Literature DB >> 23872518

Annotating temporal information in clinical narratives.

Weiyi Sun1, Anna Rumshisky2, Ozlem Uzuner3.   

Abstract

Temporal information in clinical narratives plays an important role in patients' diagnosis, treatment and prognosis. In order to represent narrative information accurately, medical natural language processing (MLP) systems need to correctly identify and interpret temporal information. To promote research in this area, the Informatics for Integrating Biology and the Bedside (i2b2) project developed a temporally annotated corpus of clinical narratives. This corpus contains 310 de-identified discharge summaries, with annotations of clinical events, temporal expressions and temporal relations. This paper describes the process followed for the development of this corpus and discusses annotation guideline development, annotation methodology, and corpus quality.
Copyright © 2013 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Annotation; Corpus Building; Medical Informatics; Natural Language Processing; Temporal Reasoning

Mesh:

Year:  2013        PMID: 23872518      PMCID: PMC3855581          DOI: 10.1016/j.jbi.2013.07.004

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  17 in total

1.  Extracting medication information from clinical text.

Authors:  Ozlem Uzuner; Imre Solti; Eithon Cadag
Journal:  J Am Med Inform Assoc       Date:  2010 Sep-Oct       Impact factor: 4.497

Review 2.  Temporal reasoning for decision support in medicine.

Authors:  Juan Carlos Augusto
Journal:  Artif Intell Med       Date:  2005-01       Impact factor: 5.326

3.  Finding temporal order in discharge summaries.

Authors:  Philip Bramsen; Pawan Deshpande; Yoong Keok Lee; Regina Barzilay
Journal:  AMIA Annu Symp Proc       Date:  2006

Review 4.  Temporal abstraction in intelligent clinical data analysis: a survey.

Authors:  Michael Stacey; Carolyn McGregor
Journal:  Artif Intell Med       Date:  2006-09-29       Impact factor: 5.326

5.  The evaluation of a temporal reasoning system in processing clinical discharge summaries.

Authors:  Li Zhou; Simon Parsons; George Hripcsak
Journal:  J Am Med Inform Assoc       Date:  2007-10-18       Impact factor: 4.497

Review 6.  Extracting information from textual documents in the electronic health record: a review of recent research.

Authors:  S M Meystre; G K Savova; K C Kipper-Schuler; J F Hurdle
Journal:  Yearb Med Inform       Date:  2008

7.  Towards temporal relation discovery from the clinical narrative.

Authors:  Guergana Savova; Steven Bethard; Will Styler; James Martin; Martha Palmer; James Masanz; Wayne Ward
Journal:  AMIA Annu Symp Proc       Date:  2009-11-14

Review 8.  Temporal reasoning over clinical text: the state of the art.

Authors:  Weiyi Sun; Anna Rumshisky; Ozlem Uzuner
Journal:  J Am Med Inform Assoc       Date:  2013-05-15       Impact factor: 4.497

9.  Extracting timing and status descriptors for colonoscopy testing from electronic medical records.

Authors:  Joshua C Denny; Josh F Peterson; Neesha N Choma; Hua Xu; Randolph A Miller; Lisa Bastarache; Neeraja B Peterson
Journal:  J Am Med Inform Assoc       Date:  2010 Jul-Aug       Impact factor: 4.497

10.  TN-TIES: A system for extracting temporal information from emergency department triage notes.

Authors:  Ann K Irvine; Stephanie W Haas; Tessa Sullivan
Journal:  AMIA Annu Symp Proc       Date:  2008-11-06
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  18 in total

1.  Chronology of your health events: approaches to extracting temporal relations from medical narratives.

Authors:  Özlem Uzuner; Amber Stubbs; Weiyi Sun
Journal:  J Biomed Inform       Date:  2013-12       Impact factor: 6.317

2.  Normalization of relative and incomplete temporal expressions in clinical narratives.

Authors:  Weiyi Sun; Anna Rumshisky; Ozlem Uzuner
Journal:  J Am Med Inform Assoc       Date:  2015-04-12       Impact factor: 4.497

3.  Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events.

Authors:  Fang Li; Jingcheng Du; Yongqun He; Hsing-Yi Song; Mohcine Madkour; Guozheng Rao; Yang Xiang; Yi Luo; Henry W Chen; Sijia Liu; Liwei Wang; Hongfang Liu; Hua Xu; Cui Tao
Journal:  J Am Med Inform Assoc       Date:  2020-07-01       Impact factor: 4.497

4.  CMedTEX: A Rule-based Temporal Expression Extraction and Normalization System for Chinese Clinical Notes.

Authors:  Zengjian Liu; Buzhou Tang; Xiaolong Wang; Qingcai Chen; Haodi Li; Junzhao Bu; Jingzhi Jiang; Qiwen Deng; Suisong Zhu
Journal:  AMIA Annu Symp Proc       Date:  2017-02-10

Review 5.  Temporal reasoning over clinical text: the state of the art.

Authors:  Weiyi Sun; Anna Rumshisky; Ozlem Uzuner
Journal:  J Am Med Inform Assoc       Date:  2013-05-15       Impact factor: 4.497

6.  A general approach for improving deep learning-based medical relation extraction using a pre-trained model and fine-tuning.

Authors:  Tao Chen; Mingfen Wu; Hexi Li
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

7.  Extraction of Temporal Information from Clinical Narratives.

Authors:  Gandhimathi Moharasan; Tu-Bao Ho
Journal:  J Healthc Inform Res       Date:  2019-02-27

8.  A pattern learning-based method for temporal expression extraction and normalization from multi-lingual heterogeneous clinical texts.

Authors:  Tianyong Hao; Xiaoyi Pan; Zhiying Gu; Yingying Qu; Heng Weng
Journal:  BMC Med Inform Decis Mak       Date:  2018-03-22       Impact factor: 2.796

Review 9.  Evaluating temporal relations in clinical text: 2012 i2b2 Challenge.

Authors:  Weiyi Sun; Anna Rumshisky; Ozlem Uzuner
Journal:  J Am Med Inform Assoc       Date:  2013-04-05       Impact factor: 4.497

Review 10.  Temporal data representation, normalization, extraction, and reasoning: A review from clinical domain.

Authors:  Mohcine Madkour; Driss Benhaddou; Cui Tao
Journal:  Comput Methods Programs Biomed       Date:  2016-02-23       Impact factor: 5.428

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