Cancer Causes & Control

, Volume 21, Issue 11, pp 1887–1894 | Cite as

Pattern-based information extraction from pathology reports for cancer registration

  • Giulio Napolitano
  • Colin Fox
  • Richard Middleton
  • David Connolly
Original paper

Abstract

Objective

To evaluate precision and recall rates for the automatic extraction of information from free-text pathology reports. To assess the impact that implementation of pattern-based methods would have on cancer registration completeness.

Method

Over 300,000 electronic pathology reports were scanned for the extraction of Gleason score, Clark level and Breslow depth, by a number of Perl routines progressively enhanced by a trial-and-error method. An additional test set of 915 reports potentially containing Gleason score was used for evaluation.

Results

Values for recall and precision of over 98 and 99%, respectively, were easily reached. Potential increase in cancer staging completeness of up to 32% was proved.

Conclusions

In cancer registration, simple pattern matching applied to free-text documents can be effectively used to improve completeness and accuracy of pathology information.

Keywords

Surgical pathology Automatic data processing Cancer registries Pattern matching Information extraction Text mining Unstructured data management Pathology report Cancer registration Regular expression 

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Giulio Napolitano
    • 1
    • 2
  • Colin Fox
    • 1
  • Richard Middleton
    • 1
  • David Connolly
    • 3
  1. 1.Northern Ireland Cancer Registry, Centre for Public HealthQueen’s University of BelfastBelfastNorthern Ireland (UK)
  2. 2.Centre for Statistical Science and Operational ResearchQueen’s University BelfastBelfastNorthern Ireland (UK)
  3. 3.Department of UrologyBelfast City HospitalBelfastNorthern Ireland (UK)

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