Using discordance to improve classification in narrative clinical databases: An application to community-acquired pneumonia

Computers in Biology and Medicine

Volumn 37, Issue 3, 2007, Pages 296-304

  Hripcsak, George ^a   Knirsch, Charles ^b   Zhou, Li ^a   Wilcox, Adam ^a   Melton, Genevieve B ^c  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b PFIZER INC   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Classification; Community acquired pneumonia; Data mining; Discordance; Electronic medical records; Natural language processing; Similarity metrics

Indexed keywords

DATA MINING; DATABASE SYSTEMS; DISEASES; NATURAL LANGUAGE PROCESSING SYSTEMS; PATTERN RECOGNITION; QUERY LANGUAGES;

CLINICAL DATABASES; ELECTRONIC MEDICAL RECORDS; NATURAL LANGUAGE PROCESSING; PNEUMONIA;

MEDICAL COMPUTING;

ACCURACY; ARTICLE; COMMUNITY ACQUIRED PNEUMONIA; DATA ANALYSIS; DATA BASE; ELECTRONIC MEDICAL RECORD; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; NARRATIVE; PRIORITY JOURNAL; STATISTICAL SIGNIFICANCE;

ADULT; AGED; ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; COMMUNITY-ACQUIRED INFECTIONS; FEMALE; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNATIONAL CLASSIFICATION OF DISEASES; MALE; MEDICAL RECORDS SYSTEMS, COMPUTERIZED; MIDDLE AGED; NATURAL LANGUAGE PROCESSING; PNEUMONIA, BACTERIAL;

EID: 33846018355     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2006.02.001     Document Type: Article

References (57)

