MetaMap Lite: an evaluation of a new Java implementation of MetaMap.

MetaMap is a widely used named entity recognition tool that identifies concepts from the Unified Medical Language System Metathesaurus in text. This study presents MetaMap Lite, an implementation of some of the basic MetaMap functions in Java. On several collections of biomedical literature and clinical text, MetaMap Lite demonstrated real-time speed and precision, recall, and F1 scores comparable to or exceeding those of MetaMap and other popular biomedical text processing tools, clinical Text Analysis and Knowledge Extraction System (cTAKES) and DNorm. Published by Oxford University Press on behalf of the American Medical Informatics Association 2017. This work is written by US Government employees and is in the public domain in the US.