title: Fine-grained information extraction from German transthoracic echocardiography reports.
abstract: BACKGROUND
  Information extraction techniques that get structured representations out of unstructured data make a large amount of clinically relevant information about patients accessible for semantic applications. These methods typically rely on standardized terminologies that guide this process. Many languages and clinical domains, however, lack appropriate resources and tools, as well as evaluations of their applications, especially if detailed conceptualizations of the domain are required. For instance, German transthoracic echocardiography reports have not been targeted sufficiently before, despite of their importance for clinical trials. This work therefore aimed at development and evaluation of an information extraction component with a fine-grained terminology that enables to recognize almost all relevant information stated in German transthoracic echocardiography reports at the University Hospital of Würzburg.
  
  
  METHODS
  A domain expert validated and iteratively refined an automatically inferred base terminology. The terminology was used by an ontology-driven information extraction system that outputs attribute value pairs. The final component has been mapped to the central elements of a standardized terminology, and it has been evaluated according to documents with different layouts.
  
  
  RESULTS
  The final system achieved state-of-the-art precision (micro average.996) and recall (micro average.961) on 100 test documents that represent more than 90 % of all reports. In particular, principal aspects as defined in a standardized external terminology were recognized with f 1=.989 (micro average) and f 1=.963 (macro average). As a result of keyword matching and restraint concept extraction, the system obtained high precision also on unstructured or exceptionally short documents, and documents with uncommon layout.
  
  
  CONCLUSIONS
  The developed terminology and the proposed information extraction system allow to extract fine-grained information from German semi-structured transthoracic echocardiography reports with very high precision and high recall on the majority of documents at the University Hospital of Würzburg. Extracted results populate a clinical data warehouse which supports clinical research.
authors.affiliation: Chair of Computer Science VI, University of Würzburg, Am Hubland, Würzburg, D-97074, Germany. martin.toepfer@uni-wuerzburg.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Toepfer
authors.affiliation: Comprehensive Heart Failure Center, University of Würzburg, Straubmühlweg 2a, Würzburg, D-97078, Germany.
authors.forename: Hamo
authors.initials: H
authors.lastname: Corovic
authors.affiliation: Chair of Computer Science VI, University of Würzburg, Am Hubland, Würzburg, D-97074, Germany.|Comprehensive Heart Failure Center, University of Würzburg, Straubmühlweg 2a, Würzburg, D-97078, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Fette
authors.affiliation: Chair of Computer Science VI, University of Würzburg, Am Hubland, Würzburg, D-97074, Germany.|Averbis GmbH, Tennenbacher Straße 11, Freiburg, D-79106, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Klügl
authors.affiliation: Comprehensive Heart Failure Center, University of Würzburg, Straubmühlweg 2a, Würzburg, D-97078, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Störk
authors.affiliation: Chair of Computer Science VI, University of Würzburg, Am Hubland, Würzburg, D-97074, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Puppe
mesh_terms: D004452:Echocardiography / Q000706:statistics & numerical data*; D005858:Germany; D006801:Humans; D016247:Information Storage and Retrieval / Q000706:statistics & numerical data*; D007256:Information Systems / Q000706:statistics & numerical data*; D013909:Thorax / Q000000981:diagnostic imaging