1. Sittig D.F. Grand challenges in medical informatics?. J. Am. Med. Inf. Assoc. 1 5 (1994) 412-413
2. Adriaans P., and Zantinge D. Data Mining (1996), Addison-Wesley, Longman, Harlow, England
3. Fayyad U.M., Piatetsky-Shapiro G., Smyth P., and Uthurusamy R. Advances in Knowledge Discovery and Data Mining (1996), AAAI Press, Menlo Park, CA
4. Bellazzi R., and Zupan B. Intelligent data analysis-special issue. Methods Inf. Med. 40 5 (2001) 362-364
5. R. Bellazzi, B. Zupan (Eds.), Special issue on intelligent data analysis in medicine and pharmacology, Methods Inf. Med. 40(5) (2001) 362-424.
6. Nadkarni P.M., Brandt C.M., and Marenco L. WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases. J. Am. Med. Inf. Assoc. 7 4 (2000) 343-356
7. Coulter D.M., Bate A., Meyboom R.H., Lindquist M., and Edwards I.R. Antipsychotic drugs and heart muscle disorder in international pharmacovigilance: data mining study. BMJ 322 7296 (2001) 1207-1209
8. Harris Jr. J.M. Coronary angiography and its complications: the search for risk factors. Arch. Intern. Med. 144 2 (1984) 337-341
9. Markey M.K., Lo J.Y., Tourassi G.D., and Floyd Jr. C.E. Self-organizing map for cluster analysis of a breast cancer database. Artif. Intell. Med. 27 2 (2003) 113-127
10. Safran C. Using routinely collected data for clinical research. Stat. Med. 10 4 (1991) 559-564
11. E. Krusinska, A. Babic, S. Chowdhury, O. Wigertz, G. Bodemar, U. Mathiesen, Integrated approach for designing medical decision support systems with knowledge extracted from clinical databases by statistical methods, Proc. Annu. Symp. Comput. Appl. Med. Care (1991) 353-357.
12. McDonald J.M., Brossette S., and Moser S.A. Pathology information systems: data mining leads to knowledge discovery. Arch. Pathol. Lab. Med. 122 5 (1998) 409-411
13. Nadkarni P.M., and Brandt C. Data extraction and ad hoc query of an entity-attribute-value database. J. Am. Med. Inf. Assoc. 5 6 (1998) 511-527
14. L. Ohno-Machado, H.S. Fraser, A. Ohrn, Improving machine learning performance by removing redundant cases in medical data sets, Proc. AMIA Symp. (1998) 523-527.
15. J.C. Prather, D.F. Lobach, L.K. Goodwin, J.W. Hales, M.L. Hage, W.E. Hammond, Medical data mining: knowledge discovery in a clinical data warehouse, Proc. AMIA Annu. Fall Symp. (1997) 101-105.
16. Sakamoto N. Object-oriented development of a concept learning system for time-centered clinical data. J. Med. Syst. 20 4 (1996) 183-196
17. Goodwin L., Prather J., Schlitz K., Iannacchione M.A., Hage M., Hammond W.E., et al. Data mining issues for improved birth outcomes. Biomed. Sci. Instrum. 34 (1997) 291-296
18. K.C. Abston, T.A. Pryor, P.J. Haug, J.L. Anderson, Inducing practice guidelines from a hospital database. Proc. AMIA Annu. Fall Symp. (1997) 168-172.
19. Tierney W.M., Murray M.D., Gaskins D.L., and Zhou X.H. Using computer-based medical records to predict mortality risk for inner-city patients with reactive airways disease. J. Am. Med. Inf. Assoc. 4 4 (1997) 313-321
20. Iezzoni L.I. Assessing quality using administrative data. Ann. Intern. Med. 127 8 Part 2 (1997) 666-674
21. Jollis J.G., Ancukiewicz M., DeLong E.R., Pryor D.B., Muhlbaier L.H., and Mark D.B. Discordance of databases designed for claims payment versus clinical information systems: implications for outcomes research. Ann. Intern. Med. 119 8 (1993) 844-850
22. Malenka D.J., McLerran D., Roos N., Fisher E.S., and Wennberg J.E. Using administrative data to describe casemix: a comparison with the medical record. J. Clin. Epidemiol. 47 9 (1994) 1027-1032
23. Preen D., Holman C., Lawrence D., Baynham N., and Semmens J. Hospital chart review provided more accurate comorbidity information than data from a general practitioner survey or an administrative database. J. Clin. Epidemiol. 57 12 (2004) 1295-1304
24. Hsia D.C., Krushat W.M., Fagan A.B., Tebbutt J.A., and Kusserow R.P. Accuracy of diagnostic coding for medicare patients under the prospective-payment system. N. Engl. J. Med. 318 6 (1988) 352-355
25. Peabody J., Luck J., Jain S., Bertenthal D., and Glassman P. Assessing the accuracy of administrative data in health information systems. Med. Care 42 11 (2004) 1066-1072
26. Hersh W., Turpin A., Price S., Kraemer D., Sacherek L., Olson D., et al. Challenging conventional assumptions of information retrieval with real users: boolean searching and batch retrieval evaluations. Inf. Proces. Manage. 37 (2001) 383-402
27. D.A. Giuse, A. Mickish, Increasing the availability of the computerized patient record, Proc. AMIA Annu. Fall Symp. (1996) 633-637.
28. Aronow D.B., Fangfang F., and Croft W.B. Ad hoc classification of radiology reports. J. Am. Med. Inf. Assoc. 6 5 (1999) 393-411
