Observational Research with EHR Data

Communities, Platforms, and Organizations

All of Us

The All of Us Research Program seeks to accelerate health research and medical breakthroughs by collecting and analyzing data from one million or more individuals living in the United States. The program was designed to engage historically underrepresented groups in biomedical research, with an emphasis on community outreach and transparency in research.

Research participants self-selectively enroll and share their data with the program. Data may include electronic health records (EHR), data from wearable devices, physical measurements, surveys, and whole genome sequencing and genotyping arrays. The data are curated and made available within a secure data repository. [1]

Anyone may visit the Research Hub to learn about the data and explore aggregated participant data with the Data Browser. Researchers may register for access to the Researcher Workbench and conduct research within the secure environment.

Brown University researchers interested in accessing the the All of Us Researcher Workbench should review the Brown University Library website for more information.

i2b2

Established in 2004, Informatics for Integrating Biology and the Bedside (i2b2) is an NIH-funded National Center for Biomedical Computing (NCBC) based in Boston, MA. i2b2 seeks to enable clinical researchers to accelerate the translation of genomic and clinical findings into novel diagnostics, prognostics, and therapeutics through the creation of software and a methodological framework. [2]

The i2b2 tranSMART Foundation is "an Open-Source Community Enabling collaboration for precision medicine, through sharing, integration, standardization, and analysis of heterogeneous data from healthcare and research." [3]

4CE

Led by the i2b2 international academics users group, the Consortium for Clinical Characterization of COVID-19 by EHR (4CE) is an international consortium for electronic health record (EHR) data-driven studies of the COVID-19 pandemic. 4CE seeks to inform doctors, epidemiologists, and the public about COVID-19 treatments and patient outcomes. [4]

National Clinical Cohort Collaborative (N3C)

The National Clinical Cohort Collaborative (N3C) has four enclaves (as of 10/18/2024): N3C COVID, N3C Education, N3C Cancer, and N3C Renal. The Education Enclave provides simulated datasets for researchers to develop and practice the skills needed to analyze real-world data. The Cancer and Renal Enclaves are part of a broader feasibility testing initiative being done to refine the overall governance, data linkage, and institutional partnership components of N3C. These domain-specific enclaves are governed by their data contributors.

N3Covid

"The National COVID Cohort Collaborative (N3C) is a collaboration among the NCATS-supported Clinical and Translational Science Awards (CTSA) Program hubs, distributed clinical data networks (PCORnet, OHDSI, ACT, TriNetX), and other partner organizations, with overall stewardship by NIH’s National Center for Advancing Translational Sciences (NCATS). The N3C aims to improve the efficiency and accessibility of analyses with COVID-19 clinical data, expand our ability to analyze and understand COVID, and demonstrate a novel approach for collaborative data sharing." [5]

OHDSI

Founded in 2014, the Observational Health Data Sciences and Informatics (OHDSI, pronounced “Odyssey”) is a multi-stakeholder, interdisciplinary, open-science collaborative. [6] OHDSI's mission is "To improve health by empowering a community to collaboratively generate the evidence that promotes better health decisions and better care." [7] OHDSI produces large-scale, real-world analytics through an international network of researchers and observational health databases and a central coordinating center at Columbia University. [8]

For more information about OHDSI, refer to OHDSI's website and the Book of OHDSI.

PCORI

The Patient-Centered Outcomes Research Institute (PCORI®) is an independent, non-profit research funding organization that funds comparative clinical effectiveness research (CER). [9]

For more information about PCORI, please visit their website.

PCORnet

The National Patient-Centered Clinical research Network, PCORnet®, is a distributed network of organizations and standardized health data for patient-centered health research, particularly CER. PCORnet® was developed with funding from the Patient-Centered Outcomes Research Institute® (PCORI®). [10]

For more information, please see their website.

TriNetX

TriNetX is a global health research network which enables researchers to perform large-scale observational studies with real-world data. Data from electronic health records (EHRs) are aggregated, anonymized, and made available through a secure analytics platform. Through TriNetX, researchers can assess study feasibility and identify eligible patient cohorts. TriNetX is used by pharmaceutical companies and academic and clinical research institutions to perform cohort analyses, conduct comparative effectiveness and epidemiological studies. [11]

For more information, visit their website.

References

  1. All of Us. [Accessed 2024-11-11]; https://allofus.nih.gov/

  2. i2b2. [Accessed 2024-11-11]; https://www.i2b2.org/about/index.html

  3. i2b2 tranSMART Foundation. [Accessed 2024-11-11]; https://i2b2transmart.org/

  4. 4CE. [Accessed 2024-11-11]; https://covidclinical.net/index.html

  5. N3C. (n.d.). Covid About. [Accessed 2024-10-07]; https://covid.cd2h.org/about/

  6. OHDSI Who We Are. [Accessed 2024-09-30]; https://ohdsi.org/who-we-are/

  7. OHDSI Mission, Vision & Values. [Accessed 2024-09-30]; https://ohdsi.org/who-we-are/mission-vision-values/

  8. Hripcsak G, Duke JD, Shah NH, Reich CG, Huser V, Schuemie MJ, Suchard MA, Park RW, Wong IC, Rijnbeek PR, van der Lei J, Pratt N, Norén GN, Li YC, Stang PE, Madigan D, Ryan PB. Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. Stud Health Technol Inform. 2015;216:574-8. PMID: 26262116; PMCID: PMC4815923.

