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. 2008 Sep-Oct;15(5):601-10.
doi: 10.1197/jamia.M2702. Epub 2008 Jun 25.

A software tool for removing patient identifying information from clinical documents

F Jeff Friedlin  1 , Clement J McDonald
Affiliations

A software tool for removing patient identifying information from clinical documents

F Jeff Friedlin et al. J Am Med Inform Assoc. 2008 Sep-Oct.

Abstract

We created a software tool that accurately removes all patient identifying information from various kinds of clinical data documents, including laboratory and narrative reports. We created the Medical De-identification System (MeDS), a software tool that de-identifies clinical documents, and performed 2 evaluations. Our first evaluation used 2,400 Health Level Seven (HL7) messages from 10 different HL7 message producers. After modifying the software based on the results of this first evaluation, we performed a second evaluation using 7,190 pathology report HL7 messages. We compared the results of MeDS de-identification process to a gold standard of human review to find identifying strings. For both evaluations, we calculated the number of successful scrubs, missed identifiers, and over-scrubs committed by MeDS and evaluated the readability and interpretability of the scrubbed messages. We categorized all missed identifiers into 3 groups: (1) complete HIPAA-specified identifiers, (2) HIPAA-specified identifier fragments, (3) non-HIPAA-specified identifiers (such as provider names and addresses). In the results of the first-pass evaluation, MeDS scrubbed 11,273 (99.06%) of the 11,380 HIPAA-specified identifiers and 38,095 (98.26%) of the 38,768 non-HIPAA-specified identifiers. In our second evaluation (status postmodification to the software), MeDS scrubbed 79,993 (99.47%) of the 80,418 HIPAA-specified identifiers and 12,689 (96.93%) of the 13,091 non-HIPAA-specified identifiers. Approximately 95% of scrubbed messages were both readable and interpretable. We conclude that MeDS successfully de-identified a wide range of medical documents from numerous sources and creates scrubbed reports that retain their interpretability, thereby maintaining their usefulness for research.

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Figures

Figure 1
Figure 1
Nineteen patient identifiers that require removal for de-identification per HIPAA regulations.
Figure 2
Figure 2
Processing schema of the de-identification software.
Figure 3
Figure 3
Examples of alternative date display formats found in sample messages.
Figure 4
Figure 4
Algorithm used by the name scrubbing process.
Figure 5
Figure 5
Example of a scrubbed HL7 narrative report message (endoscopy report).
See this image and copyright information in PMC

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