parseMedEx: Parse MedEx NLP Output

In EHR: Electronic Health Record (EHR) Data Processing and Analysis Tool

Parse MedEx NLP Output

Description

Takes files with the raw medication extraction output generated by the MedEx natural language processing system and converts it into a standardized format.

Usage

parseMedEx(filename)

Arguments

filename

File name for a single file containing MedEx output.

Details

Output from different medication extraction systems is formatted in different ways. In order to be able to process the extracted information, we first need to convert the output from different systems into a standardized format. Extracted expressions for various drug entities (e.g., drug name, strength, frequency, etc.) each receive their own column formatted as "extracted expression::start position::stop position". If multiple expressions are extracted for the same entity, they will be separated by backticks.

MedEx output files anchor extractions to a specific drug name extraction.

See EHR Vignette for Extract-Med and Pro-Med-NLP as well as Dose Building Using Example Vanderbilt EHR Data for details.

Value

A data.table object with columns for filename, drugname, strength, dose, route, and freq. The filename contains the file name corresponding to the clinical note. Each of the entity columns are of the format "extracted expression::start position::stop position".

EHR documentation built on Dec. 28, 2022, 1:31 a.m.