Annotating temporal information in clinical narratives

Journal of Biomedical Informatics

Volumn 46, Issue SUPPL., 2013, Pages

  Sun, Weiyi ^a   Rumshisky, Anna ^b   Uzuner, Ozlem ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b University of Massachusetts Lowell   (United States)

Author keywords

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

Indexed keywords

DIAGNOSIS; LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS; PATIENT TREATMENT;

ANNOTATION; DISCHARGE SUMMARY; MEDICAL INFORMATICS; NATURAL LANGUAGE PROCESSING; TEMPORAL EXPRESSIONS; TEMPORAL INFORMATION; TEMPORAL REASONING; TEMPORAL RELATION;

MEDICAL INFORMATION SYSTEMS;

ELECTRONIC MEDICAL RECORD; HUMAN; INFORMATION SCIENCE; MACHINE LEARNING; MEDICAL DOCUMENTATION; MEDICAL INFORMATION; METHODOLOGY; NARRATIVE; NATURAL LANGUAGE PROCESSING; PRIORITY JOURNAL; PROCESS DEVELOPMENT; QUALITY CONTROL PROCEDURES; REVIEW; TRAINING;

ANNOTATION; CORPUS BUILDING; MEDICAL INFORMATICS; NATURAL LANGUAGE PROCESSING; TEMPORAL REASONING;

DOCUMENTATION; ELECTRONIC HEALTH RECORDS; HUMANS; MEDICAL INFORMATICS; NARRATION; NATURAL LANGUAGE PROCESSING;

EID: 84896968842     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2013.07.004     Document Type: Review

References (37)

