Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator

Bioinformatics
Andon TchechmedjievClement Jonquet

Abstract

Second use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical data, but not very suitable for clinical text annotation. In order to add new functionalities to the NCBO Annotator without hosting or modifying the original Web service, we have designed a proxy architecture that enables seamless extensions by pre-processing of the input text and parameters, and post processing of the annotations. We have then implemented enhanced functionalities for annotating and indexing free text such as: scoring, detection of context (negation, experiencer, temporality), new output formats and coarse-grained concept recognition (with UMLS Semantic Groups). In this paper, we present the NCBO Annotator+, a Web service which incorporates these new functionalities as well as a small set of evaluation results for concept recognition and clinical context detection on two standard evaluation tasks (Clef eHealth 2017, SemEval 2014). The Annotator+ has been successfully integrated into the SIFR BioPortal platform-an implementation of NCBO BioPortal for French biomedical terminolog...Continue Reading

References

Dec 19, 2003·Nucleic Acids Research·Olivier Bodenreider
Mar 6, 2009·Journal of the American Medical Informatics Association : JAMIA·Bonnie Kaplan, Kimberly D Harris-Salamone
May 14, 2009·Journal of Biomedical Informatics·Henk HarkemaWendy W Chapman
Sep 26, 2009·BMC Bioinformatics·Nigam H ShahMark A Musen
Oct 21, 2010·Critical Care Medicine·Vitaly HerasevichOgnjen Gajic
Jan 1, 2008·Acta Crystallographica. Section E, Structure Reports Online·Jing Dai, Wei Dai
Feb 2, 2009·Macromolecular Rapid Communications·Qi ZengBen Zhong Tang
Oct 13, 2012·Journal of the American Medical Informatics Association : JAMIA·John F HurdleSamir J Courdy
Dec 15, 2012·The Mount Sinai Journal of Medicine, New York·Brian RothmanMichael M Vigoda
Sep 13, 2017·Journal of Biomedical Semantics·Louise DelégerAurélie Névéol

❮ Previous
Next ❯

Citations

Nov 8, 2018·BMC Bioinformatics·Andon TchechmedjievClement Jonquet
May 21, 2019·Nucleic Acids Research·Cong LiuChunhua Weng
Sep 5, 2021·Journal of Biomedical Informatics·Krist ShingjergjiMichel Dumontier

❮ Previous
Next ❯

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.

Related Papers

Summit on Translational Bioinformatics
Clement JonquetMark A Musen
AMIA Joint Summits on Translational Science Proceedings
Dezhao SongCui Tao
AMIA ... Annual Symposium Proceedings
Joshua D FranklinJames F Brinkley
© 2022 Meta ULC. All rights reserved