Bootstrapping a de-identification system for narrative patient records: Cost-performance tradeoffs

International Journal of Medical Informatics

Volumn 82, Issue 9, 2013, Pages 821-831

  Hanauer, David ^a   Aberdeen, John ^b   Bayer, Samuel ^b   Wellner, Benjamin ^b   Clark, Cheryl ^b   Zheng, Kai ^a   Hirschman, Lynette ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b MITRE CORPORATION   (United States)

Author keywords

Computerized E05.318.308.940.968.625 ; Electronic health records E05.318.308.940.968.625.500 ; Medical informatics L01.313.500 ; Medical record systems; Natural language processing L01.224.065.580 ; NLP; Privacy I01.880.604.473.352.500

Indexed keywords

COMPUTERIZED [E05.318.308.940.968.625]; ELECTRONIC HEALTH RECORD; MEDICAL INFORMATICS; MEDICAL RECORD SYSTEMS; NATURAL LANGUAGE PROCESSING; NLP;

ITERATIVE METHODS; NATURAL LANGUAGE PROCESSING SYSTEMS;

OPEN SYSTEMS;

ARTICLE; BOOTSTRAPPING; COST; MEASUREMENT ACCURACY; MEDICAL HISTORY; MEDICAL INFORMATION; MEDICAL RECORD; PERFORMANCE MEASUREMENT SYSTEM; PRIORITY JOURNAL; SOCIAL WORK; TIME; TRAINING;

EID: 84881374654     PISSN: 13865056     EISSN: 18728243     Source Type: Journal    
DOI: 10.1016/j.ijmedinf.2013.03.005     Document Type: Article

References (33)

