Evidence map›Paper›PMID 39974073›Full record

ArticlemedRxiv : the preprint server for health sciences2025

Development and Validation of Natural Language Processing Algorithms in the ENACT National Electronic Health Record Research Network.

Yanshan Wang, Jordan Hilsman, Chenyu Li, Michele Morris, Paul M Heider, Sunyang Fu, Min Ji Kwak, Andrew Wen, Joseph R Applegate, Liwei Wang and 26 more

Abstract readPreprint
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

36 authors.

Yanshan WangClinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA.
Jordan HilsmanClinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA.
Chenyu LiClinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA.
Michele MorrisDepartment of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA.
Paul M HeiderBiomedical Informatics Center and Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
Sunyang FuMcWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.
Min Ji KwakMcGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
Andrew WenMcWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.
Joseph R ApplegateMcWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.
Liwei WangMcWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.
Elmer BernstamMcWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.
Hongfang LiuMcWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.
Jack ChangClinical and Translational Science Institute, University of Rochester Medical Center, Rochester, NY, USA.
Daniel R HarrisInstitute for Biomedical Informatics, University of Kentucky, Lexington, KY, USA.
Alexandria CorbeauInstitute for Biomedical Informatics, University of Kentucky, Lexington, KY, USA.
Darren HendersonInstitute for Biomedical Informatics, University of Kentucky, Lexington, KY, USA.
John D OsborneDepartment of Biomedical Informatics and Data Science, University of Alabama at Birmingham, Birmingham, AL, USA.
Richard E KennedyDivision of Gerontology, Geriatrics, and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
Nelly-Estefanie Garduno-RappClinical Informatics Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Justin F RousseauClinical Informatics Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Chao YanDepartment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
You ChenDepartment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
Mayur B PatelDepartment of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.
Tyler J MurphyDepartment of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.
Bradley A MalinDepartment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
Chan Mi ParkDepartment of Gerontology, Hebrew SeniorLife, Marcus Institute for Aging Research, Boston, MA, USA.
Jungwei W FanDepartment of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA.
Sunghwan SohnDepartment of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA.
Sandeep PagaliDepartment of Medicine, Mayo Clinic, Rochester, MN, USA.
Yifan PengDepartment of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA.
Aman PathakDepartment of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL, USA.
Yonghui WuDepartment of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL, USA.
Zongqi XiaDepartment of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
Salvatore LoguercioScripps Research Translational Institute, Scripps Research, La Jolla, CA, USA.
Steven E ReisClinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA.
Shyam VisweswaranClinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA.

Funding

University of Pittsburgh Clinical and Translational Science InstituteUL1TR001857 · NCATS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI REIS, STEVEN E · 2016 to 2025
$129.3M
Mayo Clinic Center for Clinical and Translational Science (CCaTS UL1 Supplement - Dr. Timothy Curry)UL1TR002377 · NCATS · MAYO CLINIC ROCHESTER · PI VESNA D GAROVIC · 2017 to 2026
$78.4M
UT Southwestern Center for Translational MedicineUL1TR003163 · NCATS · UT SOUTHWESTERN MEDICAL CENTER · PI TOTO, ROBERT DANIEL · 2021 to 2025
$39.3M
The University of Rochester's Clinical and Translational Science InstituteUL1TR002001 · NCATS · UNIVERSITY OF ROCHESTER · PI WILSON, KAREN M., ZAND, MARTIN S · 2016 to 2024
$34.6M
Kentucky Center for Clinical and Translational ScienceUL1TR001998 · NCATS · UNIVERSITY OF KENTUCKY · PI HARTMANN, KATHERINE E, KERN, PHILIP A · 2016 to 2025
$34.2M
Scripps Clinical and Translational Science HubUM1TR004407 · NCATS · SCRIPPS RESEARCH INSTITUTE, THE · PI Eric Jeffrey Topol · 2023 to 2026
$24.2M
ENACT: Translating Health Informatics Tools to Research and Clinical Decision MakingU24TR004111 · NCATS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI STEVEN E REIS, SHYAM VISWESWARAN · 2022 to 2026
$23.3M
Center for Clinical and Translational SciencesUM1TR004906 · NCATS · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI Maria Eulalia Fernandez, LORNA H. MCNEILL · 2024 to 2026
$16.7M
Open Health Natural Language Processing CollaboratoryU01TR002062 · NCATS · MAYO CLINIC ROCHESTER · PI JIANG, XIAOQIAN, LIU, HONGFANG · 2017 to 2021
$7.6M
Early Detection of Mild Cognitive Impairment, Alzheimer’s Disease and Other Dementias using EHRR01AG068007 · NIA · MAYO CLINIC ROCHESTER · PI Yonas E Geda, Sunghwan Sohn · 2020 to 2026
$3.8M
Enhancing Infrastructure for Clinical and Translational Research to Address the Opioid EpidemicU01TR002628 · NCATS · MEDICAL UNIVERSITY OF SOUTH CAROLINA · PI LENERT, LESLIE A. · 2019 to 2023
$3.7M
Predictive modeling of Alzheimer's Disease Related Dementias (ADRD) in the elderly population empowered by knowledge-driven data miningR01HG012748 · NHGRI · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI HONGFANG LIU · 2023 to 2026
$3.1M
NCATS NIH HHS L30 TR002103NCATS NIH HHS U01 TR002062NCATS NIH HHS U01 TR002628NCATS NIH HHS U24 TR004111NCATS NIH HHS UL1 TR001857NCATS NIH HHS UL1 TR001998NCATS NIH HHS UL1 TR002001NCATS NIH HHS UL1 TR002377NCATS NIH HHS UL1 TR003163NCATS NIH HHS UM1 TR004407NCATS NIH HHS UM1 TR004906NHGRI NIH HHS R01 HG012748NIA NIH HHS R01 AG060993NIA NIH HHS R01 AG068007NIA NIH HHS R01 AG077017NIA NIH HHS RF1 AG072799NIGMS NIH HHS R01 GM141476NLM NIH HHS R01 LM014306
6 · The paper itself

Abstract

Electronic health record (EHR) data are a rich and invaluable source of real-world clinical information, enabling detailed insights into patient populations, treatment outcomes, and healthcare practices. The availability of large volumes of EHR data are critical for advancing translational research and developing innovative technologies such as artificial intelligence. The Evolve to Next-Gen Accrual to Clinical Trials (ENACT) network, established in 2015 with funding from the National Center for Advancing Translational Sciences (NCATS), aims to accelerate translational research by democratizing access to EHR data for all Clinical and Translational Science Awards (CTSA) hub investigators. The present ENACT network provides access to structured EHR data, enabling cohort discovery and translational research across the network. However, a substantial amount of critical information is contained in clinical narratives, and natural language processing (NLP) is required for extracting this information to support research. To address this need, the ENACT NLP Working Group was formed to make NLP-derived clinical information accessible and queryable across the network. This article describes the implementation and deployment of NLP infrastructure across ENACT. First, we describe the formation and goals of the Working Group, the practices and logistics involved in implementation and deployment, and the specific NLP tools and technologies utilized. Then, we describe how we extended the ENACT ontology to standardize and query NLP-derived data, as well as how we conducted multisite evaluations of the NLP algorithms. Finally, we reflect on the experience and lessons learnt, which may be useful for other national data networks that are deploying NLP to unlock the potential of clinical text for research.

Indexed as

electronic health recordsenactnatural language processingnetworktranslational research

Identifiers

PMID39974073
PMCPMC11839006

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.