZhiyong Lu

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