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A corpus of clinical narratives annotated with temporal information

Authors:

Lucian Galescu,

Nate BlaylockAuthors Info & Claims

IHI '12: Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium

Pages 715 - 720

https://doi.org/10.1145/2110363.2110446

Published: 28 January 2012 Publication History

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Abstract

Clinical reports often include descriptions of events in the patient's medical history, as well as explicit or implicit temporal information about these events. We are working towards applying deep Natural Language Processing tools towards understanding such narratives. This requires both the extraction and classification of the relevant events, and the placing of those events in time, or at least in relation to one another. Although several corpora of news data exist that have been annotated using the TimeML schema, similar corpora of clinical reports are not readily available.

In this paper we report on the design of a small corpus and the annotation schema we developed, based on data from the fourth i2b2/VA challenge. These data include, among others, annotations for medical problems, tests, and treatments in clinical reports from several healthcare institutions. We have selected a subset of clinical reports and added annotations similar to those used in the TempEval tasks for the annotation of events, time expressions and temporal relations for the news domain. The annotations have been made freely available to the research community.

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Tan XLiu DQi XBin LChen S(2023)Construction of Chinese Electronic Medical Record Entity and Entity Relation Annotation Corpus for Pediatric Bronchopneumonia Disease2023 IEEE International Conference on Medical Artificial Intelligence (MedAI)10.1109/MedAI59581.2023.00040(260-265)Online publication date: 18-Nov-2023
https://doi.org/10.1109/MedAI59581.2023.00040
Moharasan GHo T(2019)Extraction of Temporal Information from Clinical NarrativesJournal of Healthcare Informatics Research10.1007/s41666-019-00049-0Online publication date: 27-Feb-2019
https://doi.org/10.1007/s41666-019-00049-0
Moharasan GHo T(2017)Extraction of Temporal Events from Clinical Text Using Semi-supervised Conditional Random FieldsData Mining and Big Data10.1007/978-3-319-61845-6_41(409-421)Online publication date: 24-Jun-2017
https://doi.org/10.1007/978-3-319-61845-6_41
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Index Terms

A corpus of clinical narratives annotated with temporal information
1. Computing methodologies
  1. Artificial intelligence
    1. Natural language processing

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Published In

IHI '12: Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium

January 2012

914 pages

ISBN:9781450307819

DOI:10.1145/2110363

General Chairs:
Gang Luo
IBM Research, USA
,
Jiming Liu
Hong Kong Baptist University
,
Program Chair:
Christopher C. Yang
Drexel University

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 28 January 2012

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IHI '12: ACM International Health Informatics Symposium

January 28 - 30, 2012

Florida, Miami, USA

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Tan XLiu DQi XBin LChen S(2023)Construction of Chinese Electronic Medical Record Entity and Entity Relation Annotation Corpus for Pediatric Bronchopneumonia Disease2023 IEEE International Conference on Medical Artificial Intelligence (MedAI)10.1109/MedAI59581.2023.00040(260-265)Online publication date: 18-Nov-2023
https://doi.org/10.1109/MedAI59581.2023.00040
Moharasan GHo T(2019)Extraction of Temporal Information from Clinical NarrativesJournal of Healthcare Informatics Research10.1007/s41666-019-00049-0Online publication date: 27-Feb-2019
https://doi.org/10.1007/s41666-019-00049-0
Moharasan GHo T(2017)Extraction of Temporal Events from Clinical Text Using Semi-supervised Conditional Random FieldsData Mining and Big Data10.1007/978-3-319-61845-6_41(409-421)Online publication date: 24-Jun-2017
https://doi.org/10.1007/978-3-319-61845-6_41
Madkour MHsing-yi Song Jingcheng Du Tao C(2016)A representational analysis of a temporal indeterminancy display in clinical events2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)10.1109/BIBM.2016.7822673(1089-1095)Online publication date: Dec-2016
https://doi.org/10.1109/BIBM.2016.7822673
Madkour MBenhaddou DTao C(2016)Temporal data representation, normalization, extraction, and reasoningComputer Methods and Programs in Biomedicine10.1016/j.cmpb.2016.02.007128:C(52-68)Online publication date: 1-May-2016
https://dl.acm.org/doi/10.1016/j.cmpb.2016.02.007
Cormack JNath CMilward DRaja KJonnalagadda S(2015)Agile text mining for the 2014 i2b2/UTHealth Cardiac risk factors challengeJournal of Biomedical Informatics10.5555/2869975.287035558:S(S120-S127)Online publication date: 1-Dec-2015
https://dl.acm.org/doi/10.5555/2869975.2870355
Xu DZhang MZhao TGe CGao WWei JZhu K(2015)Data-Driven Information Extraction from Chinese Electronic Medical RecordsPLOS ONE10.1371/journal.pone.013627010:8(e0136270)Online publication date: 21-Aug-2015
https://doi.org/10.1371/journal.pone.0136270
Lin CDligach DMiller TBethard SSavova G(2015)Multilayered temporal modeling for the clinical domainJournal of the American Medical Informatics Association10.1093/jamia/ocv11323:2(387-395)Online publication date: 31-Oct-2015
https://doi.org/10.1093/jamia/ocv113
Uzuner ÖStubbs A(2015)Practical applications for natural language processing in clinical researchJournal of Biomedical Informatics10.1016/j.jbi.2015.10.00758:S(S1-S5)Online publication date: 1-Dec-2015
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Cormack JNath CMilward DRaja KJonnalagadda S(2015)Agile text mining for the 2014 i2b2/UTHealth Cardiac risk factors challengeJournal of Biomedical Informatics10.1016/j.jbi.2015.06.03058(S120-S127)Online publication date: Dec-2015
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A French clinical corpus with comprehensive semantic annotations: development of the Medical Entity and Relation LIMSI annOtated Text corpus (MERLOT)

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A French clinical corpus with comprehensive semantic annotations: development of the Medical Entity and Relation LIMSI annOtated Text corpus (MERLOT)

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Enrichment of Arabic TimeML Corpus

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