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Centralized Interactive Phenomics Resource (CIPHER)


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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). EHR based phenotypes are clinical conditions, diseases, or characteristics that are derived from information contained within EHR systems. This can include data from the clinical health records system itself, claims data, registries, surveys, or a combination of data sources. The creation of EHR-based phenotypes allows for standardization across various patient populations, electronic health systems, research projects, and operations.

CIPHER Phenotype Example

CIPHER improves upon existing phenomics library models to help advance innovation in clinical research by using the CIPHER phenotype collection standard. The CIPHER phenotype collection standard is an adaptable metadata collection method that enables reproducibility of EHR-based phenotypes. The CIPHER standard was iteratively developed with phenomics experts and has been used to capture thousands of phenotypes. This standard provides both detailed information on the phenotype algorithm and a high-level picture of the development and validation process. Its framework includes standard vocabularies, enabling the interoperability of the phenotype knowledgebase across various healthcare systems. (JAMIA 2023)

What initially began as a collective effort to drive collaboration and innovation within the largest healthcare system in the United States is now being made available as a public resource.

To learn more about CIPHER, please see our Cyberseminar: Centralized Interactive Phenomics Resource (CIPHER): Overview and Demonstration of the VA Phenomics Library (6/5/2023)- Kelly Cho, PhD, MPH; Jacqueline Honerlaw, RN, MPH


Accelerate health data innovation by providing an integrated and interactive knowledge sharing platform.


  • Provide an easy-to-use platform to develop, collect, store, and share computable phenotypes, metadata, and resources.
  • Establish and maintain a standardized and scalable metadata collection process to optimize phenotype reproducibility and interoperability across health systems.
  • Encourage and facilitate collaboration across the data science community.

CIPHER Features

  • Phenotype Knowledgebase: Browse by domain or utilize our complex search to identify and compare phenotypes to find the one most applicable for your use case.
  • Phenotype Entry Webform: You can now contribute your phenotypes by using our electronic webform and communicate directly with CIPHER through the online dashboard. Learn more about how to contribute your phenotypes to CIPHER.
  • Data Visualization Tools: Tools are available to enable users to visualize data results and to aid in development of phenotypes.

Additional Resources for VA Investigators

Please note, these resources are for VA Investigators only. You must be logged onto the VA network to access the following:


For more information on CIPHER, please contact

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Any health information on this website is strictly for informational purposes and is not intended as medical advice. It should not be used to diagnose or treat any condition.