Development and validation of MicrobEx: an open-source package for microbiology culture concept extraction.

ABSTRACT:

Objective

Microbiology culture reports contain critical information for important clinical and public health applications. However, microbiology reports often have complex, semistructured, free-text data that present a barrier for secondary use. Here we present the development and validation of an open-source package designed to ingest free-text microbiology reports, determine whether the culture is positive, and return a list of Systemized Nomenclature of Medicine (SNOMED)-CT mapped bacteria.

Materials and methods

Our concept extraction Python package, MicrobEx, is built upon a rule-based natural language processing algorithm and was developed using microbiology reports from 2 different electronic health record systems in a large healthcare organization, and then ext

SUBMITTER: Eickelberg G 

PROVIDER: S-EPMC9150069 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature