{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T02:46:06Z","timestamp":1780109166251,"version":"3.54.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"5","funder":[{"name":"Department of Veterans Affairs Office of Research and Development"},{"name":"Office of Science of the US Department of Energy"},{"name":"Department of Veterans Affairs Office of Information Technology Inter-Agency","award":["VA118-16-M-1062"],"award-info":[{"award-number":["VA118-16-M-1062"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,4,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Objective<\/jats:title>\n                  <jats:p>Development of clinical phenotypes from electronic health records (EHRs) can be resource intensive. Several phenotype libraries have been created to facilitate reuse of definitions. However, these platforms vary in target audience and utility. We describe the development of the Centralized Interactive Phenomics Resource (CIPHER) knowledgebase, a comprehensive public-facing phenotype library, which aims to facilitate clinical and health services research.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Materials and Methods<\/jats:title>\n                  <jats:p>The platform was designed to collect and catalog EHR-based computable phenotype algorithms from any healthcare system, scale metadata management, facilitate phenotype discovery, and allow for integration of tools and user workflows. Phenomics experts were engaged in the development and testing of the site.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The knowledgebase stores phenotype metadata using the CIPHER standard, and definitions are accessible through complex searching. Phenotypes are contributed to the knowledgebase via webform, allowing metadata validation. Data visualization tools linking to the knowledgebase enhance user interaction with content and accelerate phenotype development.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Discussion<\/jats:title>\n                  <jats:p>The CIPHER knowledgebase was developed in the largest healthcare system in the United States and piloted with external partners. The design of the CIPHER website supports a variety of front-end tools and features to facilitate phenotype development and reuse. Health data users are encouraged to contribute their algorithms to the knowledgebase for wider dissemination to the research community, and to use the platform as a springboard for phenotyping.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>CIPHER is a public resource for all health data users available at https:\/\/phenomics.va.ornl.gov\/ which facilitates phenotype reuse, development, and dissemination of phenotyping knowledge.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jamia\/ocae042","type":"journal-article","created":{"date-parts":[[2024,3,14]],"date-time":"2024-03-14T05:26:26Z","timestamp":1710393986000},"page":"1126-1134","source":"Crossref","is-referenced-by-count":11,"title":["Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users"],"prefix":"10.1093","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5872-359X","authenticated-orcid":false,"given":"Jacqueline","family":"Honerlaw","sequence":"first","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuk-Lam","family":"Ho","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Fontin","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Murray","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley","family":"Galloway","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Heise","sequence":"additional","affiliation":[{"name":"Oak Ridge National Laboratory (ORNL) , Oak Ridge, TN 37830, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keith","family":"Connatser","sequence":"additional","affiliation":[{"name":"Oak Ridge National Laboratory (ORNL) , Oak Ridge, TN 37830, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Davies","sequence":"additional","affiliation":[{"name":"Oak Ridge National Laboratory (ORNL) , Oak Ridge, TN 37830, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey","family":"Gosian","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monika","family":"Maripuri","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Russo","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"},{"name":"Department of Computer Science, Landmark College , Putney, VT 05346, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rahul","family":"Sangar","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vidisha","family":"Tanukonda","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Atlanta Healthcare System , Decatur, GA 30033, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward","family":"Zielinski","sequence":"additional","affiliation":[{"name":"Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"},{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maureen","family":"Dubreuil","sequence":"additional","affiliation":[{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"},{"name":"Section of Rheumatology, Boston University Chobanian and Avedisian School of Medicine , Boston, MA 02118, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0973-5639","authenticated-orcid":false,"given":"Andrew J","family":"Zimolzak","sequence":"additional","affiliation":[{"name":"Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center , Houston, TX 77030, United States"},{"name":"Department of Medicine, Baylor College of Medicine , Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vidul A","family":"Panickan","sequence":"additional","affiliation":[{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Su-Chun","family":"Cheng","sequence":"additional","affiliation":[{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stacey B","family":"Whitbourne","sequence":"additional","affiliation":[{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"},{"name":"Million Veteran Program (MVP) Coordinating Center, VA Boston , Boston, MA 02111, United States"},{"name":"Division of Aging, Department of Medicine, Brigham and Women\u2019s Hospital , Boston, MA 02115, United States"},{"name":"Department of Medicine, Harvard Medical School , Boston, MA 02115, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R","family":"Gagnon","sequence":"additional","affiliation":[{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"},{"name":"Department of Biostatistics, Boston University School of Public Health , Boston, MA 02118, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianxi","family":"Cai","sequence":"additional","affiliation":[{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, United States"},{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA 02115, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine P","family":"Liao","sequence":"additional","affiliation":[{"name":"VA Boston Healthcare System , Boston, MA 02111, United States"},{"name":"Department of Medicine, Harvard Medical School , Boston, MA 02115, United States"},{"name":"Division of Rheumatology, Inflammation, and Immunity, Brigham and Women\u2019s Hospital , Boston, MA 02115, United States"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1459-9638","authenticated-orcid":false,"given":"Rachel B","family":"Ramoni","sequence":"additional","affiliation":[{"name":"Office of Research and Development, Veterans Health Administration , Washington, DC 20002, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J 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