Development and evaluation of an open source software tool for deidentification of pathology reports

BMC Medical Informatics and Decision Making
Bruce A BeckwithFrank Kuo

Abstract

Electronic medical records, including pathology reports, are often used for research purposes. Currently, there are few programs freely available to remove identifiers while leaving the remainder of the pathology report text intact. Our goal was to produce an open source, Health Insurance Portability and Accountability Act (HIPAA) compliant, deidentification tool tailored for pathology reports. We designed a three-step process for removing potential identifiers. The first step is to look for identifiers known to be associated with the patient, such as name, medical record number, pathology accession number, etc. Next, a series of pattern matches look for predictable patterns likely to represent identifying data; such as dates, accession numbers and addresses as well as patient, institution and physician names. Finally, individual words are compared with a database of proper names and geographic locations. Pathology reports from three institutions were used to design and test the algorithms. The software was improved iteratively on training sets until it exhibited good performance. 1800 new pathology reports were then processed. Each report was reviewed manually before and after deidentification to catalog all identifiers and no...Continue Reading

References

Jun 3, 1998·Journal of the American Medical Informatics Association : JAMIA·M E FrisseW W Stead
May 14, 2003·Archives of Pathology & Laboratory Medicine·Jules J Berman
Feb 27, 2004·American Journal of Clinical Pathology·Dilip GuptaJohn Gilbertson
Jul 27, 2005·International Journal of Medical Informatics·Frank MengBernard M Churchill
May 11, 2007·Human Pathology·Thomas A DrakeUNKNOWN Shared Pathology Informatics Network

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Citations

Mar 2, 2010·Journal of the American Medical Informatics Association : JAMIA·Reyyan YeniterziBradley Malin
Aug 4, 2010·BMC Medical Research Methodology·Stephane M MeystreMatthew H Samore
Jul 31, 2012·BMC Medical Research Methodology·Oscar FerrándezStéphane M Meystre
Jun 23, 2010·BMC Medical Informatics and Decision Making·Karen TuJoel Martin
Oct 3, 2013·BMC Medical Informatics and Decision Making·Andrew J McMurryBen Y Reis
Jul 12, 2013·BMC Medical Informatics and Decision Making·Andrea C FernandesFelicity Callard
Jul 26, 2008·BMC Medical Informatics and Decision Making·Ishna NeamatullahGari D Clifford
Jun 27, 2008·Journal of the American Medical Informatics Association : JAMIA·F Jeff Friedlin, Clement J McDonald
Jun 30, 2007·Journal of the American Medical Informatics Association : JAMIA·Ozlem UzunerPeter Szolovits
Apr 27, 2007·Journal of the American Medical Informatics Association : JAMIA·Andrew J McMurryKenneth D Mandl
Sep 13, 2013·Journal of the American Medical Informatics Association : JAMIA·Mehmet KayaalpClement J McDonald
May 6, 2010·Journal of the American Medical Informatics Association : JAMIA·Rebecca S CrowleyMichael Feldman
Aug 4, 2012·Journal of the American Medical Informatics Association : JAMIA·Louise DelegerImre Solti
Sep 6, 2012·Journal of the American Medical Informatics Association : JAMIA·Oscar FerrándezStéphane M Meystre
May 28, 2010·Journal of Medical Systems·Lu-Chou HuangTsair Kao
Aug 2, 2015·Journal of Biomedical Informatics·Hui Yang, Jonathan M Garibaldi
Jul 28, 2016·Journal of Clinical Pathology·Gerard BurgerRonald Cornet
Jul 11, 2009·Computers in Biology and Medicine·Lu-Chou HuangTsair Kao
May 11, 2007·Human Pathology·Thomas A DrakeUNKNOWN Shared Pathology Informatics Network
May 21, 2016·Health Informatics Journal·Kostas PantazosSoren Lippert
Jan 2, 2015·Journal of Korean Medical Science·Soo-Yong ShinJae Ho Lee
Mar 29, 2018·BMC Medical Informatics and Decision Making·Yue-Shu ZhaoKun Li
Sep 9, 2019·BMC Medical Informatics and Decision Making·Md Nazmus SadatXiaoqian Jiang
Jan 4, 2017·Journal of the American Medical Informatics Association : JAMIA·Franck DernoncourtPeter Szolovits
Jun 6, 2017·Journal of Biomedical Informatics·Zengjian LiuQingcai Chen
Jun 13, 2017·Journal of Biomedical Informatics·Hee-Jin LeeKirk Roberts
Dec 7, 2007·Artificial Intelligence in Medicine·Ozlem UzunerPeter Szolovits
Jan 16, 2008·Clinics in Laboratory Medicine·Jason A LymanJames H Harrison

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Methods Mentioned

BETA
electron microscopy
used
in

Software Mentioned

Windows
JDOM
HMS Scrubber
MySQL
JDK
SPIN
MySQL ODBC Bridge
Java

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