title: Secondary use of electronic health records for building cohort studies through top-down information extraction.
abstract: Controlled clinical trials are usually supported with an in-front data aggregation system, which supports the storage of relevant information according to the trial context within a highly structured environment. In contrast to the documentation of clinical trials, daily routine documentation has many characteristics that influence data quality. One such characteristic is the use of non-standardized text, which is an indispensable part of information representation in clinical information systems. Based on a cohort study we highlight challenges for mining electronic health records targeting free text entry fields within semi-structured data sources. Our prototypical information extraction system achieved an F-measure of 0.91 (precision=0.90, recall=0.93) for the training set and an F-measure of 0.90 (precision=0.89, recall=0.92) for the test set. We analyze the obtained results in detail and highlight challenges and future directions for the secondary use of routine data in general.
authors.affiliation: Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria. Electronic address: markus.kreuzthaler@medunigraz.at.
authors.forename: Markus
authors.initials: M
authors.lastname: Kreuzthaler
authors.affiliation: Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schulz
authors.affiliation: Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria.
authors.forename: Andrea
authors.initials: A
authors.lastname: Berghold
mesh_terms: D000465:Algorithms; D015331:Cohort Studies; D003196:Computer Graphics; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D057286:Electronic Health Records; D005060:Europe; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D008490:Medical Informatics / Q000379:methods*; D009323:Natural Language Processing; D015203:Reproducibility of Results; D012107:Research Design; D012984:Software; D014481:United States; D014584:User-Computer Interface
keywords: Clinical narrative; Information extraction; Secondary use