Representing and utilizing clinical textual data for real world studies: An OHDSI approach.

Humans Data Science Electronic Health Records Medical Informatics Natural Language Processing Narration
Electronic health records Natural language processing Real-world study

Journal

Journal of biomedical informatics
ISSN: 1532-0480
Titre abrégé: J Biomed Inform
Pays: United States
ID NLM: 100970413

Informations de publication

Date de publication:
06 2023
Historique:
received: 25 05 2022
revised: 21 01 2023
accepted: 13 03 2023
pmc-release: 01 06 2024
medline: 5 6 2023
pubmed: 20 3 2023
entrez: 19 3 2023
Statut: ppublish

Résumé

Clinical documentation in electronic health records contains crucial narratives and details about patients and their care. Natural language processing (NLP) can unlock the information conveyed in clinical notes and reports, and thus plays a critical role in real-world studies. The NLP Working Group at the Observational Health Data Sciences and Informatics (OHDSI) consortium was established to develop methods and tools to promote the use of textual data and NLP in real-world observational studies. In this paper, we describe a framework for representing and utilizing textual data in real-world evidence generation, including representations of information from clinical text in the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM), the workflow and tools that were developed to extract, transform and load (ETL) data from clinical notes into tables in OMOP CDM, as well as current applications and specific use cases of the proposed OHDSI NLP solution at large consortia and individual institutions with English textual data. Challenges faced and lessons learned during the process are also discussed to provide valuable insights for researchers who are planning to implement NLP solutions in real-world studies.

Identifiants

DOI: 10.1016/j.jbi.2023.104343 PMID: 36935011 PMC: PMC10428170
pubmed: 36935011
pii: S1532-0464(23)00064-3
doi: 10.1016/j.jbi.2023.104343
pmc: PMC10428170
mid: NIHMS1897646
pii:
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

104343

Subventions

Organisme : NIA NIH HHS
ID : P30 AG059307
Pays : United States
Organisme : NLM NIH HHS
ID : R00 LM013001
Pays : United States
Organisme : NCATS NIH HHS
ID : U01 TR002062
Pays : United States
Organisme : NCCIH NIH HHS
ID : R01 AT009457
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NLM NIH HHS
ID : R01 LM006910
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR002494
Pays : United States

Informations de copyright

Copyright © 2023 Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of Competing Interest Dr. Hua Xu and The University of Texas Health Science Center at Houston have research related financial interests at Melax Technologies Inc. Dr. Xiaoyan Wang has related financial interests at Sema4 Mount Sinai Genomics Inc.

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Auteurs

Vipina K Keloth (VK)

Section of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA.

Juan M Banda (JM)

Department of Computer Science, Georgia State University, Atlanta, GA, USA.

Michael Gurley (M)

Lurie Cancer Center, Northwestern University, Chicago, Illinois, USA.

Paul M Heider (PM)

Biomedical Informatics Center, Medical University of South Carolina, Charleston, SC, USA.

Georgina Kennedy (G)

Ingham Institute for Applied Medical Research, Sydney, Australia.

Hongfang Liu (H)

Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA.

Feifan Liu (F)

Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA.

Timothy Miller (T)

Computational Health Informatics Program, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA.

Karthik Natarajan (K)

Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.

Olga V Patterson (O)

VA Informatics and Computing Infrastructure, Department of Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA; Division of Epidemiology, Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, Utah, USA; Verily Life Sciences, Mountain View, CA, USA.

Yifan Peng (Y)

Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA.

Kalpana Raja (K)

Section of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA.

Ruth M Reeves (RM)

TN Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, TN, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.

Masoud Rouhizadeh (M)

Department of Pharmaceutical Outcomes & Policy, University of Florida, Gainesville, FL, USA; Biomedical Informatics and Data Science, Johns Hopkins University, Baltimore, MD, USA.

Jianlin Shi (J)

VA Informatics and Computing Infrastructure, Department of Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA; Division of Epidemiology, Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, Utah, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, USA.

Xiaoyan Wang (X)

Sema4 Mount Sinai Genomics Incorporation, Stamford, CT, USA.

Yanshan Wang (Y)

Department of Health Information Management, Department of Biomedical Informatics, and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA.

Wei-Qi Wei (WQ)

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.

Andrew E Williams (AE)

School of Medicine, Tufts University, Boston, MA, USA.

Rui Zhang (R)

Institute for Health Informatics, and Department of Pharmaceutical Care & Health Systems, University of Minnesota, Minneapolis, MN, USA.

Rimma Belenkaya (R)

Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Christian Reich (C)

Real World Solutions, IQVIA, Durham, NC, USA.

Clair Blacketer (C)

Janssen Pharmaceutical Research and Development LLC, Titusville, NJ, USA; Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, the Netherlands.

Patrick Ryan (P)

Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA; Janssen Pharmaceutical Research and Development LLC, Titusville, NJ, USA.

George Hripcsak (G)

Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.

Noémie Elhadad (N)

Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA. Electronic address: noemie.elhadad@columbia.edu.

Hua Xu (H)

Section of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA. Electronic address: hua.xu@yale.edu.

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