1. Blumenthal D. Stimulating the adoption of health information technology. N. Engl. J. Med. 2009, 360(April (15)):1477-1479.
2. Blumenthal D. EHR Adoption Set to Soar. 2010 [cited 17 February 2010]; Available from:. http://healthit.hhs.gov/portal/server.pt%3Fopen=512%26mode=2%26objID=3357.
3. Bates D.W., Bitton A. The future of health information technology in the patient-centered medical home. Health Aff. (Millwood) 2010, 29(April (4)):614-621.
4. Friedman C.P., Wong A.K., Blumenthal D. Achieving a nationwide learning health system. Sci. Transl. Med. 2010, 2(November (57)):57cm29.
5. Gray B.H., Bowden T., Johansen I., Koch S. Issues in international health policy: electronic health records: an international perspective on "meaningful use". Issue Brief (Commonwealth Fund) 2011, 1-18.
6. Jha A.K., Doolan D., Grandt D., Scott T., Bates D.W. The use of health information technology in seven nations. Int. J. Med. Inform. 2008, 77(12):848-854.
7. Rosenbloom S.T., Denny J.C., Xu H., Lorenzi N., Stead W.W., Johnson K.B. Data from clinical notes: a perspective on the tension between structure and flexible documentation. J. Am.Med.Inform.Assoc. 2011, 18(March-April (2)):181-186.
8. Zheng K., Mei Q., Hanauer DA Collaborative search in electronic health records. J. Am.Med.Inform.Assoc. 2011, 18(May (3)):282-291.
9. Standards for privacy of individually identifiable health information. 65th ed. Federal Register: US Department of Health and Human Services; 2000. p. 82462-510.
10. Tu K., Klein-Geltink J., Mitiku T., Mihai C., Martin J. De-identification of primary care electronic medical records free-text data in Ontario, Canada. BMC Med. Inform. Decis. Mak. 2010, 10(1):35.
11. Neamatullah I., Douglass M.M., Lehman L.W., Reisner A., Villarroel M., Long W.J., Szolovits P., Moody G.B., Mark R.G., Clifford G.D. Automated de-identification of free-text medical records. BMC Med. Inform. Decis. Mak. 2008, 8:32.
12. Friedlin F.J., McDonald C.J. A software tool for removing patient identifying information from clinical documents. J. Am. Med. Inform. Assoc. 2008, 15(September-October (5)):601-610.
13. Szarvas G., Farkas R., Busa-Fekete R. State-of-the-art anonymization of medical records using an iterative machine learning framework. J. Am. Med. Inform. Assoc. 2007, 14(September-October (5)):574-580.
14. Uzuner Ö., Sibanda T.C., Luo Y., Szolovits P. A de-identifier for medical discharge summaries. Artif. Intell. Med. 2008, 42(January (1)):13-35.
15. Aberdeen J., Bayer S., Yeniterzi R., Wellner B., Clark C., Hanauer D., Malin B., Hirschman L. The MITRE Identification Scrubber Toolkit: design, training, and assessment. Int. J. Med. Inform. 2010, 79(December (12)):849-859.
16. Yeniterzi R., Aberdeen J., Bayer S., Wellner B., Hirschman L., Malin B. Effects of personal identifier resynthesis on clinical text de-identification. J. Am. Med. Inform. Assoc. 2010, 17(March-April (2)):159-168.
17. Bria W. Web-enabled clinical information systems: a new era begins. Clinical Informatics 2000, 103-111. Healthcare Information and Management Systems Society, Chicago, IL. M. Brady, M. Hassett (Eds.).
18. Zheng K., Mei Q., Yang L., Manion F.J., Balis U.J., Hanauer D.A. Voice-dictated versus typed-in clinician notes: linguistic properties and the potential implications on natural language processing. AMIA Annual Symposium proceedings/AMIA Symposium AMIA Symposium 2011, 1630-1638.
19. Ghani R., Jones R. A comparison of efficacy and assumptions of bootstrapping algorithms for training information extraction systems. Workshop on Linguistic Knowledge Acquisition and Representation: Bootstrapping Annotated Data at the Linguistic Resources and Evaluation Conference (LREC 2002) 2002.
20. Uzuner Ö., Luo Y., Szolovits P. Evaluating the state-of-the-art in automatic de-identification. J. Am. Med. Inform. Assoc. 2007, 14(September-October (5)):550-563.
21. Laws F., Schätze H. Stopping criteria for active learning of named entity recognition. Proceedings of the 22nd International Conference on Computational Linguistics 2008, 465-472.
22. Patterson O., Hurdle J.F. Document clustering of clinical narratives: a systematic study of clinical sublanguages. AMIA Annual Symposium proceedings/AMIA Symposium AMIA Symposium 2011, 1099-1107.
23. Meystre S.M., Friedlin F.J., South B.R., Shen S., Samore M.H. Automatic de-identification of textual documents in the electronic health record: a review of recent research. BMC Med. Res. Methodol. 2010, 10:70.
24. Wellner B., Huyck M., Mardis S., Aberdeen J., Morgan A., Peshkin L., Yeh A., Hitzeman J., Hirschman L. Rapidly retargetable approaches to de-identification in medical records. J. Am. Med. Inform. Assoc. 2007, 14(January (5)):564-573.
25. Dalianis H., Velupillai S. De-identifying Swedish clinical text - refinement of a gold standard and experiments with Conditional random fields. J. Biomed. Semantics 2010, 1(April (1)):6. doi:10.1186/2041-1480-1-6.
26. Douglass M.M., Clifford G.D., Reisner A., Moody G.B., Mark R.G. Computer-assisted deidentification of free text in the MIMIC II database. Comput. Cardiol. 2004, 31:341-344.
27. Dorr D.A., Phillips W.F., Phansalkar S., Sims S.A., Hurdle J.F. Assessing the difficulty and time cost of de-identification in clinical narratives. Methods Inf. Med. 2006, 45:246-252.
28. Arnott Smith C. Effect of XML markup on retrieval of clinical documents. AMIA Annual Symposium proceedings/AMIA Symposium AMIA Symposium 2003, 614-618.
29. Dolin R.H., Alschuler L., Beebe C., Biron P.V., Boyer S.L., Essin D., Kimber E., Lincoln T., Mattison J.E. The HL7 clinical document architecture. Journal of the American Medical Informatics Association: JAMIA. 2001, 8(November-December (6)):552-569.
30. Shen S., South B.R., Friedlin F.J., Meystre S. Coverage of manual de-identification on VA clinical documents. AMIA Annual Symposium proceedings/AMIA Symposium AMIA Symposium 2011.
31. Velupillai S., Dalianis H., Hassel M., Nilsson G.H. Developing a standard for de-identifying electronic patient records written in Swedish: precision, recall and F-measure in a manual and computerized annotation trial. Int. J. Med. Inform. 2009, 78(December (12)):e19-e26.
32. Mayer J., Shen S., South B.R., Meystre S., Friedlin F.J., Ray W.R., Samore M. Inductive creation of an annotation schema and a reference standard for de-identification of VA electronic clinical notes. AMIA Annual Symposium proceedings/AMIA Symposium AMIA Symposium 2009.
33. Carrell D., Malin B., Aberdeen J., Bayer S., Clark C., Wellner B., Hirschman L. Hiding in plain sight: use of realistic surrogates to reduce exposure of protected health information in clinical text. J. Am. Med. Inform. Assoc. 2013, 20(March-April (2)):342-348.