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Development of Data Infrastructure for Use of Electronic Health Records (EHRs) in Comparative Effectiveness Research (CER)

Establishing an infrastructure for the use of electronic health records in clinical comparative effectiveness research.
  • Office of the National Coordinator for Health Information Technology (ONC)
  • National Institutes of Health's National Library of Medicine (NLM)


Start Date
  • NLM FY 2012: 06/01/2012
  • ONC FY 2012: 08/29/2012
  • ONC FY 2013: 07/15/2013
  • NLM FY 2013: 07/20/2013


  • Standardized Collection of Standardized Clinical Data
  • Use of Enhanced Publicly-Funded Data Systems for Research


STATUS: Completed Project


It is challenging to define and collect patient data (e.g., lab test results, marital status, and patient-reported depression) in a standardized way in different comparative effectiveness research (CER) studies. This makes it difficult to enable the comparison of results and facilitate the use of electronic health record (EHR) systems as a source of valid CER data.


At the onset of this project, various clinical and health service research groups were already engaged in independent initiatives to standardize electronic data collection. Work was needed to build on these individual efforts to make it easier to conduct CER in diverse community health care settings, reduce data collection burden on health care providers and patients, and make site-specific modifications to EHR system capabilities in order to enable community participation. The infrastructure that would accommodate this goal consists of two components: 1) an authoritative repository to maintain and distribute up-to-date common data elements (CDEs) and patient assessment specifications with underlying terminology values sets for researchers and EHR developers: and 2) a standardized mechanism that would enable an EHR to capture structured data for a specified use case. With this infrastructure in place, researchers would readily have access to standardized electronic versions of data collection instruments relevant to CER.

Project Objectives:

  • Select and require the use of health information technology (IT) standards-based CDEs and patient assessment instruments in CER and patient-centered outcomes research (PCOR).

  • Develop and validate a health IT standards-based extensible electronic case report form (eCRF) to be used within EHRs to enable efficient capture of data on individual patients for specified use cases. This data will be merged with comparable data for other relevant patients and used in CER.

  • Enhance health IT standards infrastructure to support effective maintenance, distribution, and use of the definitions of CDEs and patient assessment instruments, with particular emphasis on the standard terminology value sets required to define them.

  • Establish the standards, services, and policies that integrate PCOR activities into the clinical health IT.


  • ONC’s role in this project was to identify a community of public and private stakeholder groups and facilitate their active participation and contribution to the identification and development of standards through a public and virtual platform called the Standards & Interoperability Framework (S&I). Through this initiative, ONC developed CDEs and the standards for eCRF structures/templates in a human-readable and machine-readable format. During the project’s timeframe, lack of consensus among the project’s national stakeholders precluded the identification of the particular CDEs that could population any eCRF. Stakeholder consensus was crucial, and it was later accomplished. The results of this endeavor were the initial entries into the NIH/NLM’s CDE Repository.

  • The NLM created and populated the NIH CDE Repository. The NIH CDE Repository has been designed to provide access to structured human and machine-readable definitions of data elements that have been recommended or required by NIH Institutes and Centers and other organizations for use in research and for other purposes. The CDE Repository currently contains 12 classifications of CDEs totaling 1,131,344 elements across the classifications.



  • The project team published a journal article in December 2016 in Clinical Trials titled, “Improving the Value of Clinical Research Through the Use of Common Data Elements.” The article can be found here:



Below is a list of ASPE-funded PCORTF projects that are related to this project

Expanding Data Collection for the National Program of Cancer Registries (NPCR) for Comparative Effectiveness Research (CER) – Enhanced data collection and data linkages between central cancer registries and other health related datasets can provide researchers with essential real-world and population-based data for CER. This project built upon previous funding provided to central cancer registries operated by 10 states—part of the National Program of Cancer Registries (NPCR)—to collect detailed treatment and outcomes data from electronic data sources. The PCORTF funding extended longitudinal data collection for a subset of cancer patients in these 10 states, enabling patient-level CER of cancer outcomes, and to improve the tools and timeliness of cancer reporting to the Centers for Disease Control.

Strengthening and Expanding the Community Health Applied Research Network (CHARN) Registry to Conduct Patient-Centered Outcomes Research (PCOR) – CHARN is a network of the Health Resources and Services Administration’s (HRSA) community health centers (CHCs) and universities that was established in 2010 to create an infrastructure for this safety-net community to carry out patient-centered outcomes research (PCOR), including observational and interventional studies among underserved populations, ultimately leading to improved patient care and outcomes. To realize the full potential of the CHARN infrastructure for information sharing and research, CHARN wanted to expand and enhance its data registries and to make its data available to non-CHARN researchers conducting PCOR.