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The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment 

This on-demand webinar does not offer CE credit.

A JAMIA Journal Club webinar – part of AMIA’s COVID-19 Resource Center

Haendel M., Chute C., Gersing K., The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment [published online ahead of print, 2020 Aug 17]. J Am Med Inform Assoc. 2020;ocaa196. doi:10.1093/jamia/ocaa196.

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Melissa A. Haendel, PhD
Professor of Medical Informatics and Clinical Epidemiology, School of Medicine
Director of the Center for Data to Health, Oregon Clinical and Translational Research Institute
Biomedical Informatics Graduate Program, School of Medicine
Christopher G. Chute, MD, DrPH
Bloomberg Distinguished Professor
Johns Hopkins Bloomberg School of Public Health


Maryam Zolnoori , PhD
Postdoctoral Research Fellow
Department of Digital Health Sciences and Department of Psychiatry and Psychology
Mayo Clinic
Hannah Burkhardt
PhD Candidate, University of Washington School of Medicine
Biomedical Informatics and Medical Education


Yizhen Zhong
PhD candidate in Computational biology
Northwestern University

Statement of Purpose

COVID-19 poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical data are abundant, these are largely inaccessible to outside researchers. Statistical, machine learning, and causal analyses are most successful with largescale data beyond what is available in any given organization. Here, we introduce the National COVID Cohort Collaborative (N3C), an open science community focused on analyzing patient level data from many centers. The Clinical and Translational Science Award (CTSA) Program and scientific community created N3C to overcome technical, regulatory, policy, and governance barriers to sharing and harmonizing individual-level clinical data. We developed solutions to extract, aggregate, and harmonize data across organizations and data models, and created a secure data enclave to enable efficient, transparent, and reproducible collaborative analytics.

Organized in inclusive workstreams, in two months we created: legal agreements and governance for organizations and researchers; data extraction scripts to identify and ingest positive, negative, and possible COVID-19 cases; a data quality assurance and harmonization pipeline to create a single harmonized dataset; population of the secure data enclave with data, machine learning, and statistical analytics tools; dissemination mechanisms; and a synthetic data pilot to democratize data access.

The N3C has demonstrated that a multi-site collaborative learning health network can overcome barriers to rapidly build a scalable infrastructure incorporating multi-organizational clinical data for COVID-19 analytics. We expect this effort to save lives by enabling rapid collaboration among clinicians, researchers, and data scientists to identify treatments and specialized care and thereby reduce the immediate and long-term impacts of COVID-19.

Target Audience

The target audience for this activity is professionals and students interested in health informatics.

Learning Objectives

After this live activity, the participant should be better able to:

  • Understand the informatics and regulatory challenges of establishing a large-scale collection of centralized EHR data
  • Articulate the common data models used as source data for N3C integration, and how they are harmonized in the project
  • Describe the N3C data enclave, both from a security/confidential projection perspective and as a rich analytic environment

Commercial Support

No commercial support was received for this activity.

Disclosures for this Activity 

The following presenters, planners, and staff who are in a position to control the content of this activity disclose that they and their life partners have no relevant financial relationships with commercial interests: 

JAMIA Journal Club Presenters: Christopher Chute
JAMIA Journal Club planners: Hannah Burkhardt, Kirk E. Roberts, Yizhen Zhong, Maryam Zolnoori
AMIA staff: Susanne Arnold, Pesha Rubinstein

JAMIA Journal Club presenter Melissa Haendel discloses that she is founding shareholder of Pryzm Health.


Dates and Times: -
Type: Webinar
Course Format(s): On Demand