NOBLE - Flexible concept recognition for large-scale biomedical natural language processing

BMC Bioinformatics
Eugene TseytlinRebecca S Jacobson

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

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Citations

Sep 16, 2016·BMC Medical Informatics and Decision Making·Harry HochheiserRebecca S Jacobson
May 30, 2017·Journal of Biomedical Informatics·John CuzzolaEbrahim Bagheri
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
Jan 23, 2019·Journal of Cheminformatics·Lenz FurrerFabio Rinaldi
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
Nov 8, 2018·BMC Bioinformatics·Andon TchechmedjievClement Jonquet
Jan 31, 2020·Frontiers in Plant Science·Ian R Braun, Carolyn J Lawrence-Dill
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
Oct 28, 2019·Journal of Biomedical Informatics·Cong LiuChunhua Weng
Feb 18, 2020·Computer Methods and Programs in Biomedicine·Zhe WangJing Zhang
May 19, 2021·Journal of Biomedical Semantics·Ivano LauriolaFabio Rinaldi
Jun 18, 2021··Chuan LeiAlina Vretinaris

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Software Mentioned

cTAKES Dictionary Lookup Annotator ( DLA )
GATE
cTAKES UIMA Processing
cTAKES Fast Dictionary Lookup Annotator ( FDLA )
cTAKES Fast Dictionary Lookup Annotator
Concept Mapper
MMTx MetamorphoSys
MGrep
OBA
AnnotDiffTool

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