1. Meystre S., Savova G., Kipper-Schuler K., Hurdle J., et al. Extracting information from textual documents in the electronic health record: a review of recent research. Yearb Med Inform 2008, 35:128-144.
2. Sun W, Rumshisky A, Uzuner O. Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. Journal of the American Medical Informatics Association 2013.
3. Augusto J.C. Temporal reasoning for decision support in medicine. Artif Intell Med 2005, 33(1):1-24.
4. Stacey Michael, McGregor Carolyn Temporal abstraction in intelligent clinical data analysis: a survey. Artif Intell Med 2007, 39(1):1-24.
5. Denny Joshua C, Peterson Josh F, Choma Neesha N, Hua Xu, Miller Randolph A, Bastarache Lisa, et al. Extracting timing and status descriptors for colonoscopy testing from electronic medical records. J Am Med Inform Assoc 2010;17(4):383-8.
6. Liu Mei, Jiang Min, Kawai Vivian K, Stein Charles M, Roden Dan M, Denny Joshua C, et al. Modeling drug exposure data in electronic medical records: an application to warfarin. In: AMIA annual symposium proceedings, volume 2011. American Medical Informatics Association; 2011. p. 815.
7. Irvine Ann K, Haas Stephanie W, Sullivan Tessa. Tn-ties: A system for extracting temporal information from emergency department triage notes. In: AMIA Annual symposium proceedings, volume 2008. American Medical Informatics Association; 2008. p. 328.
8. Zhou Li, Parsons Simon, Hripcsak George The evaluation of a temporal reasoning system in processing clinical discharge summaries. J Am Med Inform Assoc 2008, 15(1):99-106.
9. Clark Kimberly K, Sharma Deepak K, Chute Christopher G, Tao Cui. Application of a temporal reasoning framework tool in analysis of medical device adverse events. In: AMIA annual symposium proceedings, volume 2011. American Medical Informatics Association; 2011. p. 1366.
10. Li M., Patrick J. Extracting temporal information from electronic patient records. AMIA Annu Sympos Proc 2012, 2012:542.
11. Pustejovsky J., Castano J., Ingria R., Sauri R., Gaizauskas R., Setzer A., et al. Timeml: Robust specification of event and temporal expressions in text. New Direct Question Answer 2003, 3:28-34.
12. Augusto J.C. The logical approach to temporal reasoning. Artif Intell Rev 2001, 16(4):301-333.
13. Mani I, Pustejovsky J, Gaizauskas R. The language of time: a reader. Oxford University Press; 2005.
14. Allen JF. An interval-based representation of temporal knowledge. In: Proc. 7th international joint conference on artificial intelligence. Canada: Vancouver; 1981. p. 221-6.
15. Mani I., Pustejovsky J., Sundheim B. Introduction to the special issue on temporal information processing. ACM Trans Asian Lang Inform Process (TALIP) 2004, 3(1):1-10.
16. Pustejovsky J, Hanks P, Sauri R, See A, Gaizauskas R, Setzer A et al. The TimeBank corpus. In: Corpus linguistics, volume 2003; 2003. p. 40.
17. Verhagen M, Gaizauskas R, Schilder F, Hepple M, Katz G, Pustejovsky J. Semeval-2007 task 15: Tempeval temporal relation identification. In: Proceedings of the 4th international workshop on semantic evaluations; 2007. p. 75-80.
18. Verhagen M, Sauri R, Caselli T, Pustejovsky J. Semeval-2010 task 13: Tempeval-2. In: Proceedings of the 5th international workshop on semantic evaluation. Association for, Computational Linguistics; 2010. p. 57-62.
19. UzZaman N, Llorens H, Allen J, Derczynski L, Verhagen M, Pustejovsky J. Tempeval-3: Evaluating events, time expressions, and temporal relations. arXiv, preprint arXiv:1206.5333; 2012.
20. Roberts A, Gaizauskas R, Hepple M, Demetriou G, Guo Y, Setzer A et al. Semantic annotation of clinical text: the clef corpus. In: Proceedings of building and evaluating resources for biomedical text mining: workshop at LREC; 2008.
21. Galescu L, Blaylock N. A corpus of clinical narratives annotated with temporal information. In: Proceedings of the 2nd ACM SIGHIT symposium on international health informatics. ACM; 2012. p. 715-20.
22. Castaño J, Gaizauskas R, Ingria B, Katz G, Knippen B, Littman J et al. 1.2.1 a formal specification language for events and temporal expressions; 2005. p. 10.
23. UzZaman N, Allen JF. Trips and trios system for tempeval-2: Extracting temporal information from text. In: Proceedings of the 5th international workshop on semantic evaluation. Association for, Computational Linguistics; 2010. p. 276-83.
24. Llorens H, Saquete E, Navarro B. Tipsem (English and Spanish): evaluating crfs and semantic roles in tempeval-2. In: Proceedings of the 5th international workshop on semantic, evaluation; 2010. p. 284-91.
25. Graff D., Cieri C. English Gigaword 2003, Linguistic Data Consortium, Philadelphia.
26. Uzuner O., Solti I., Cadag E. Extracting medication information from clinical text. J Am Med Inform Assoc 2010, 17(5):514-518.
27. Savova G, Bethard S, Styler W, Martin J, Palmer M, Masanz et al. Towards temporal relation discovery from the clinical narrative. In: AMIA annual symposium proceedings, volume 2009. American Medical Informatics Association; 2009. p. 568.
28. Jordan P.W., Mowery D.L., Wiebe J., Chapman W.W. Annotating conditions in clinical narratives to support temporal classification. Proc Am Med Inform Assoc Sympos 2010, 2010:1005.
29. Bramsen P, Deshpande P, Lee YK, Barzilay R. Finding temporal order in discharge summaries. In: AMIA annual symposium proceedings, volume 2006. American Medical Informatics Association; 2006. p. 81.
30. Uzuner O., South B., Shen S., DuVall S. 2010 i2b2/va challenge on concepts, assertions, and relations in clinical text. J Am Med Inform Assoc 2011, 18(5):552-556.
31. Uzuner O., Bodnari A., Shen S., Forbush T., Pestian J., South B. Evaluating the state of the art in coreference resolution for electronic medical records. J Am Med Inform Assoc 2012, 19(5):786-791.
32. Temporal histories of your medical events, thyme.
33. Stubbs A. Mae and mai: lightweight annotation and adjudication tools. In: Proceedings of the 5th linguistic annotation workshop. Association for, Computational Linguistics; 2011. p. 129-33.
34. Fleiss Joseph L, Levin Bruce, Paik Myunghee Cho. Statistical methods for rates and proportions. John Wiley & Sons; 2013.
35. Hripcsak George, Rothschild Adam S. Agreement, the f-measure, and reliability in information retrieval. J Am Med Inform Assoc 2005, 12(3):296-298.
36. Setzer A, Gaizauskas R, Hepple M. Using semantic inferences for temporal annotation comparison. In: Proceedings of the fourth international workshop on inference in computational semantics (ICOS-4); 2003. p. 25-6.
37. UzZaman N, Allen J. Temporal evaluation. In: Proceedings of the 49th annual meeting of the association for computational linguistics. Human Language Technologies; 2011. p. 351-6.