Various criteria in the evaluation of biomedical named entity recognition

BMC Bioinformatics
Richard Tzong-Han TsaiWen-Lian Hsu

Abstract

Text mining in the biomedical domain is receiving increasing attention. A key component of this process is named entity recognition (NER). Generally speaking, two annotated corpora, GENIA and GENETAG, are most frequently used for training and testing biomedical named entity recognition (Bio-NER) systems. JNLPBA and BioCreAtIvE are two major Bio-NER tasks using these corpora. Both tasks take different approaches to corpus annotation and use different matching criteria to evaluate system performance. This paper details these differences and describes alternative criteria. We then examine the impact of different criteria and annotation schemes on system performance by retesting systems participated in the above two tasks. To analyze the difference between JNLPBA's and BioCreAtIvE's evaluation, we conduct Experiment 1 to evaluate the top four JNLPBA systems using BioCreAtIvE's classification scheme. We then compare them with the top four BioCreAtIvE systems. Among them, three systems participated in both tasks, and each has an F-score lower on JNLPBA than on BioCreAtIvE. In Experiment 2, we apply hypothesis testing and correlation coefficient to find alternatives to BioCreAtIvE's evaluation scheme. It shows that right-match and lef...Continue Reading

References

Jul 27, 2001·Bioinformatics·V HatzivassiloglouA Rzhetsky
Aug 15, 2002·Bioinformatics·Lorraine Tanabe, W John Wilbur
Dec 4, 2002·International Journal of Medical Informatics·Kristofer FranzénJoakim Cöster
Jul 9, 2004·The British Journal of Radiology·S AhnE Choi
Nov 24, 2004·Computational Biology and Chemistry·Zhang-Zhi HuCathy H Wu
Apr 9, 2005·Bioinformatics·Yu SongByoung-Kee Yi
Jun 18, 2005·BMC Bioinformatics·Christian BlaschkeAlfonso Valencia
Jun 18, 2005·BMC Bioinformatics·Alexander YehLynette Hirschman
Jun 18, 2005·BMC Bioinformatics·Lorraine TanabeW John Wilbur
Jun 18, 2005·BMC Bioinformatics·Jenny FinkelClaire Grover
Jun 18, 2005·BMC Bioinformatics·Ryan McDonald, Fernando Pereira
Jun 18, 2005·BMC Bioinformatics·GuoDong ZhouSoonHeng Tan
Aug 23, 2005·International Journal of Medical Informatics·G D Zhou

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Citations

Sep 30, 2008·Briefings in Bioinformatics·Pankaj Agarwal, David B Searls
Oct 29, 2010·Journal of Bioinformatics and Computational Biology·Yue WangJun'ichi Tsujii
Dec 10, 2009·BMC Bioinformatics·Yue WangJun'ichi Tsujii
May 9, 2008·BMC Bioinformatics·Antonio JimenoDietrich Rebholz-Schuhmann
Apr 27, 2013·BMC Medical Informatics and Decision Making·Qi LiImre Solti
Mar 11, 2015·Journal of the American Medical Informatics Association : JAMIA·Azadeh NikfarjamGraciela Gonzalez
Mar 25, 2017·Journal of the American Medical Informatics Association : JAMIA·Anne CocosAaron J Masino
Jun 14, 2018·BMC Bioinformatics·Shashank GuptaVasudeva Varma
Jun 29, 2018·Bioinformatics·Arjun MaggeGraciela Gonzalez-Hernandez
Sep 29, 2020·Frontiers in Cell and Developmental Biology·Nadeesha PereraFrank Emmert-Streib
Jan 1, 2012·ISRN Bioinformatics·Tiago GregoFrancisco M Couto
Jul 27, 2021·Briefings in Bioinformatics·Bosheng SongXiangxiang Zeng
Apr 13, 2018··Chenwei ZhangPhilip S. Yu
Dec 18, 2017··Guadalupe Aguado-de-CeaPablo Calleja

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Software Mentioned

GENETAG
AbGene
Bio
iProLINK
Kex
JNLPBA
GENIA
NEWGENE
Yapex
BioCreAtIvE

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