Evidence map›Paper›PMID 36935011›Full record

ArticleJournal of biomedical informatics2023

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

Vipina K Keloth, Juan M Banda, Michael Gurley, Paul M Heider, Georgina Kennedy, Hongfang Liu, Feifan Liu, Timothy Miller, Karthik Natarajan, Olga V Patterson and 17 more

Abstract read
In one paragraph

Article in Journal of biomedical informatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

  1. Article
  2. Accelerating real-world prediction and research in Alzheimer's: The M3AD study.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026
    Article
  3. Review
  4. Article
  5. Article
  6. Generative Artificial Intelligence for Health Technology Assessment: Opportunities, Challenges, and Policy Considerations: An ISPOR Working Group Report.Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research · 2025
    Review
  7. Review
  8. Clinical Research Informatics: Contributions from 2023.Yearbook of medical informatics · 2024
    Review
  9. Clinical Research Informatics: a Decade-in-Review.Yearbook of medical informatics · 2024
    Review
  10. Article
  11. Review
  12. The Growing Impact of Natural Language Processing in Healthcare and Public Health.Inquiry : a journal of medical care organization, provision and financing
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

27 authors.

Vipina K KelothSection of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA.
Juan M BandaDepartment of Computer Science, Georgia State University, Atlanta, GA, USA.
Michael GurleyLurie Cancer Center, Northwestern University, Chicago, Illinois, USA.
Paul M HeiderBiomedical Informatics Center, Medical University of South Carolina, Charleston, SC, USA.
Georgina KennedyIngham Institute for Applied Medical Research, Sydney, Australia.
Hongfang LiuDepartment of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA.
Feifan LiuDepartment of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Timothy MillerComputational Health Informatics Program, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
Karthik NatarajanDepartment of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
Olga V PattersonVA 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 PengDepartment of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA.
Kalpana RajaSection of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA.
Ruth M ReevesTN Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, TN, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
Masoud RouhizadehDepartment of Pharmaceutical Outcomes & Policy, University of Florida, Gainesville, FL, USA; Biomedical Informatics and Data Science, Johns Hopkins University, Baltimore, MD, USA.
Jianlin ShiVA 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 WangSema4 Mount Sinai Genomics Incorporation, Stamford, CT, USA.
Yanshan WangDepartment of Health Information Management, Department of Biomedical Informatics, and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA.
Wei-Qi WeiDepartment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
Andrew E WilliamsSchool of Medicine, Tufts University, Boston, MA, USA.
Rui ZhangInstitute for Health Informatics, and Department of Pharmaceutical Care & Health Systems, University of Minnesota, Minneapolis, MN, USA.
Rimma BelenkayaMemorial Sloan Kettering Cancer Center, New York, NY, USA.
Christian ReichReal World Solutions, IQVIA, Durham, NC, USA.
Clair BlacketerJanssen Pharmaceutical Research and Development LLC, Titusville, NJ, USA; Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, the Netherlands.
Patrick RyanDepartment of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA; Janssen Pharmaceutical Research and Development LLC, Titusville, NJ, USA.
George HripcsakDepartment of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
Noémie ElhadadDepartment of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA. Electronic address: noemie.elhadad@columbia.edu.
Hua XuSection of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA. Electronic address: hua.xu@yale.edu.

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
University of Minnesota Clinical and Translational Science Institute (UMN CTSI)UL1TR002494 · NCATS · UNIVERSITY OF MINNESOTA · PI BLAZAR, BRUCE R, WEISDORF, DANIEL J · 2018 to 2022
$34.9M
Stanford Alzheimer's Disease Research CenterAdmin Supp: Developing iPSC models for AD and PDP30AG066515 · NIA · STANFORD UNIVERSITY · PI Lisa Goldman Rosas · 2020 to 2026
$29.0M
DISCOVERING AND APPLYING KNOWLEDGE IN CLINICAL DATABASESR01LM006910 · NLM · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI HRIPCSAK, GEORGE M · 2000 to 2023
$10.6M
Open Health Natural Language Processing CollaboratoryU01TR002062 · NCATS · MAYO CLINIC ROCHESTER · PI JIANG, XIAOQIAN, LIU, HONGFANG · 2017 to 2021
$7.6M
Stanford Medicine Center for Longevity and Healthy Aging Research Education CoreP30AG059307 · NIA · STANFORD UNIVERSITY · PI PERIYAKOIL, VYJEYANTHI S, YESAVAGE, JEROME A · 2018 to 2025
$4.9M
A Translational Informatics Framework to Mine Efficacy and Safety of Dietary SupplementsR01AT009457 · NCCIH · UNIVERSITY OF MINNESOTA · PI RUI ZHANG · 2017 to 2026
$4.1M
A framework to enhance radiology structured report by invoking NLP and DL: Models and ApplicationsR00LM013001 · NLM · WEILL MEDICAL COLL OF CORNELL UNIV · PI PENG, YIFAN · 2020 to 2022
$710k
NCATS NIH HHS U01 TR002062NCATS NIH HHS UL1 TR002494NCCIH NIH HHS R01 AT009457NCI NIH HHS P30 CA008748NIA NIH HHS P30 AG059307NIA NIH HHS P30 AG066515NLM NIH HHS R00 LM013001NLM NIH HHS R01 LM006910
6 · The paper itself

Abstract

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.

Indexed as

Data ScienceMedical InformaticsElectronic Health RecordsHumansNarrationNatural Language ProcessingElectronic health recordsNatural language processingReal-world study

Identifiers

PMID36935011
PMCPMC10428170

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.