The deid software package includes code and dictionaries for automated location and removal of protected health information (PHI) in free text from medical records. The gold-standard corpus is a collection of deidentified nursing notes that have been reidentified with realistic surrogate data, for use in developing and evaluating software such as deid.
For additional discussion of the methods used by the software described here, see
Neamatullah I, Douglass M, Lehman LH, Reisner A, Villarroel M, Long WJ, Szolovits P, Moody GB, Mark RG, Clifford GD. Automated De-Identification of Free-Text Medical Records. BMC Medical Informatics and Decision Making, 2008, 8:32. doi:10.1186/1472-6947-8-32
Please cite the above paper when referencing this material, and also include the standard citation for PhysioNet:
Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG, Mietus JE, Moody GB, Peng C-K, Stanley HE. PhysioBank, PhysioToolkit, and Physionet: Components of a New Research Resource for Complex Physiologic Signals. Circulation 101(23):e215-e220 [Circulation Electronic Pages; http://circ.ahajournals.org/cgi/content/full/101/23/e215]; 2000 (June 13).
In the USA, the HIPAA Privacy Rule restricts exchange of medical data containing protected health information (PHI), defined as any information that might be used to identify the individual(s) from whom the data were collected. Data known to contain PHI can be shared for research purposes only under tightly controlled circumstances, typically involving data use agreements under which the researchers involved must obtain IRB or equivalent approvals for use of the data.
By contrast, medical data that do not contain PHI are exempt from the restrictions of the HIPAA Privacy Rule and may be shared freely. The data available on PhysioNet fall into this category.
Many of the research data sets currently being collected by PhysioNet are accompanied by PHI, and the process of removing this PHI ("de-identification" in the language of HIPAA, or "anonymization") is tedious and error-prone. For many research projects, the cost of de-identification is a significant barrier to data sharing.
The MIMIC II project has invested several years' effort to develop and evaluate software that is capable of removing PHI from text and, where appropriate, replacing it by realistic surrogate PHI. (For example, names are replaced by fictitious names, medical record numbers by fictitious medical record numbers, dates by fictitious dates, geographic locations by other geographic locations, etc.) The MIMIC II project has contributed to PhysioNet both its deidentification software, which may be useful to other researchers needing to remove PHI from their own data, and a large corpus of text drawn from ICU nursing notes that were gathered simultaneously with the signals, trends, laboratory reports, discharge summaries and other data in the MIMIC II clinical and waveform databases.
As is the case with all software available on PhysioNet, the de-identification software (deid) is provided in source form so that its workings can be studied, customized, and improved. This software is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
The authors of the deid software package are Margaret M Douglass,
Li-wei H Lehman, William J Long, and Ishna Neamatullah. An experimental
prototype by Jason M Levine provided useful guidance in the design of
The deid package requires Perl (version 5 or later), which is freely available for all popular platforms here if you don't have it already.
The current version of the deid software package was
developed and tested using perl 5.8.8 and perl 5.10 on GNU/Linux
(Fedora Core 10). It has also been tested on Fedora 6, 7 and 8,
Ubuntu 8.04, MacOS X 10.4.5, and on MS-Windows XP.
Downloading and installing deid
The deid software package can be downloaded as a single file, deid-1.1.tar.gz. (Instructions on unpacking tar.gz files are here.) The contents of deid-1.1.tar.gz unpack into a directory named deid-1.1, which contains the files listed below.
The deid software package is command-line (text mode) software that must be run in a terminal emulator (console) window.
If you wish to test deid, see Data: the gold-standard corpus of deidentified medical text below for information on obtaining id.text. Copy id.text into the deid-1.1 directory (created when deid-1.1.tar.gz was unpacked in the previous step), and enter that directory. Type the command
perl deid.pl id deid.config
The software will print a greeting message:
******************************************************************************************************************* De-Identification Algorithm: Identifies Protected Health Information (PHI) in Discharge Summaries and Nursing Notes ******************************************************************************************************************* Starting de-identification (version 1.1) ... Running deid in output mode. Output files will be: id.phi: the PHI locations found by the code. id.res: the scrubbed text. id.info: debug info about the PHI locations.
