Journal of Pathology Informatics Journal of Pathology Informatics
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Year : 2015  |  Volume : 6  |  Issue : 1  |  Page : 62

Extraction and analysis of discrete synoptic pathology report data using R

Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, K7L 3N6, Canada

Correspondence Address:
Alexander Boag
Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, K7L 3N6
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/2153-3539.170649

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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. Conclusion: This approach provides a simple solution at minimal cost that can make discrete synoptic report data readily available for quality assurance and research activities.

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