title: Symbolic rule-based classification of lung cancer stages from free-text pathology reports.
abstract: OBJECTIVE
  To classify automatically lung tumor-node-metastases (TNM) cancer stages from free-text pathology reports using symbolic rule-based classification.
  
  
  METHODS
  By exploiting report substructure and the symbolic manipulation of systematized nomenclature of medicine-clinical terms (SNOMED CT) concepts in reports, statements in free text can be evaluated for relevance against factors relating to the staging guidelines. Post-coordinated SNOMED CT expressions based on templates were defined and populated by concepts in reports, and tested for subsumption by staging factors. The subsumption results were used to build logic according to the staging guidelines to calculate the TNM stage.
  
  
  METHODS
  The accuracy measure and confusion matrices were used to evaluate the TNM stages classified by the symbolic rule-based system. The system was evaluated against a database of multidisciplinary team staging decisions and a machine learning-based text classification system using support vector machines.
  
  
  RESULTS
  Overall accuracy on a corpus of pathology reports for 718 lung cancer patients against a database of pathological TNM staging decisions were 72%, 78%, and 94% for T, N, and M staging, respectively. The system's performance was also comparable to support vector machine classification approaches.
  
  
  CONCLUSIONS
  A system to classify lung TNM stages from free-text pathology reports was developed, and it was verified that the symbolic rule-based approach using SNOMED CT can be used for the extraction of key lung cancer characteristics from free-text reports. Future work will investigate the applicability of using the proposed methodology for extracting other cancer characteristics and types.
authors.affiliation: The Australian e-Health Research Centre, CSIRO ICT Centre, Brisbane, Australia. anthony.nguyen@csiro.au
authors.forename: Anthony N
authors.initials: AN
authors.lastname: Nguyen
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Lawley
authors.forename: David P
authors.initials: DP
authors.lastname: Hansen
authors.forename: Rayleen V
authors.initials: RV
authors.lastname: Bowman
authors.forename: Belinda E
authors.initials: BE
authors.lastname: Clarke
authors.forename: Edwina E
authors.initials: EE
authors.lastname: Duhig
authors.forename: Shoni
authors.initials: S
authors.lastname: Colquist
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001315:Australia; D057225:Data Mining; D020000:Decision Support Systems, Clinical; D006801:Humans; D008175:Lung Neoplasms / Q000473:pathology*; D009367:Neoplasm Staging / Q000145:classification*; D012042:Registries / Q000706:statistics & numerical data; D039061:Systematized Nomenclature of Medicine