Patient Identification for Clinical Trials with Ontology-based Information Extraction from Documents

In this paper, we describe the use of ontologies in the context of a system for recruiting patients for clinical trials, which is currently being tested at the Charité – Universitätsmedizin Berlin, one of the largest university hospitals in Europe. The main purpose of the CRDW (Clinical Research Data Warehouse) is to support patient recruitment for clinical trials 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 that is 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 focus of this paper is the description of our ontology model, which we tailored to the particular requirements of our application. In the article, we will also provide an evaluation of the system based on experimental data obtained from the daily routine work of the study assistants.