A temporal constraint structure for extracting temporal information from clinical narrative

Journal of Biomedical Informatics

Volumn 39, Issue 4, 2006, Pages 424-439

  Zhou, Li ^a   Melton, Genevieve B ^a   Parsons, Simon ^b   Hripcsak, George ^a  

^a Howard Hughes Medical Institute   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

Discharge summary; Natural language processing; Simple Temporal Problem; Temporal constraints; Temporal model; Temporal reasoning; Temporal representation

Indexed keywords

CONSTRAINT THEORY; DATA STRUCTURES; ELECTRIC DISCHARGES; INFORMATION RETRIEVAL; KNOWLEDGE ENGINEERING; NATURAL LANGUAGE PROCESSING SYSTEMS;

DISCHARGE SUMMARY; SIMPLE TEMPORAL PROBLEM (STP); TEMPORAL CONSTRAINTS; TEMPORAL MODEL; TEMPORAL REASONING; TEMPORAL REPRESENTATION;

BIOMEDICAL ENGINEERING;

ANALYTIC METHOD; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOMEDICINE; COMPUTER PROGRAM; INFORMATION PROCESSING; MEDICAL INFORMATION; PRIORITY JOURNAL; RANDOMIZATION; TIME;

DATABASE MANAGEMENT SYSTEMS; INFORMATION STORAGE AND RETRIEVAL; MEDICAL HISTORY TAKING; MEDICAL RECORDS SYSTEMS, COMPUTERIZED; NARRATION; NATURAL LANGUAGE PROCESSING; TIME FACTORS;

EID: 33745845169     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2005.07.002     Document Type: Article

References (42)