On a typical current PC, the process will run to completion in approximately 10 to 20 minutes. The three output files will be written into the current directory; they should be identical to the files of the same names that are included in the GSoutput directory.
The program runStat.pl can be used to derive performance statistics by comparing the id.phi file generated by deid.pl with the reference id.deid file provided with the deid software package. To do this, type the command
perl runStat.pl id.deid id.phiwhich should produce the output
========================== Num of true positives = 1720 Num of false positives = 546 Num of false negatives = 59 Sensitivity/Recall = 0.967 PPV/Specificity = 0.748 ==========================To use the gold standard corpus to test the performance of another deidentifier, arrange for that deidentifier to produce a file in the format of id.phi, then use runStat.pl as above.
Examine the configuration file, deid.config, to see how to modify the behavior of deid.pl. For additional information, see the user manual.
In order to customize this software to de-identify free text in other medical records, you may replace our filter modules with your data-specific filters. Additionally, at a minimum, you will have to replace the six files that contain a priori information (see below).
Depending on the text you wish to de-identify, you may wish to re-classify names as ambiguous or not. For example, "Mae" is an unambiguous name in most contexts, but in nursing and discharge notes, it may be an acronym (meaning "moving all extremities") and it is therefore ambiguous in those contexts.
Except for functions related to calculating performance statistics (in stats.pm), the deidentification code is contained in a perl script (deid.pl). Its configuration file, deid.config, can be used to set parameters of the deidentification process at run time. Associated word and phrase lists are in lists/ (containing known and possible PHI) and dict/ (containing probable non-PHI).
If the date shift filter is on, deid replaces all dates in its input with surrogate dates. The shift.txt file contains a randomly assigned date shift (between 1000 and 3000 days) for each patient in the gold standard corpus; surrogate dates are generated by adding the specified number of days to the dates in the input file. The method used to generate the date shifts in shift.txt differs from that used in PhysioBank databases.
The file id-phi.phrase is provided as a convenient index to the PHI in the gold standard corpus; it is not used by the deid software. Each line of this file contains 6 fields: PID, Record_Number, PHI_Start_Location, PHI_End_Location, PHI_Type, and PHI_Text.
The file id.deid also contains PHI locations in the gold standard corpus, and it is used as a reference for calculating performance statistics by the functions in stats.pm. It contains two types of lines. The first type is of the form
Patient PID Note Record_Numberand the second type is of the form
PHI_Start_Location PHI_Start_Location PHI_End_Location
Evaluating software for de-identification turns out to be quite difficult. As in many of the projects contributing to PhysioNet, a reference database is highly useful. Ideally the developer of de-identification software needs an appropriate corpus of text in which all of the PHI has been labelled, so that the software's PHI detection performance can be assessed quickly and quantitatively. To compare different approaches to PHI removal objectively, we need a standard corpus. And here's the dilemma: we can't share such a corpus if it has any PHI in it!
The deid software package was developed and tested using a gold standard corpus of 2,434 nursing notes that have been thoroughly deidentified by a multi-pass process that included meticulous reviews by three or more experts working independently, as well as by a variety of automated methods. All detected instances of PHI in these nursing notes have been replaced by realistic surrogate data in the gold standard corpus. Although the deid software, as noted above, may be redistributed under the terms of the GPL, the gold standard corpus, because of the very small possibility that it may contain one or more instances of undetected PHI, is currently available only under terms that do not permit it to be redistributed. This corpus is available only under the following conditions:
To download the corpus, login to PhysioNetWorks, then follow the "Deidentified Medical Text" link on your PhysioNetWorks home page. (You can create a free PhysioNetWorks account in a few minutes here if you don't have one already.)
This work was performed with support from the National Institute of Biomedical Imaging and Bioengineering (NIBIB), under grant R01 EB001659.