Abstract
Natural language processing (NLP) applications are increasingly important in biomedical data analysis, knowledge engineering, and decision support. Concept recognition is an important component task for NLP pipelines, and can be either general-purpose or domain-specific. We describe a novel, flexible, and general-purpose concept recognition component for NLP pipelines, and compare its speed and accuracy against five commonly used alternatives on both a biological and clinical corpus. NOBLE Coder implements a general algorithm for matching terms to concepts from an arbitrary vocabulary set. The system's matching options can be configured individually or in combination to yield specific system behavior for a variety of NLP tasks. The software is open source, freely available, and easily integrated into UIMA or GATE. We benchmarked speed and accuracy of the system against the CRAFT and ShARe corpora as reference standards and compared it to MMTx, MGrep, Concept Mapper, cTAKES Dictionary Lookup Annotator, and cTAKES Fast Dictionary Lookup Annotator. We describe key advantages of the NOBLE Coder system and associated tools, including its greedy algorithm, configurable matching strategies, and multiple terminology input formats. Thes...Continue Reading
References
Jun 10, 2004·Journal of the American Medical Informatics Association : JAMIA·Carol FriedmanGeorge Hripcsak
Sep 17, 2004·BMC Medical Informatics and Decision Making·Jules J Berman
Jun 18, 2005·BMC Bioinformatics·Tomohiro MitsumoriHirohumi Doi
Oct 20, 2005·BMC Medical Informatics and Decision Making·Jules J Berman
Jan 30, 2008·PLoS Computational Biology·K Bretonnel Cohen, Lawrence Hunter
Jul 1, 2008·Bioinformatics·Chun-Nan HsuI-Fang Chung
Feb 28, 2009·BMC Bioinformatics·Yael Garten, Russ B Altman
Sep 26, 2009·BMC Bioinformatics·Nigam H ShahMark A Musen
May 6, 2010·Journal of the American Medical Informatics Association : JAMIA·Alan R Aronson, François-Michel Lang
May 6, 2010·Journal of the American Medical Informatics Association : JAMIA·Rebecca S CrowleyMichael Feldman
Jun 15, 2010·Journal of Biomedical Informatics·Mark Stevenson, Yikun Guo
Jul 22, 2010·Journal of Biomedical Informatics·Kaihong LiuRebecca S Crowley
Sep 8, 2010·Journal of the American Medical Informatics Association : JAMIA·Guergana K SavovaChristopher G Chute
Sep 8, 2010·Journal of the American Medical Informatics Association : JAMIA·Domonkos Tikk, Illés Solt
Nov 9, 2010·Methods of Information in Medicine·K LiuR S Crowley
Aug 19, 2011·Journal of the American Medical Informatics Association : JAMIA·Prakash M NadkarniWendy W Chapman
Dec 22, 2011·BMC Bioinformatics·Zhiyong LuW John Wilbur
Feb 3, 2012·Journal of the American Medical Informatics Association : JAMIA·Jiaping ZhengGuergana K Savova
May 9, 2012·BMC Medical Informatics and Decision Making·Son DoanMinh Phuong Tu
Jul 11, 2012·BMC Bioinformatics·Michael BadaLawrence E Hunter
May 7, 2013·International Journal of Medical Informatics·David HanauerLynette Hirschman
May 15, 2013·Methods of Information in Medicine·K LiuR S Crowley
Feb 28, 2014·BMC Bioinformatics·Christopher FunkKarin Verspoor
Aug 10, 2016·Database : the Journal of Biological Databases and Curation·Jitendra JonnagaddalaHong-Jie Dai
Citations
Sep 16, 2016·BMC Medical Informatics and Decision Making·Harry HochheiserRebecca S Jacobson
Sep 20, 2016·PloS One·Noha AlnazzawiSophia Ananiadou
May 30, 2017·Journal of Biomedical Informatics·John CuzzolaEbrahim Bagheri
Nov 15, 2017·PeerJ·Paul Groth, Jessica Cox
Nov 11, 2017·Journal of Biomedical Semantics·Marco BasaldellaFabio Rinaldi
Dec 9, 2017·Database : the Journal of Biological Databases and Curation·Luís CamposFrancisco Couto
Apr 13, 2018·Journal of the American Medical Informatics Association : JAMIA·John CuzzolaJelena Jovanovic
Jan 20, 2018·The Journal of Rural Health : Official Journal of the American Rural Health Association and the National Rural Health Care Association·Barbara MarlengaWilliam Pickett
Dec 7, 2018·Proteomics·Mansheng LiTao Chen
Oct 19, 2016·Digestive Diseases and Sciences·Alyce J M AndersonDavid G Binion
Jan 23, 2019·Journal of Cheminformatics·Lenz FurrerFabio Rinaldi
Jan 28, 2020·JAMIA Open·Jose-Franck Diaz-GarelliUmit Topaloglu
Sep 17, 2020·Journal of the American Medical Informatics Association : JAMIA·Tiago K ColicchioJames J Cimino
Sep 25, 2017·Journal of Biomedical Semantics·Jelena Jovanović, Ebrahim Bagheri
Jun 14, 2018·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Jing ChenGe Zhang
Apr 5, 2019·JAMIA Open·Meijian GuanUmit Topaloglu
Nov 8, 2018·BMC Bioinformatics·Andon TchechmedjievClement Jonquet
Jan 31, 2020·Frontiers in Plant Science·Ian R Braun, Carolyn J Lawrence-Dill
Feb 7, 2020·JAMIA Open·Albee Y LingSuzanne R Tamang
Jan 29, 2017·Journal of the American Medical Informatics Association : JAMIA·Dina Demner-FushmanAlan R Aronson
Jan 1, 2017·Database : the Journal of Biological Databases and Curation·Michael BadaLawrence E Hunter
Jan 15, 2020·Journal of Biomedical Semantics·Sara AlthubaitiRobert Hoehndorf
Aug 10, 2019·Cancer Research·Guergana K SavovaJeremy L Warner
Oct 28, 2019·Journal of Biomedical Informatics·Cong LiuChunhua Weng
Dec 10, 2020·Journal of Medical Internet Research·Borim RyuSooyoung Yoo
Feb 18, 2020·Computer Methods and Programs in Biomedicine·Zhe WangJing Zhang
Sep 11, 2019·Bioinformatics·Ginger TsuengAndrew I Su
May 19, 2021·Journal of Biomedical Semantics·Ivano LauriolaFabio Rinaldi
May 25, 2018··Beng Chin OoiJu Fan
Jun 18, 2021··Chuan LeiAlina Vretinaris