• Time event ontology (TEO): to...

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

Title:
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events.
Authors:
Li F; School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA., Du J; School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA., He Y; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA., Song HY; School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA., Madkour M; Advanced Analytics, Cummins Inc, Columbus, Indiana, USA., Rao G; College of Intelligence and Computing, Tianjin University, Tianjin, China., Xiang Y; School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA., Luo Y; School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA., Chen HW; School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA.; University of Texas Southwestern Medical Center, Dallas, Texas, USA., Liu S; Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA., Wang L; Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA., Liu H; Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA., Xu H; School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA., Tao C; School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA.
Source:
Journal of the American Medical Informatics Association : JAMIA [J Am Med Inform Assoc] 2020 Jul 01; Vol. 27 (7), pp. 1046-1056.
Publication Type:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9430800 Publication Model: Print Cited Medium: Internet ISSN: 1527-974X (Electronic) Linking ISSN: 10675027 NLM ISO Abbreviation: J Am Med Inform Assoc Subsets: MEDLINE
Imprint Name(s):
Publication: 2015- : Oxford : Oxford University Press
Original Publication: Philadelphia, PA : Hanley & Belfus, c1993-
MeSH Terms:
Biological Ontologies* , Electronic Health Records* , Time*, Decision Support Systems, Clinical ; Humans ; Natural Language Processing ; Semantic Web
References:
JMIR Med Inform. 2018 Feb 22;6(1):e7. (PMID: 29472179)
J Am Med Inform Assoc. 2013 Sep-Oct;20(5):806-13. (PMID: 23564629)
J Biomed Semantics. 2012 Dec 20;3(1):13. (PMID: 23256916)
J Am Med Inform Assoc. 2015 Jul;22(4):872-80. (PMID: 25896647)
AMIA Annu Symp Proc. 2005;:869-73. (PMID: 16779164)
Trans Assoc Comput Linguist. 2018;6:343-356. (PMID: 32432133)
J Am Med Inform Assoc. 2013 Sep-Oct;20(5):814-9. (PMID: 23676245)
AMIA Annu Symp Proc. 2010 Nov 13;2010:787-91. (PMID: 21347086)
AMIA Jt Summits Transl Sci Proc. 2011;2011:64-8. (PMID: 22211182)
J Am Med Inform Assoc. 2013 Sep-Oct;20(5):836-42. (PMID: 23558168)
Comput Biol Med. 1997 Sep;27(5):353-68. (PMID: 9397339)
Am J Case Rep. 2018 Sep 29;19:1152-1161. (PMID: 30266895)
J Am Med Inform Assoc. 2015 Apr;22(e1):e151-61. (PMID: 25344930)
J Biomed Inform. 2013 Dec;46 Suppl:S5-12. (PMID: 23872518)
JMIR Med Inform. 2020 Jan 31;8(1):e15510. (PMID: 32012067)
N Engl J Med. 2018 Oct 11;379(15):1452-1462. (PMID: 30304648)
Grant Information:
R01 AI130460 United States AI NIAID NIH HHS; R01 LM011829 United States LM NLM NIH HHS
Contributed Indexing:
Keywords: Allen’s interval algebra; basic time relations; clinical decision support; clinical event; temporal relational reasoning; time event ontology
Entry Date(s):
Date Created: 20200707 Date Completed: 20210405 Latest Revision: 20210707
Update Code:
20250114
PubMed Central ID:
PMC7647306
DOI:
10.1093/jamia/ocaa058
PMID:
32626903
Database:
MEDLINE

Weitere Informationen

Objective: The goal of this study is to develop a robust Time Event Ontology (TEO), which can formally represent and reason both structured and unstructured temporal information.
Materials and Methods: Using our previous Clinical Narrative Temporal Relation Ontology 1.0 and 2.0 as a starting point, we redesigned concept primitives (clinical events and temporal expressions) and enriched temporal relations. Specifically, 2 sets of temporal relations (Allen's interval algebra and a novel suite of basic time relations) were used to specify qualitative temporal order relations, and a Temporal Relation Statement was designed to formalize quantitative temporal relations. Moreover, a variety of data properties were defined to represent diversified temporal expressions in clinical narratives.
Results: TEO has a rich set of classes and properties (object, data, and annotation). When evaluated with real electronic health record data from the Mayo Clinic, it could faithfully represent more than 95% of the temporal expressions. Its reasoning ability was further demonstrated on a sample drug adverse event report annotated with respect to TEO. The results showed that our Java-based TEO reasoner could answer a set of frequently asked time-related queries, demonstrating that TEO has a strong capability of reasoning complex temporal relations.
Conclusion: TEO can support flexible temporal relation representation and reasoning. Our next step will be to apply TEO to the natural language processing field to facilitate automated temporal information annotation, extraction, and timeline reasoning to better support time-based clinical decision-making.
(© The Author(s) 2020. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)