ExaCT: automatic extraction of clinical trial characteristics from journal publications
1 Institute for Information Technology, National Research Council, Ottawa, Ontario, Canada
2 University of California San Francisco, San Francisco, CA, USA
BMC Medical Informatics and Decision Making 2010, 10:56 doi:10.1186/1472-6947-10-56Published: 28 September 2010
Clinical trials are one of the most important sources of evidence for guiding evidence-based practice and the design of new trials. However, most of this information is available only in free text - e.g., in journal publications - which is labour intensive to process for systematic reviews, meta-analyses, and other evidence synthesis studies. This paper presents an automatic information extraction system, called ExaCT, that assists users with locating and extracting key trial characteristics (e.g., eligibility criteria, sample size, drug dosage, primary outcomes) from full-text journal articles reporting on randomized controlled trials (RCTs).
ExaCT consists of two parts: an information extraction (IE) engine that searches the article for text fragments that best describe the trial characteristics, and a web browser-based user interface that allows human reviewers to assess and modify the suggested selections. The IE engine uses a statistical text classifier to locate those sentences that have the highest probability of describing a trial characteristic. Then, the IE engine's second stage applies simple rules to these sentences to extract text fragments containing the target answer. The same approach is used for all 21 trial characteristics selected for this study.
We evaluated ExaCT using 50 previously unseen articles describing RCTs. The text classifier (first stage) was able to recover 88% of relevant sentences among its top five candidates (top5 recall) with the topmost candidate being relevant in 80% of cases (top1 precision). Precision and recall of the extraction rules (second stage) were 93% and 91%, respectively. Together, the two stages of the extraction engine were able to provide (partially) correct solutions in 992 out of 1050 test tasks (94%), with a majority of these (696) representing fully correct and complete answers.
Our experiments confirmed the applicability and efficacy of ExaCT. Furthermore, they demonstrated that combining a statistical method with 'weak' extraction rules can identify a variety of study characteristics. The system is flexible and can be extended to handle other characteristics and document types (e.g., study protocols).