Development of the Centralized Interactive Phenomics Resource (CIPHER) Standard for Electronic Health Data-Based Phenomics Knowledgebase

The development of phenotypes using electronic health records is a resource intensive process. Therefore, the cataloging of phenotype algorithm metadata for reuse is critical to accelerate clinical research. The Department of Veterans Affairs Office of Research and Development has developed a phenomics knowledgebase library, CIPHER (Centralized Interactive Phenomics Research), which improves upon existing phenomics library models to help advance innovation in clinical research by using the CIPHER phenotype collection standard. The CIPHER standard was iteratively developed with phenomics experts and has been used to capture over 5,000 phenotypes. We describe the development of the CIPHER standard for phenotype metadata collection, its current application to the largest healthcare system in the United States, and the future expansion of the CIPHER knowledgebase as a public resource for phenotyping. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement CIPHER is funded by the Department of Veterans Affairs Office of Research and Development ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present work are contained in the manuscript