A new algorithmic approach for the extraction of temporal associations from clinical narratives with an application to medical product safety surveillance reports

Wang, Wei; Kreimeyer, Kory; Woo, Emily Jane; Ball, Robert; Foster, Matthew; Pandey, Abhishek; Scott, John; Botsis, Taxiarchis

doi:10.1016/j.jbi.2016.06.006

Title: A new algorithmic approach for the extraction of temporal associations from clinical narratives with an application to medical product safety surveillance reports

Journal Article · Fri Jun 17 00:00:00 EDT 2016 · Journal of Biomedical Informatics

DOI:https://doi.org/10.1016/j.jbi.2016.06.006· OSTI ID:1373441

Wang, Wei; Kreimeyer, Kory; Woo, Emily Jane; Ball, Robert; Foster, Matthew; Pandey, Abhishek; Scott, John; Botsis, Taxiarchis

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Sponsoring Organization:: USDOE

Grant/Contract Number:: U54LM008748

OSTI ID:: 1373441

Alternate ID(s):: OSTI ID: 1350780

Journal Information:: Journal of Biomedical Informatics, Journal Name: Journal of Biomedical Informatics Vol. 62 Journal Issue: C; ISSN 1532-0464

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 15 works

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References (19)

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Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification Sohn, Sunghwan; Wagholikar, Kavishwar B.; Li, Dingcheng Journal of the American Medical Informatics Association, Vol. 20, Issue 5 https://doi.org/10.1136/amiajnl-2013-001622	journal	September 2013
Chronology of your health events: Approaches to extracting temporal relations from medical narratives Uzuner, Özlem; Stubbs, Amber; Sun, Weiyi Journal of Biomedical Informatics, Vol. 46 https://doi.org/10.1016/j.jbi.2013.11.005	journal	December 2013
Vaccine adverse event text mining system for extracting features from vaccine safety reports Botsis, Taxiarchis; Buttolph, Thomas; Nguyen, Michael D. Journal of the American Medical Informatics Association, Vol. 19, Issue 6 https://doi.org/10.1136/amiajnl-2012-000881	journal	November 2012
Detecting temporal expressions in medical narratives Reeves, Ruth M.; Ong, Ferdo R.; Matheny, Michael E. International Journal of Medical Informatics, Vol. 82, Issue 2 https://doi.org/10.1016/j.ijmedinf.2012.04.006	journal	February 2013
Knowledge-rich temporal relation identification and classification in clinical notes D'Souza, J.; Ng, V. Database, Vol. 2014, Issue 0 https://doi.org/10.1093/database/bau109	journal	January 2014
A temporal constraint structure for extracting temporal information from clinical narrative Zhou, Li; Melton, Genevieve B.; Parsons, Simon Journal of Biomedical Informatics, Vol. 39, Issue 4 https://doi.org/10.1016/j.jbi.2005.07.002	journal	August 2006
Temporal reasoning over clinical text: the state of the art Sun, Weiyi; Rumshisky, Anna; Uzuner, Ozlem Journal of the American Medical Informatics Association, Vol. 20, Issue 5 https://doi.org/10.1136/amiajnl-2013-001760	journal	September 2013
Multilingual and cross-domain temporal tagging Strötgen, Jannik; Gertz, Michael Language Resources and Evaluation, Vol. 47, Issue 2 https://doi.org/10.1007/s10579-012-9179-y	journal	May 2012
Use of data mining at the Food and Drug Administration Duggirala, Hesha J.; Tonning, Joseph M.; Smith, Ella Journal of the American Medical Informatics Association, Vol. 23, Issue 2 https://doi.org/10.1093/jamia/ocv063	journal	July 2015
Towards generating a patient’s timeline: Extracting temporal relationships from clinical notes Nikfarjam, Azadeh; Emadzadeh, Ehsan; Gonzalez, Graciela Journal of Biomedical Informatics, Vol. 46 https://doi.org/10.1016/j.jbi.2013.11.001	journal	December 2013
TEMPTING system: A hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries Chang, Yung-Chun; Dai, Hong-Jie; Wu, Johnny Chi-Yang Journal of Biomedical Informatics, Vol. 46 https://doi.org/10.1016/j.jbi.2013.09.007	journal	December 2013
Information extraction from research papers using conditional random fields Peng, Fuchun; McCallum, Andrew Information Processing & Management, Vol. 42, Issue 4 https://doi.org/10.1016/j.ipm.2005.09.002	journal	July 2006
Understanding vaccine safety information from the Vaccine Adverse Event Reporting System Varricchio, Frederick; Iskander, John; Destefano, Frank The Pediatric Infectious Disease Journal, Vol. 23, Issue 4 https://doi.org/10.1097/00006454-200404000-00002	journal	January 2004
Evaluating temporal relations in clinical text: 2012 i2b2 Challenge Sun, Weiyi; Rumshisky, Anna; Uzuner, Ozlem Journal of the American Medical Informatics Association, Vol. 20, Issue 5 https://doi.org/10.1136/amiajnl-2013-001628	journal	September 2013
Eventual situations for timeline extraction from clinical reports Grouin, Cyril; Grabar, Natalia; Hamon, Thierry Journal of the American Medical Informatics Association, Vol. 20, Issue 5 https://doi.org/10.1136/amiajnl-2013-001627	journal	September 2013
Temporal Annotation in the Clinical Domain Styler, William F.; Bethard, Steven; Finan, Sean Transactions of the Association for Computational Linguistics, Vol. 2 https://doi.org/10.1162/tacl_a_00172	journal	December 2014
Annotating temporal information in clinical narratives Sun, Weiyi; Rumshisky, Anna; Uzuner, Ozlem Journal of Biomedical Informatics, Vol. 46 https://doi.org/10.1016/j.jbi.2013.07.004	journal	December 2013
A hybrid system for temporal information extraction from clinical text Tang, Buzhou; Wu, Yonghui; Jiang, Min Journal of the American Medical Informatics Association, Vol. 20, Issue 5 https://doi.org/10.1136/amiajnl-2013-001635	journal	September 2013

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