Extraction and analysis of discrete synoptic pathology report data using R
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...
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| Format: | Article |
| Language: | English |
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Wolters Kluwer Medknow Publications
2015-01-01
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| Series: | Journal of Pathology Informatics |
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| Online Access: | http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2015;volume=6;issue=1;spage=62;epage=62;aulast=Boag |
| Summary: | 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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| ISSN: | 2153-3539 |