{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T07:56:30Z","timestamp":1775202990949,"version":"3.50.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T00:00:00Z","timestamp":1593561600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01LM011829"],"award-info":[{"award-number":["R01LM011829"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI130460"],"award-info":[{"award-number":["R01AI130460"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UTHealth Innovation for Cancer Prevention Research Training Program Pre-Doctoral Fellowship"},{"DOI":"10.13039\/100004917","name":"Cancer Prevention and Research Institute of Texas","doi-asserted-by":"publisher","award":["# RP160015"],"award-info":[{"award-number":["# RP160015"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Objective<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Materials and Methods<\/jats:title>\n                  <jats:p>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\u2019s 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jamia\/ocaa058","type":"journal-article","created":{"date-parts":[[2020,4,13]],"date-time":"2020-04-13T19:13:18Z","timestamp":1586805198000},"page":"1046-1056","source":"Crossref","is-referenced-by-count":21,"title":["Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8865-7717","authenticated-orcid":false,"given":"Fang","family":"Li","sequence":"first","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0322-4566","authenticated-orcid":false,"given":"Jingcheng","family":"Du","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA"}]},{"given":"Yongqun","family":"He","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA"}]},{"given":"Hsing-Yi","family":"Song","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA"}]},{"given":"Mohcine","family":"Madkour","sequence":"additional","affiliation":[{"name":"Advanced Analytics, Cummins Inc, Columbus, Indiana, USA"}]},{"given":"Guozheng","family":"Rao","sequence":"additional","affiliation":[{"name":"College of Intelligence and Computing, Tianjin University, Tianjin, China"}]},{"given":"Yang","family":"Xiang","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA"}]},{"given":"Yi","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6199-0736","authenticated-orcid":false,"given":"Henry W","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA"},{"name":"University of Texas Southwestern Medical Center, Dallas, Texas, USA"}]},{"given":"Sijia","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA"}]},{"given":"Liwei","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA"}]},{"given":"Hongfang","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5274-4672","authenticated-orcid":false,"given":"Hua","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA"}]},{"given":"Cui","family":"Tao","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,7,6]]},"reference":[{"issue":"5","key":"2020110613082748600_ocaa058-B1","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/S0010-4825(96)00010-8","article-title":"Temporal reasoning and temporal data maintenance in medicine: issues and challenges","volume":"27","author":"Combi","year":"1997","journal-title":"Comput Biol Med"},{"key":"2020110613082748600_ocaa058-B2","first-page":"869","article-title":"System architecture for temporal information extraction, representation and reasoning in clinical narrative reports","volume":"2005","author":"Zhou","year":"2005","journal-title":"AMIA Annu Symp Proc"},{"key":"2020110613082748600_ocaa058-B3","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1016\/j.jbi.2013.07.004","article-title":"Annotating temporal information in clinical narratives","volume":"46","author":"Sun","year":"2013","journal-title":"J Biomed Inform"},{"issue":"5","key":"2020110613082748600_ocaa058-B4","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1136\/amiajnl-2013-001628","article-title":"Evaluating temporal relations in clinical text: 2012 i2b2 Challenge","volume":"20","author":"Sun","year":"2013","journal-title":"J Am Med Inform Assoc"},{"issue":"4","key":"2020110613082748600_ocaa058-B5","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1093\/jamia\/ocv024","article-title":"Risk prediction for chronic kidney disease progression using heterogeneous electronic health record data and time series analysis","volume":"22","author":"Perotte","year":"2015","journal-title":"J Am Med Inform Assoc"},{"issue":"e1","key":"2020110613082748600_ocaa058-B6","doi-asserted-by":"crossref","first-page":"e151","DOI":"10.1136\/amiajnl-2014-002642","article-title":"Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record","volume":"22","author":"Lin","year":"2015","journal-title":"J Am Med Inform Assoc"},{"issue":"1","key":"2020110613082748600_ocaa058-B7","doi-asserted-by":"crossref","first-page":"e15510","DOI":"10.2196\/15510","article-title":"Longitudinal risk prediction of chronic kidney disease in diabetic patients using temporal-enhanced gradient boosting machine: retrospective cohort study","volume":"8","author":"Song","year":"2020","journal-title":"JMIR Med Inform"},{"issue":"5","key":"2020110613082748600_ocaa058-B8","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1136\/amiajnl-2013-001760","article-title":"Temporal reasoning over clinical text: the state of the art","volume":"20","author":"Sun","year":"2013","journal-title":"J Am Med Inform Assoc"},{"key":"2020110613082748600_ocaa058-B9","first-page":"28","article-title":"TimeML: Robust specification of event and temporal expressions in text","author":"Pustejovsky","year":"2003","journal-title":"New Directions in Question Answering"},{"key":"2020110613082748600_ocaa058-B10","first-page":"806","author":"Bethard"},{"key":"2020110613082748600_ocaa058-B11","first-page":"1052","author":"Bethard"},{"key":"2020110613082748600_ocaa058-B12","first-page":"565","author":"Bethard"},{"key":"2020110613082748600_ocaa058-B13","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1007\/978-94-024-0881-2_35","volume-title":"Handbook