  9. PCORI. [Accessed 2024-11-11]; https://www.pcori.org/

  10. PCORnet. [Accessed 2024-11-11]; https://pcornet.org/

  11. TriNetX. [Accessed 2024-11-11]; https://trinetx.com/#signe

Resources

Books

  • O’Neil ST, Beasley W, Loomba J, Patrick S, Wilkins KJ, Crowley KM., Anzalone, AJ (Eds.) (2023). The Researcher’s Guide to N3C: A National Resource for Analyzing Real-World Health Data. DOI: 10.5281/zenodo.7749367

Articles

  • All of Us Research Program Genomics Investigators. Genomic data in the All of Us Research Program. Nature. 2024 Mar;627(8003):340-346. doi: 10.1038/s41586-023-06957-x. Epub 2024 Feb 19. PMID: 38374255; PMCID: PMC10937371.

  • Cronin RM, Jerome RN, Mapes B, Andrade R, Johnston R, Ayala J, Schlundt D, Bonnet K, Kripalani S, Goggins K, Wallston KA, Couper MP, Elliott MR, Harris P, Begale M, Munoz F, Lopez-Class M, Cella D, Condon D, AuYoung M, Mazor KM, Mikita S, Manganiello M, Borselli N, Fowler S, Rutter JL, Denny JC, Karlson EW, Ahmedani BK, O'Donnell CJ; Vanderbilt University Medical Center Pilot Team, and the Participant Provided Information Committee. Development of the Initial Surveys for the All of Us Research Program. Epidemiology. 2019 Jul;30(4):597-608. doi: 10.1097/EDE.0000000000001028. PMID: 31045611; PMCID: PMC6548672.

  • Turner SP, Pompea ST, Williams KL, Kraemer DA Jr, Sholle ET, Chen C, Cole CL, Kaushal R, Campion TR Jr. Implementation of Informatics to Support the NIH All of Us Research Program in a Healthcare Provider Organization. AMIA Jt Summits Transl Sci Proc. 2019 May 6;2019:602-609. PMID: 31259015; PMCID: PMC6568061.

  • Doerr M, Grayson S, Moore S, Suver C, Wilbanks J, Wagner J. Implementing a universal informed consent process for the All of Us Research Program. Pac Symp Biocomput. 2019;24:427-438. PMID: 30963079; PMCID: PMC6417826.

  • Haendel MA, Chute CG, Bennett TD, Eichmann DA, Guinney J, Kibbe WA, Payne PRO, Pfaff ER, Robinson PN, Saltz JH, Spratt H, Suver C, Wilbanks J, Wilcox AB, Williams AE, Wu C, Blacketer C, Bradford RL, Cimino JJ, Clark M, Colmenares EW, Francis PA, Gabriel D, Graves A, Hemadri R, Hong SS, Hripscak G, Jiao D, Klann JG, Kostka K, Lee AM, Lehmann HP, Lingrey L, Miller RT, Morris M, Murphy SN, Natarajan K, Palchuk MB, Sheikh U, Solbrig H, Visweswaran S, Walden A, Walters KM, Weber GM, Zhang XT, Zhu RL, Amor B, Girvin AT, Manna A, Qureshi N, Kurilla MG, Michael SG, Portilla LM, Rutter JL, Austin CP, Gersing KR; N3C Consortium. The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. J Am Med Inform Assoc. 2021 Mar 1;28(3):427-443. doi: 10.1093/jamia/ocaa196. PMID: 32805036; PMCID: PMC7454687.

  • Suver C, Harper J, Loomba J, Saltz M, Solway J, Anzalone AJ, Walters K, Pfaff E, Walden A, McMurry J, Chute CG, Haendel M. The N3C governance ecosystem: A model socio-technical partnership for the future of collaborative analytics at scale. J Clin Transl Sci. 2023 Nov 14;7(1):e252. doi: 10.1017/cts.2023.681. PMID: 38229902; PMCID: PMC10789985.

  • Hripcsak G, Schuemie MJ, Madigan D, Ryan PB, Suchard MA. Drawing Reproducible Conclusions from Observational Clinical Data with OHDSI. Yearb Med Inform. 2021 Aug;30(1):283-289. doi: 10.1055/s-0041-1726481. Epub 2021 Apr 21. PMID: 33882595; PMCID: PMC8416226.

  • Reich C, Ostropolets A, Ryan P, Rijnbeek P, Schuemie M, Davydov A, Dymshyts D, Hripcsak G. OHDSI Standardized Vocabularies-a large-scale centralized reference ontology for international data harmonization. J Am Med Inform Assoc. 2024 Feb 16;31(3):583-590. doi: 10.1093/jamia/ocad247. PMID: 38175665; PMCID: PMC10873827.

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