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

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...

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Autores principales: Eickelberg, Garrett, Luo, Yuan, Sanchez-Pinto, L Nelson
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9150069/
https://www.ncbi.nlm.nih.gov/pubmed/35651524
http://dx.doi.org/10.1093/jamiaopen/ooac026
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author Eickelberg, Garrett
Luo, Yuan
Sanchez-Pinto, L Nelson
author_facet Eickelberg, Garrett
Luo, Yuan
Sanchez-Pinto, L Nelson
author_sort Eickelberg, Garrett
collection PubMed
description 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 externally validated on the reports of 2 other institutions with manually reviewed results as a benchmark. RESULTS: MicrobEx achieved F1 scores >0.95 on all classification tasks across 2 independent validation sets with minimal customization. Additionally, MicrobEx matched or surpassed our MetaMap-based benchmark algorithm performance across positive culture classification and species capture classification tasks. DISCUSSION: Our results suggest that MicrobEx can be used to reliably estimate binary bacterial culture status, extract bacterial species, and map these to SNOMED organism observations when applied to semistructured, free-text microbiology reports from different institutions with relatively low customization. CONCLUSION: MicrobEx offers an open-source software solution (available on both GitHub and PyPI) for bacterial culture status estimation and bacterial species extraction from free-text microbiology reports. The package was designed to be reused and adapted to individual institutions as an upstream process for other clinical applications such as: machine learning, clinical decision support, and disease surveillance systems.
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spelling pubmed-91500692022-05-31 Development and validation of MicrobEx: an open-source package for microbiology culture concept extraction Eickelberg, Garrett Luo, Yuan Sanchez-Pinto, L Nelson JAMIA Open Application Notes 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 externally validated on the reports of 2 other institutions with manually reviewed results as a benchmark. RESULTS: MicrobEx achieved F1 scores >0.95 on all classification tasks across 2 independent validation sets with minimal customization. Additionally, MicrobEx matched or surpassed our MetaMap-based benchmark algorithm performance across positive culture classification and species capture classification tasks. DISCUSSION: Our results suggest that MicrobEx can be used to reliably estimate binary bacterial culture status, extract bacterial species, and map these to SNOMED organism observations when applied to semistructured, free-text microbiology reports from different institutions with relatively low customization. CONCLUSION: MicrobEx offers an open-source software solution (available on both GitHub and PyPI) for bacterial culture status estimation and bacterial species extraction from free-text microbiology reports. The package was designed to be reused and adapted to individual institutions as an upstream process for other clinical applications such as: machine learning, clinical decision support, and disease surveillance systems. Oxford University Press 2022-04-22 /pmc/articles/PMC9150069/ /pubmed/35651524 http://dx.doi.org/10.1093/jamiaopen/ooac026 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of the American Medical Informatics Association. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Application Notes
Eickelberg, Garrett
Luo, Yuan
Sanchez-Pinto, L Nelson
Development and validation of MicrobEx: an open-source package for microbiology culture concept extraction
title Development and validation of MicrobEx: an open-source package for microbiology culture concept extraction
title_full Development and validation of MicrobEx: an open-source package for microbiology culture concept extraction
title_fullStr Development and validation of MicrobEx: an open-source package for microbiology culture concept extraction
title_full_unstemmed Development and validation of MicrobEx: an open-source package for microbiology culture concept extraction
title_short Development and validation of MicrobEx: an open-source package for microbiology culture concept extraction
title_sort development and validation of microbex: an open-source package for microbiology culture concept extraction
topic Application Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9150069/
https://www.ncbi.nlm.nih.gov/pubmed/35651524
http://dx.doi.org/10.1093/jamiaopen/ooac026
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