BoB, a best-of-breed automated text de-identification system for VHA clinical documents.

Ferrández O, South BR, Shen S, Friedlin FJ, Samore MH, Meystre SM. BoB, a best-of-breed automated text de-identification system for VHA clinical documents. Journal of the American Medical Informatics Association : JAMIA. 2013 Jan 1; 20(1):77-83.

Related HSR&D Project(s)

• HIR 09-006 – Consortium for Healthcare Informatics Research - De-Identification

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Abstract:

OBJECTIVE: De-identification allows faster and more collaborative clinical research while protecting patient confidentiality. Clinical narrative de-identification is a tedious process that can be alleviated by automated natural language processing methods. The goal of this research is the development of an automated text de-identification system for Veterans Health Administration (VHA) clinical documents. MATERIALS AND METHODS: We devised a novel stepwise hybrid approach designed to improve the current strategies used for text de-identification. The proposed system is based on a previous study on the best de-identification methods for VHA documents. This best-of-breed automated clinical text de-identification system (aka BoB) tackles the problem as two separate tasks: (1) maximize patient confidentiality by redacting as much protected health information (PHI) as possible; and (2) leave de-identified documents in a usable state preserving as much clinical information as possible. RESULTS: We evaluated BoB with a manually annotated corpus of a variety of VHA clinical notes, as well as with the 2006 i2b2 de-identification challenge corpus. We present evaluations at the instance- and token-level, with detailed results for BoB's main components. Moreover, an existing text de-identification system was also included in our evaluation. DISCUSSION: BoB's design efficiently takes advantage of the methods implemented in its pipeline, resulting in high sensitivity values (especially for sensitive PHI categories) and a limited number of false positives. CONCLUSIONS: Our system successfully addressed VHA clinical document de-identification, and its hybrid stepwise design demonstrates robustness and efficiency, prioritizing patient confidentiality while leaving most clinical information intact.