Launching in June 2023, the public website for the VA’s centralized interactive phenomics resource, known as CIPHER, provides an online knowledge-sharing platform designed to improve the use of electronic health records (EHRs) for research and clinical care.
“CIPHER has revolutionized the way researchers use EHR data in research by providing a standardized and streamlined platform to look up phenotypes, gain an edge in healthcare research, and support portability across healthcare systems,” said Dr. Sumitra Muralidhar, director of the VA Million Veteran Program and lead sponsor of CIPHER.
The CIPHER library contains definitions of computable phenotypes—clinical conditions, diseases, or traits derived from health data—data mappings, programming code, and data visualization tools. The library is open to both VA and non-VA researchers and enables broader sharing of research findings within the scientific community. The goal of this universal access is to accelerate research and facilitate the use of complex health data to improve care for veterans and others.
The platform serves as an online searchable library of EHR-based phenotypes that are anonymized to protect patient privacy – VA has strict safeguards in place to protect veterans’ privacy. Data sources may include health registries, claims data, physician notes, and patient surveys.
VA is the largest integrated healthcare system in the United States, with over 170 medical centers. Its EHR system contains billions of records, including laboratory tests, diagnoses, and medical procedures. EHR-based phenotypes can help standardize health definitions across different populations, research projects, and hospital operations.
EHR-based phenotypes are used in research, quality improvement initiatives, and clinical patient care. However, phenotype creation can be time-intensive due to disparate data sources and healthcare systems. The process also requires expertise in handling large, complex data sets. CIPHER helps address these challenges by optimizing healthcare data sources and establishing standards for capturing phenotype definitions. To date, the CIPHER platform has cataloged more than 6,000 phenotypes using an internally developed phenotype capture standard.
CIPHER was created through a VA partnership with the U.S. Department of Energy’s Oak Ridge National Laboratory. The collaboration leverages the laboratory’s computational resources and expertise on large, complex data sets.
“We expect the CIPHER knowledge base to improve the accuracy and efficiency of research using code-based phenotypes. Contributing to CIPHER will expand the impact of our work by making our phenotypes more readily available to other researchers,” said Maureen Dubreuil, MD, a rheumatologist at the VA Boston Healthcare System and associate professor of medicine at Boston University Chobanian & Avedisian School of Medicine.
CIPHER is available to the public at phenomics.va.ornl.gov. Details about the resources and standards that enable CIPHER can be found in the Journal of the American Medical Informatics Association (CIPHER Resources, PMID: 38481028; CIPHER Metadata Standard, PMID: 36882092).
