Natural language processing in aid of FlyBase curators.

BMC Bioinformatics
Nikiforos KaramanisTed Briscoe

Abstract

Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities ...Continue Reading

References

Jul 1, 2004·Nature Genetics·Robert Hoffmann, Alfonso Valencia
Nov 16, 2004·Journal of Biomedical Informatics·Alexander A MorganJeff B Colombe
Apr 14, 2005·Briefings in Bioinformatics·Aaron M Cohen, William R Hersh
Nov 14, 2006·Nucleic Acids Research·Madeline A CrosbyUNKNOWN FlyBase Consortium
Jan 24, 2007·Bioinformatics·Dietrich Rebholz-SchuhmannPeter Stoehr
Jun 5, 2007·Bioinformatics·Marti A HearstJerry Ye
Jul 17, 2008·Comparative and Functional Genomics·Karen Eilbeck, Suzanna E Lewis

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Citations

Mar 22, 2012·Database : the Journal of Biological Databases and Curation·Rafal RakSophia Ananiadou
Apr 25, 2012·Database : the Journal of Biological Databases and Curation·Fabio RinaldiRuss B Altman
Nov 20, 2012·Database : the Journal of Biological Databases and Curation·Peter McQuilton, UNKNOWN FlyBase Consortium
Nov 20, 2012·Database : the Journal of Biological Databases and Curation·Chih-Hsuan WeiZhiyong Lu
Nov 20, 2012·Database : the Journal of Biological Databases and Curation·Zhiyong Lu, Lynette Hirschman
Apr 16, 2013·Database : the Journal of Biological Databases and Curation·Karin VerspoorJohn-Paul Plazzer
May 17, 2008·Nucleic Acids Research·Hodong LeeJong C Park
Dec 22, 2011·BMC Bioinformatics·Cecilia N ArighiCathy H Wu
Jul 25, 2012·BMC Bioinformatics·Jan CzarneckiAdrian J Shepherd
Dec 21, 2012·Briefings in Bioinformatics·Mariana Neves, Ulf Leser
Jun 14, 2014·Database : the Journal of Biological Databases and Curation·David CamposJosé Luís Oliveira
Dec 29, 2015·Database : the Journal of Biological Databases and Curation·Raul Rodriguez-Esteban
Apr 8, 2011·Chembiochem : a European Journal of Chemical Biology·Deanna L MendezSarah C R Elgin
May 15, 2012·Journal of Biomedical Informatics·Fabio RinaldiSimon Clematide
Feb 19, 2008·Journal of Biomedical Informatics·Ben Medlock
Apr 15, 2009·Journal of Biomedical Informatics·Hui YangGoran Nenadic
Apr 28, 2009·Journal of Biomedical Informatics·Anália LourençoMiguel Rocha
Jun 10, 2016·Database : the Journal of Biological Databases and Curation·Sérgio MatosJosé Luís Oliveira
Dec 23, 2011·Trends in Ecology & Evolution·Andrew R DeansJames P Balhoff
Apr 17, 2018·PLoS Biology·UNKNOWN International Society for Biocuration
Nov 15, 2012·Nature Reviews. Genetics·Dietrich Rebholz-SchuhmannRobert Hoehndorf
Feb 27, 2020·The FEBS Journal·Anastasia Baryshnikova
Sep 19, 2019·PLoS Computational Biology·Yang YangHong-Bin Shen
Apr 4, 2017·Database : the Journal of Biological Databases and Curation·Honghan WuRichard J B Dobson

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Software Mentioned

BioText Search Engine
Textpresso
PaperBrowsers
PaperBrowser
NER
R
JREX
MedMiner
Linux Fedora Core
iHop

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