Textractor: a hybrid system for medications and reason for their prescription extraction from clinical text documents

UNLABELLED OBJECTIVE To describe a new medication information extraction system-Textractor-developed for the 'i2b2 medication extraction challenge'. The development, functionalities, and official evaluation of the system are detailed. DESIGN Textractor is based on the Apache Unstructured Information Management Architecture (UMIA) framework, and uses methods that are a hybrid between machine learning and pattern matching. Two modules in the system are based on machine learning algorithms, while other modules use regular expressions, rules, and dictionaries, and one module embeds MetaMap Transfer. MEASUREMENTS The official evaluation was based on a reference standard of 251 discharge summaries annotated by all teams participating in the challenge. The metrics used were recall, precision, and the F(1)-measure. They were calculated with exact and inexact matches, and were averaged at the level of systems and documents. RESULTS The reference metric for this challenge, the system-level overall F(1)-measure, reached about 77% for exact matches, with a recall of 72% and a precision of 83%. Performance was the best with route information (F(1)-measure about 86%), and was good for dosage and frequency information, with F(1)-measures of about 82-85%. Results were not as good for durations, with F(1)-measures of 36-39%, and for reasons, with F(1)-measures of 24-27%. CONCLUSION The official evaluation of Textractor for the i2b2 medication extraction challenge demonstrated satisfactory performance. This system was among the 10 best performing systems in this challenge.