Ontology-based semantic annotation of documents in the context of patient identification for clinical trials

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. © 2013 Springer-Verlag.