Monday, January 14, 2008

Medical record de-identifier (using the doublet method)

Earlier today, I wrote a blog describing an identifier-free doublet list. This blog describes a scrubber use-case for the doublet list.

The de-identification of medical text is a good use of the doublet list. To share medical records (usually for the purposes of research) it is often imporant to remove all of the identifiers (that could link a patient to the record).

There are now available a variety of medical text scrubbers for this purpose. Most require the users to develop identifier lists for their site (list of patient names, doctor names, etc), run very slowly (typically, about one record per second), and do not remove anywhere close to all of the identifiers.

Not so for the doublet method. A doublet scrubber parses through any text, matching doublets from the text against an external identifier-free doublet list, preserving all matching doublets from the text, and blocking all non-matching words with an asterisk. If your list of doublets contains no identifiers, the scrubbed output should be perfectly de-identified. Though perfection can never be guaranteed, I have never encountered any "missed" identifiers in a text that was parsed under these conditions. A public domain list of doublets is available , but I cannot guarantee that the list is identifier-free or that it is the best list for your purposes. Feel free to modify the list, add to the list, or create your own list of identifier-free doublets.

The doublet method is described in Ruby Programming for Medicine and Biology.

For each citation, the list of authors is put on a line, and is immediately followed by its scrubbed version on the next line. Then the title of the article is put on the next line, followed by the scrubbed version of the title of the article. This pattern is repeated for the 1500+ citation.

The doublet scrubber is small (just a few dozen lines of code) and fast. It took approximately 2 seconds to parse the 15000 citations using a Perl script with access to a list of about 200,000 identifier-free doublets. I used my home computer (2.8 GHz, 512 MByte RAM). This is a scrubbing rate of 1 MegaByte per second. At this speed, a 1 GByte file could be parsed in about 15 minutes. It can parse a 1 Terabyte file in about a week. Large hospitals produce about 1 Terabyte of data each week, so this scrubber can, for now, "keep up" with the vast load of data produced by many hospitals (using a modest desktop computer).

The only limitation that I have found with the doublet scrubber is that it scrubs too much, blocking all doublets not found in the external doublet list. You can be the judge by reviewing the provided output file. The output attached here can be used to assess the effectiveness of the doublet method of text scrubbing.

-Jules Berman tags: common rule, data scrubbing, de-identification, deidentification, hipaa, medical records
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