News Release

VA launches public research platform to optimize use of electronic health data

The CIPHER platform serves as an online searchable library of EHR-based phenotypes, data mappings, programming code, and tools for data visualization

Reports and Proceedings

Veterans Affairs Research Communications

Accelerating the use of health data


The Centralized Interactive Phenomics Resource (CIPHER) is a knowledgebase of computable electronic health records (EHR)-based phenotypes developed by the U.S. Department of Veterans Affairs (VA). 

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Credit: Department of Veteran Affairs

The Department of Veterans Affairs has launched a public-facing website for the Centralized Interactive Phenomics Resource (CIPHER), an online knowledge-sharing platform that aims to improve the use of electronic health records (EHR) for research and clinical care.

The CIPHER library contains definitions of the observable characteristics of health conditions (phenotypes), data mappings, programming code, and tools for data visualization, and is open to both VA and non-VA investigators, allowing research findings to be shared more broadly within the scientific community. The universal access will help accelerate research and facilitate the use of complex health data, leading to improved care for Veterans and others.

The information within CIPHER is de-identified and does not contain any personal identifiable information from Veterans. VA has strong safeguards in place to protect Veteran privacy.

“CIPHER has revolutionized the way researchers use EHR data in research by providing a standardized and streamlined platform to look up phenotypes, get a head start in health research, and help with portability across health systems,” said Dr. Sumitra Muralidhar, director of the VA Million Veteran Program, and lead sponsor for CIPHER.

The platform serves as an online searchable library of EHR-based phenotypes: clinical conditions, diseases, or characteristics that are taken from information within an EHR system and de-identified to maintain patient privacy. Data sources can include health registries, claims data, physician notes, and patient surveys.

VA is the largest integrated health care system in the United States, with over 170 medical centers; its EHR system contains billions of records that include laboratory tests, diagnoses, and medical procedures. EHR-based phenotypes can help standardize health definitions across different groups, research projects, and hospital operations.

EHR-based phenotypes are used in research, quality improvement initiatives, and clinical care for patients. However, creating phenotypes can be time intensive due to variation in data sources and health systems. The process also requires expertise in the use of large, complex data sets. CIPHER helps overcome those challenges by optimizing health data sources and introducing standards for collecting phenotype definitions. To date, the CIPHER platform has cataloged over 6,000 phenotypes using a phenotype collection standard that was developed in house.

CIPHER was established through a VA partnership with the U.S. Department of Energy’s Oak Ridge National Laboratory. The collaboration leverages the lab’s computational resources and expertise in large, complex datasets.

“We expect the CIPHER knowledgebase to improve the rigor and efficiency of research that uses code-based phenotypes. Contributing to CIPHER will also extend the impact of our work by making our phenotypes more readily available to other researchers,” said physician Dr. Maureen Dubreuil, VA Boston Healthcare System, and Boston University.

Learn more about CIPHER at

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