Qualitative analysis of workflow modifications used to generate the reference standard for the 2010 i2b2/VA challenge.

The Department of Veterans Affairs (VA) and the Informatics for Integrating Biology and the Bedside (i2b2) team partnered to generate the reference standard for the 2010 i2b2/VA challenge task on concept extraction, assertion classification, and relation classification. The purpose of this paper is to report an in-depth qualitative analysis of the experience and perceptions of human annotators for these tasks. Transcripts of semi-structured interviews were analyzed using qualitative methods to identify key constructs and themes related to these annotation tasks.

Inductive creation of an annotation schema and a reference standard for de-identification of VA electronic clinical notes.

Accessing both structured and unstructured clinical data is a high priority for research efforts. However, HIPAA requires that data meet or exceed a deidentification standard to assure that protected health information (PHI) is removed. This is a particularly difficult problem in the case of unstructured clinical free text and natural language processing (NLP) systems can be trained to automatically de-identify clinical text.