of Linguistic Annotation","author":"Pustejovsky","year":"2017"},{"key":"2020110613082748600_ocaa058-B14","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1162\/tacl_a_00025","article-title":"From characters to time intervals: new paradigms for evaluation and neural parsing of time normalizations","volume":"6","author":"Laparra","year":"2018","journal-title":"Trans Assoc Comput Linguist"},{"key":"2020110613082748600_ocaa058-B15","first-page":"3779","author":"Bethard"},{"key":"2020110613082748600_ocaa058-B16","first-page":"88","author":"Laparra"},{"key":"2020110613082748600_ocaa058-B17","author":"Ning"},{"key":"2020110613082748600_ocaa058-B18","year":"2004"},{"issue":"15","key":"2020110613082748600_ocaa058-B19","doi-asserted-by":"crossref","first-page":"1452","DOI":"10.1056\/NEJMra1615014","article-title":"Classification, ontology, and precision medicine","volume":"379","author":"Haendel","year":"2018","journal-title":"N Engl J Med"},{"issue":"2","key":"2020110613082748600_ocaa058-B20","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1006\/knac.1993.1008","article-title":"A translation approach to portable ontology specifications","volume":"5","author":"Gruber","year":"1993","journal-title":"Knowl Acquis"},{"issue":"3","key":"2020110613082748600_ocaa058-B21","first-page":"57","article-title":"Ontologies of time: review and trends","volume":"11","author":"Ermolayev","year":"2014","journal-title":"Int J Comput Sci Appl"},{"key":"2020110613082748600_ocaa058-B22","year":"2017"},{"key":"2020110613082748600_ocaa058-B23","author":"O\u2019Connor"},{"issue":"1","key":"2020110613082748600_ocaa058-B24","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1145\/1017068.1017073","article-title":"An ontology of time for the semantic web","volume":"3","author":"Hobbs","year":"2004","journal-title":"ACM Trans Asian Lang Inf Process (TALIP)"},{"key":"2020110613082748600_ocaa058-B25","first-page":"1","author":"Zhou"},{"key":"2020110613082748600_ocaa058-B26","first-page":"787","article-title":"CNTRO: a semantic web ontology for temporal relation inferencing in clinical narratives","volume-title":"AMIA Annu Symp Proc","author":"Tao","year":"2010"},{"issue":"1","key":"2020110613082748600_ocaa058-B27","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/2041-1480-3-13","article-title":"Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis","volume":"3","author":"Tao","year":"2012","journal-title":"J Biomed Sem"},{"issue":"1","key":"2020110613082748600_ocaa058-B28","doi-asserted-by":"crossref","first-page":"e7","DOI":"10.2196\/medinform.8175","article-title":"Representation of time-relevant common data elements in the cancer data standards repository: statistical evaluation of an ontological approach","volume":"6","author":"Chen","year":"2018","journal-title":"JMIR Med Inform"},{"key":"2020110613082748600_ocaa058-B29","first-page":"64","article-title":"CNTRO 2.0: a harmonized semantic web ontology for temporal relation inferencing in clinical narratives","volume":"2011","author":"Tao","year":"2011","journal-title":"AMIA Summits Transl Sci Proc"},{"issue":"5","key":"2020110613082748600_ocaa058-B30","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1093\/logcom\/4.5.531","article-title":"Actions and events in interval temporal logic","volume":"4","author":"Allen","year":"1994","journal-title":"J Logic Comput"},{"key":"2020110613082748600_ocaa058-B31","first-page":"1","author":"Gr\u00fcninger"},{"key":"2020110613082748600_ocaa058-B32","author":"Drummond"},{"key":"2020110613082748600_ocaa058-B33","year":"2004"},{"key":"2020110613082748600_ocaa058-B34"},{"key":"2020110613082748600_ocaa058-B35","author":"Group","year":"2009"},{"issue":"5","key":"2020110613082748600_ocaa058-B36","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1136\/amiajnl-2013-001622","article-title":"Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification","volume":"20","author":"Sohn","year":"2013","journal-title":"J Am Med Inform Assoc"},{"key":"2020110613082748600_ocaa058-B37"},{"key":"2020110613082748600_ocaa058-B38"},{"key":"2020110613082748600_ocaa058-B39","first-page":"778","author":"Minard"},{"key":"2020110613082748600_ocaa058-B40","first-page":"792","author":"Llorens"},{"key":"2020110613082748600_ocaa058-B41"},{"key":"2020110613082748600_ocaa058-B42"},{"key":"2020110613082748600_ocaa058-B43","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.12659\/AJCR.911393","article-title":"Idiosyncratic drug-induced liver injury due to ciprofloxacin: a report of two cases and review of the literature","volume":"19","author":"Radovanovic","year":"2018","journal-title":"Am J Case Rep"},{"key":"2020110613082748600_ocaa058-B44"},{"key":"2020110613082748600_ocaa058-B45","first-page":"394","author":"Pustejovsky","year":"2010"}],"container-title":["Journal of the American Medical Informatics Association"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/27\/7\/1046\/34152889\/ocaa058.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/27\/7\/1046\/34152889\/ocaa058.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,6]],"date-time":"2020-11-06T19:20:29Z","timestamp":1604690429000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jamia\/article\/27\/7\/1046\/5867649"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,1]]},"references-count":45,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2020,7,6]]},"published-print":{"date-parts":[[2020,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/jamia\/ocaa058","relation":{},"ISSN":["1527-974X"],"issn-type":[{"value":"1527-974X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7]]},"published":{"date-parts":[[2020,7,1]]}}}