title: Extraction and analysis of discrete synoptic pathology report data using R.
abstract: BACKGROUND
  Synoptic pathology reports can serve as a rich source of cancer information, particularly when the content is available as discrete electronic data fields. Our institution generates such reports as part of a province wide program in Ontario but the resulting data is not easily extracted and analyzed at the local level.
  
  
  METHODS
  A low cost system was developed using the open sourced and freely available R scripting/data analysis environment to parse synoptic report results into a dataframe and perform basic summary statistics.
  
  
  RESULTS
  As a pilot project text reports from 427 prostate needle biopsies were successfully read into R and the data elements split out and converted into appropriated data classes for analysis.
  
  
  CONCLUSIONS
  This approach provides a simple solution at minimal cost that can make discrete synoptic report data readily available for quality assurance and research activities.
authors.affiliation: Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
authors.forename: Alexander
authors.initials: A
authors.lastname: Boag
keywords: Cancer; R; quality; synoptic