29. W.W. Chapman, W. Bridewell, P. Hanbury, G.F. Cooper, B.G. Buchanan, Evaluation of negation phrases in narrative clinical reports, Proc. AMIA Symp. (2001) 105-109.
30. Mutalik P.G., Deshpande A., and Nadkarni P.M. Use of general-purpose negation detection to augment concept indexing of medical documents: a quantitative study using the UMLS. J. Am. Med. Inf. Assoc. 8 6 (2001) 598-609
31. Baud R.H., Rassinoux A.M., and Scherrer J.R. Natural language processing and semantical representation of medical texts. Methods Inf. Med. 31 2 (1992) 117-125
32. P.J. Haug, S. Koehler, L.M. Lau, P. Wang, R. Rocha, S.M. Huff, Experience with a mixed semantic/syntactic parser, Proc. Annu. Symp. Comput. Appl. Med. Care (1995) 284-288.
33. Sager N., Lyman M., Bucknall C., Nhan N., and Tick L.J. Natural language processing and the representation of clinical data. J. Am. Med. Inf. Assoc. 1 2 (1994) 142-160
34. Zweigenbaum P. MENELAS: an access system for medical records using natural language. Comput. Methods Programs Biomed. 45 1-2 (1994) 117-120
35. W.W. Chapman, P.J. Haug, Bayesian modeling for linking causally related observations in chest X-ray reports, Proc. AMIA Symp. (1998) 587-591.
36. M. Fiszman, P.J. Haug, P.R. Frederick, Automatic extraction of PIOPED interpretations from ventilation/perfusion lung scan reports, Proc. AMIA Symp. (1998) 860-864.
37. D. Aronsky, M. Fiszman, W.W. Chapman, P.J. Haug, Combining decision support methodologies to diagnose pneumonia, Proc. AMIA Symp. (2001) 12-16.
38. 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. Inf. Assoc. 7 6 (2000) 593-604
39. Friedman C., Hripcsak G., DuMouchel W., Johnson S.B., and Clayton P.D. Natural language processing in an operational clinical information system. Natural Language Eng. 1 (1995) 83-108
40. Friedman C., Shagina L., Lussier Y., and Hripcsak G. Automated encoding of clinical documents based on natural language processing. J. Am. Med. Inf. Assoc. 11 5 (2004) 392-402
41. Wilcox A.B., and Hripcsak G. The role of domain knowledge in automating medical text report classification. J. Am. Med. Inf. Assoc. 10 4 (2003) 330-338
42. Hripcsak G., Austin J.H., Alderson P.O., and Friedman C. Use of natural language processing to translate clinical information from a database of 889,921 chest radiographic reports. Radiology 224 1 (2002) 157-163
43. Elkins J.S., Friedman C., Boden-Albala B., Sacco R.L., and Hripcsak G. Coding neuroradiology reports for the Northern Manhattan Stroke Study: a comparison of natural language processing and manual review. Comput. Biomed. Res. 33 1 (2000) 1-10
44. J.H. Chuang, C. Friedman, G. Hripcsak, A comparison of the Charlson comorbidities derived from medical language processing and administrative data. Proc. AMIA Symp. (2002) 160-164.
45. Mendonça E., Hass J., Shagina L., Larson E., and Friedman C. Extracting information on pneumonia in infants using natural language processing of radiology reports. J. Biomed. Inf. 38 4 (2005) 314-321
46. Hogan W.R., and Wagner M.M. Accuracy of data in computer-based patient records. J. Am. Med. Inf. Assoc. 4 5 (1997) 342-355
47. Aronsky D., and Haug P.J. Assessing the quality of clinical data in a computer-based record for calculating the pneumonia severity index. J. Am. Med. Inf. Assoc. 7 1 (2000) 55-65
48. Little R.J.A., and Rubin D.B. Statistical Analysis with Missing Data (1987), Wiley, New York
49. Rubin D. Multiple imputation after 18+ years. J. Am. Stat. Assoc. 91 (1996) 473-489
50. Lakshiminarayan K., Harp S.A., and Samad T. Imputation of missing data in industrial databases. Appl. Intell. 11 (1999) 259-275
51. C. Friedman, C. Knirsch, L. Shagina, G. Hripcsak, Automating a severity score guideline for community-acquired pneumonia employing medical language processing of discharge summaries, Proc. AMIA Symp. (1999) 256-260.
52. Fine M.J., Auble T.E., Yealy D.M., Hanusa B.H., Weissfeld L.A., Singer D.E., et al. A prediction rule to identify low-risk patients with community-acquired pneumonia. N. Engl. J. Med. 336 4 (1997) 243-250
53. Lindberg D.A., Humphreys B.L., and McCray A.T. The unified medical language system. Methods Inf. Med. 32 4 (1993) 281-291
54. M. Krauthammer, G. Hripcsak, A knowledge model for the interpretation and visualization of NLP-parsed discharged summaries, Proc. AMIA Symp. (2001) 339-343.
55. Caviedes J.E., and Cimino J.J. Towards the development of a conceptual distance metric for the UMLS. J. Biomed. Inf. 37 2 (2004) 77-85
56. H.R. Solbrig, P.L. Elkin, P.V. Ogren, C.G. Chute, A formal approach to integrating synonyms with a reference terminology, Proc. AMIA Symp. (2000) 814-818.
57. Charlson M.E., Pompei P., Ales K.L., and MacKenzie C.R. A new method of classifying prognostic comorbidity in longitudinal studies: development and validation. J. Chronic Dis. 40 5 (1987) 373-383