1. Augusto J.C. Temporal reasoning for decision support in medicine. Artif Intell Med 33 1 (2005) 1-24
2. Combi C., and Shahar Y. Temporal reasoning and temporal data maintenance in medicine: Issues and challenges. Computers in Biology and Medicine 27 5 (1997) 353-368
3. Kindler H., Densow D., and Fliedner T.M. A pragmatic implementation of medical temporal reasoning for clinical medicine. Comput Biol Med 28 2 (1998) 105-120
4. Deshpande A.M., Brandt C., and Nadkarni P.M. Temporal query of attribute-value patient data: utilizing the constraints of clinical studies. Int J Med Inform 70 (2003) 59-77
5. Nigrin D.J., and Kohane I.S. Temporal expressiveness in querying a time-stamp-based clinical database. J Am Med Inform Assoc 7 2 (2000) 152-163
6. Shahar Y., and Musen M.A. Knowledge-based temporal abstraction in clinical domains. Artif Intell Med 8 3 (1996) 267-298
7. Shahar Y. A framework for knowledge-based temporal abstraction. Artif Intell 90 1-2 (1997) 79-133
8. Kahn M., Fagan L., and Sheiner L. Combining physiologic models and symbolic methods to interpret time-varying patient data. Methods Inform Med 30 3 (1991) 167-178
9. Das A., and Musen M. A foundational model of time for heterogeneous clinical databases. Proc AMIA Annu Fall Symp (1997)
10. Combi C., Pinciroli F., and Pozzi G. Managing different time granularities of clinical information by an interval-based temporal data model. Methods Inform Med 34 5 (1995) 458-474
11. Combi C, Pinciroli F, Pozzi G. Managing time granularity of narrative clinical information: the temporal data model TIME-NESIS. In Proceedings of the 3rd workshop on temporal representation and reasoning (TIME'96). p. 88.
12. O'Connor M., Tu S., and Musen M. Representation of temporal indeterminacy in clinical databases. Proc AMIA Symp 1 (2000) 615-619
13. Campbell K.E., Das A.K., and Musen M.A. A logical foundation for representation of clinical data. J Am Med Inform Assoc 1 3 (1994) 218-232
14. Fiszman M., Chapman W.W., Aronsky D., Evans R.S., and Haug P.J. Automatic detection of acute bacterial pneumonia from chest X-ray reports. J Am Med Inform Assoc 7 6 (2000) 593-604
15. Friedman C., Alderson P.O., Austin J.H., Cimino J.J., and Johnson S.B. A general natural-language text processor for clinical radiology. J Am Med Inform Assoc 1 2 (1994) 161-174
16. Hripcsak G., Friedman C., Alderson P.O., DuMouchel W., Johnson S.B., and Clayton P.D. Unlocking clinical data from narrative reports: a study of natural language processing. Ann Intern Med 122 9 (1995) 681-688
17. Melton G.B., and Hripcsak G. Automated detection of adverse events using natural language processing of discharge summaries. J Am Med Inform Assoc (2005) M1794
18. Friedman C. A broad-coverage natural language processing system. Proc AMIA Symp (2000) 270-274
19. Sager N., Lyman M., Nhan N., and Tick L. Medical language processing: applications to patient data representation and automatic encoding. Methods Inform Med 34 1-2 (1995) 140-146
20. Wilcox A., and Hripcsak G. The role of domain knowledge in automating medical text report classification. J Am Med Inform Assoc 10 (2003) 330-338
21. Cao H., Stetson P., and Hripcsak G. Assessing explicit error reporting in the narrative electronic medical record using keyword searching. J Biomed Inform 36 (2003) 99-105
22. Mendonca E.A., Hass J., Shagina L., Larson E., and Friedman C. Extracting information on pneumonia in infants using natural language processing of radiology reports. J Biomed Inform 38 4 (2005) 314-321
23. Dolin R.H. Modeling the temporal complexities of symptoms. J Am Med Inform Assoc 2 5 (1995) 323-331
24. Hripcsak G., Zhou L., Parsons S., Das A.K., and Johnson S.B. Modeling electronic discharge summaries as a simple temporal constraint satisfaction problem. J Am Med Inform Assoc 12 1 (2005) 55-63
25. Jonsson P., Drakengren T., and Backstrom C. Temporal information in medical narrative. In: Sager N., Friedman C., and Lyman M.S. (Eds). Medical language processing computer management of narrative data (1987), Addison-Wesley Pub Co., Reading, MA 175-194
26. Zhou L., Friedman C., Parsons S., and Hripcsak G. System architecture for temporal information extraction representation and reasong in clinical narrative reports. Proc AMIA Symp (2005) [accepted]
27. Ceusters W, Buekens F, DeMoor G, Bernauer J, DeKeyser L, Surján G. TSMI: a CEN/TC251 standard for time specific problems in healthcare informatics and telematics. 1997;46(2):87.
28. Allen J.F. Time and time again: the many ways to represent time. Int J Intell Syst 6 4 (1991) 341-355
29. Pani A.K., and Bhattacharjee G.P. Temporal representation and reasoning in artificial intelligence: a review. Math Comput Model 34 1-2 (2001) 55-80
30. Meiri I. Combining qualitative and quantitative constraints in temporal reasoning. Artif Intell 87 1-2 (1996) 343-385
31. Dechter R., Meiri I., and Pearl J. Temporal constraint networks. Artif Intell 49 1-3 (1991) 61-95
32. Vilain M, Kautz H. Constraint propagation algorithms for temporal reasoning. In Proceedings AAAI-86, Philadephia, PA; 1986. p. 377-82.
33. Dean T., and McDermott D. Temporal data base management. Artif Intell 32 (1987) 1-55
34. Allen J. Maintaining knowledge about temporal intervals. Commun ACM 26 (1983) 832-843
35. Xu L, Choueiry B. A new efficient algorithm for solving the simple temporal problem. In Proceedings of 10th international symposium on temporal representation and reasoning and fourth international conference on temporal logic, July 08-10, 2003, Cairns, Queensland, Australia; 2003. p. P212.
36. Lisa Ferro LG. Inderjeet Mani, Beth Sundheim, George Wilson. TIDES-2003 standard for the annotation of temporal expressions. In Proceedings of the MITRE 2003.
37. ISO8601:2000(E) Data elements and interchange formats-information interchange-representation of dates and times. 2nd ed.; 2000-12-15.
38. Obermeier K. Temporal inference in medical texts. In Proceedings of 23 annual meeting of the Association for Computational Linguistics, Chicago; 1985 July.
39. Ferro L, Gerber L, Mani I, Sundheim B, Wilson G. TIDES 2003 standard for the annotation of temporal expressions, September 2003;2003.
40. Sauri R, Littman J, Knippen B, Gaizauskas R, Setzer A, Pustejovsky J. TimeML annotation guidelines; September 2004.
41. Hobbs J, Pustejovsky J. Annotating and reasoning about time and events. In Proceedings of AAAI spring symposium on logical formalizations of commonsense reasoning, Stanford, CA; March 2003.
42. Friedman C., Kra P., and Rzhetsky A. Two biomedical sublanguages: a description based on the theories of Zellig Harris. J Biomed Inform 35 4 (2002) 222-235