Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Mar 28, 2026

A User-friendly and Powerful R Analysis of Large-scale Datasets
10:56

A User-friendly and Powerful R Analysis of Large-scale Datasets

Published on: November 4, 2025

453

Extraction and analysis of discrete synoptic pathology report data using R.

Alexander Boag1

  • 1Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, K7L 3N6, Canada.

Journal of Pathology Informatics
|January 6, 2016
PubMed
Summary

A low-cost R system efficiently extracts discrete data from synoptic pathology reports, enabling easier cancer information analysis for quality assurance and research.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Evaluating the Utility and Implementation Barriers of a Liquid Biopsy Biomarker Test Early in the Lung Cancer Diagnostic Pathway to Improve Timeliness of Palliative Systemic Therapy.

Current oncology (Toronto, Ont.)·2026
Same author

Hypersensitivity pneumonitis secondary to foam exposure in mattress and pillows.

BMJ case reports·2024
Same author

Mold in Foam Pillows and Mattresses: A Novel Cause of Hypersensitivity Pneumonitis.

Chest·2021
Same author

Canadian Multicenter Project on Standardization of Programmed Death-Ligand 1 Immunohistochemistry 22C3 Laboratory-Developed Tests for Pembrolizumab Therapy in NSCLC.

Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer·2020
Same author

Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study.

BMC cancer·2018
Same author

Correction to: Use of multicolor fluorescence in situ hybridization to detect deletions in clinical tissue sections.

Laboratory investigation; a journal of technical methods and pathology·2018

Area of Science:

  • Pathology Informatics
  • Cancer Data Management
  • Health Informatics

Background:

  • Synoptic pathology reports are valuable for cancer information when data is in discrete electronic fields.
  • Provincial programs generate these reports, but local data extraction and analysis are challenging.
  • Current systems limit the accessibility of structured pathology data for local use.

Purpose of the Study:

  • To develop a cost-effective system for extracting and analyzing discrete data from synoptic pathology reports.
  • To improve the accessibility of cancer information contained within pathology reports at the local level.
  • To facilitate quality assurance and research activities through readily available structured data.

Main Methods:

  • Utilized the open-source R scripting and data analysis environment.
Keywords:
CancerRqualitysynoptic

More Related Videos

Author Spotlight: High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution
10:47

Author Spotlight: High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution

Published on: May 5, 2023

4.7K
Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies
07:47

Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies

Published on: September 15, 2023

2.4K

Related Experiment Videos

Last Updated: Mar 28, 2026

A User-friendly and Powerful R Analysis of Large-scale Datasets
10:56

A User-friendly and Powerful R Analysis of Large-scale Datasets

Published on: November 4, 2025

453
Author Spotlight: High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution
10:47

Author Spotlight: High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution

Published on: May 5, 2023

4.7K
Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies
07:47

Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies

Published on: September 15, 2023

2.4K
  • Developed a system to parse synoptic report results into a data frame.
  • Implemented basic summary statistics for data analysis.

    • Main Results:

    • Successfully processed text reports from 427 prostate needle biopsies in a pilot project.
    • Parsed data elements from synoptic reports into appropriate data classes for analysis.
    • Demonstrated the feasibility of extracting discrete data for research.

    Conclusions:

    • The developed R-based system offers a simple, low-cost solution for accessing discrete synoptic report data.
    • This approach enhances the utility of pathology reports for quality assurance and research.
    • Facilitates the use of structured cancer data for improved healthcare insights.