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Ontology-Based Semantic Annotation of Documents in the Context of Patient Identification for Clinical Trials
Peter Geibel1, Martin Trautwein4, Hebun Erdur2, Lothar Zimmermann1, Stefan Krüger1, Josef Schepers1, Kati Jegzentis3, Frank Müller1, Christian Hans Nolte2, Anne Becker4, Markus Frick4, Jochen Setz4, Jan Friedrich Scheitz2, Serdar Tütüncü2, Tatiana Usnich2, Alfred Holzgreve4, Thorsten Schaaf1, and Thomas Tolxdorff1
1Institut of Medical Informatics, Charité - Universitätsmedizin Berlin, Germany
peter.geibel@charite.de
thomas.tolxdorff@charite.de
2Department of Neurology (CBF), Charité - Universitätsmedizin Berlin, Germany
3Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Germany
4Vivantes - Netzwerk für Gesundheit GmbH, Germany
martin.trautwein@vivantes.de
Abstract. In this paper, we describe the use of ontologies in the context of a system for identifying patients that are eligible for clinical trials. The main purpose of this clinical research data warehouse (CRDW) is to support patient recruitment based on routine data from the hospital’s clinical information system (CIS). In contrast to most other systems for similar purposes, the CRDW also makes use of information present in clinical documents like admission reports, radiological findings and discharge letters. The linguistic analysis recognizes negated and coordinated phrases. It is supported by clinical domain ontologies that enable the identification of main terms and their properties, as well as semantic search with synonyms, hypernyms, and syntactic variants. The CRDW system is currently being tested at hospitals of the Charité - Universitätsmedizin Berlin and the Vivantes - Netzwerk für Gesundheit GmbH. In the paper, we provide an evaluation of the system based on real world data obtained from the daily routine work of the study assistants.
Keywords: Ontologies, RDFS, secondary use of health data, patient recruitment, clinical data warehouse
LNCS 8185, p. 719 ff.
lncs@springer.com
© Springer-Verlag Berlin Heidelberg 2013