MedXN: an open source medication extraction and normalization tool for clinical text

Abstract

Objective: We developed the Medication Extraction and Normalization (MedXN) system to extract comprehensive medication information and normalize it to the most appropriate RxNorm concept unique identifier (RxCUI) as specifically as possible.

Methods: Medication descriptions in clinical notes were decomposed into medication name and attributes, which were separately extracted using RxNorm dictionary lookup and regular expression. Then, each medication name and its attributes were combined together according to RxNorm convention to find the most appropriate RxNorm representation. To do this, we employed serialized hierarchical steps implemented in Apache's Unstructured Information Management Architecture. We also performed synonym expansion, removed false medications, and employed inference rules to improve the medication extraction and normalization performance.

Results: An evaluation on test data of 397 medication mentions showed F-measures of 0.975 for medication name and over 0.90 for most attributes. The RxCUI assignment produced F-measures of 0.932 for medication name and 0.864 for full medication information. Most false negative RxCUI assignments in full medication information are due to human assumption of missing attributes and medication names in the gold standard.

Conclusions: The MedXN system (http://sourceforge.net/projects/ohnlp/files/MedXN/) was able to extract comprehensive medication information with high accuracy and demonstrated good normalization capability to RxCUI as long as explicit evidence existed. More sophisticated inference rules might result in further improvements to specific RxCUI assignments for incomplete medication descriptions.

Keywords: Electronic Medical Records; Medication Extraction; Medication Normalization; Natural Language Processing; RxNorm.

Figure 1

MedXN algorithm flow for medication extraction and normalization. RxCUI, RxNorm concept unique identifier.

Figure 2

Medication information annotations visualized in the MedXN system.

Figure 3

MedXN evaluation on the test set (partial match).

Figure 4

MedXN versus National Center for Biomedical Computing (NCBO) annotator versus MedEx performance of RxCUI assignment on the test set.