title: TNM-O: ontology support for staging of malignant tumours.
abstract: Objectives of this work are to (1) present an ontological framework for the TNM classification system, (2) exemplify this framework by an ontology for colon and rectum tumours, and (3) evaluate this ontology by assigning TNM classes to real world pathology data.
  
  
  
  The TNM ontology uses the Foundational Model of Anatomy for anatomical entities and BioTopLite 2 as a domain top-level ontology. General rules for the TNM classification system and the specific TNM classification for colorectal tumours were axiomatised in description logic. Case-based information was collected from tumour documentation practice in the Comprehensive Cancer Centre of a large university hospital. Based on the ontology, a module was developed that classifies pathology data.
  
  
  
  TNM was represented as an information artefact, which consists of single representational units. Corresponding to every representational unit, tumours and tumour aggregates were defined. Tumour aggregates consist of the primary tumour and, if existing, of infiltrated regional lymph nodes and distant metastases. TNM codes depend on the location and certain qualities of the primary tumour (T), the infiltrated regional lymph nodes (N) and the existence of distant metastases (M). Tumour data from clinical and pathological documentation were successfully classified with the ontology.
  
  
  
  A first version of the TNM Ontology represents the TNM system for the description of the anatomical extent of malignant tumours. The present work demonstrates its representational power and completeness as well as its applicability for classification of instance data.
authors.affiliation: Institute for Medical Biometry and Statistics, Medical Center - University of Freiburg, Faculty of Medicine, Stefan-Meier-Str. 26, Freiburg i. Br., 79104, Germany. martin.boeker@uniklinik-freiburg.de.
authors.forename: Martin
authors.identifier: 0000-0003-2972-2042
authors.initials: M
authors.lastname: Boeker
authors.affiliation: Institute for Medical Biometry and Statistics, Medical Center - University of Freiburg, Faculty of Medicine, Stefan-Meier-Str. 26, Freiburg i. Br., 79104, Germany.|Department of Informatics, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal.
authors.forename: Fábio
authors.initials: F
authors.lastname: França
authors.affiliation: Tumorbank Comprehensive Cancer Center Freiburg and Center for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, Breisacher Straße 115a, Freiburg i. Br., 79106, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Bronsert
authors.affiliation: Institute of Medical Computer Sciences, Statistics and Documentation, Medical University of Graz, Auenbruggerplatz 2, Graz, 8036, Austria.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schulz
mesh_terms: D064229:Biological Ontologies; D006801:Humans; D009367:Neoplasm Staging; D009369:Neoplasms / Q000473:pathology*
keywords: Anatomical extent; Description logic; TNM classification; TNM ontology; Tumour classification; Tumour staging