{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T08:12:41Z","timestamp":1777968761712,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"5","funder":[{"name":"U.S. Department of Veterans Affairs Office of Research and Development"},{"name":"U.S. Department of Veterans Affairs or the United States Government"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 (VA) has developed a standard for phenotype metadata collection which is currently used in the VA phenomics knowledgebase library, CIPHER (Centralized Interactive Phenomics Resource), to capture over 5000 phenotypes. The CIPHER standard improves upon existing phenotype library metadata collection by capturing the context of algorithm development, phenotyping method used, and approach to validation. While the standard was iteratively developed with VA phenomics experts, it is applicable to the capture of phenotypes across healthcare systems. We describe the framework of the CIPHER standard for phenotype metadata collection, the rationale for its development, and its current application to the largest healthcare system in the United States.<\/jats:p>","DOI":"10.1093\/jamia\/ocad030","type":"journal-article","created":{"date-parts":[[2023,3,8]],"date-time":"2023-03-08T00:19:37Z","timestamp":1678234777000},"page":"958-964","source":"Crossref","is-referenced-by-count":24,"title":["Framework of the Centralized Interactive Phenomics Resource (CIPHER) standard for electronic health data-based phenomics knowledgebase"],"prefix":"10.1093","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5872-359X","authenticated-orcid":false,"given":"Jacqueline","family":"Honerlaw","sequence":"first","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuk-Lam","family":"Ho","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"Fontin","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey","family":"Gosian","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monika","family":"Maripuri","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Murray","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rahul","family":"Sangar","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashley","family":"Galloway","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"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, Texas, USA"},{"name":"Department of Medicine, Baylor College of Medicine , Houston, Texas, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stacey B","family":"Whitbourne","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"},{"name":"Department of Medicine, Harvard Medical School , Boston, Massachusetts, USA"},{"name":"Division of Aging, Department of Medicine, Brigham and Women's Hospital , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan P","family":"Casas","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"},{"name":"Department of Medicine, Harvard Medical School , Boston, Massachusetts, USA"},{"name":"Division of Aging, Department of Medicine, Brigham and Women's Hospital , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"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, District of Columbia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David R","family":"Gagnon","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"},{"name":"Department of Biostatistics, School of Public Health, Boston University , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianxi","family":"Cai","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"},{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, Massachusetts, USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katherine P","family":"Liao","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"},{"name":"Department of Medicine, Harvard Medical School , Boston, Massachusetts, USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, Massachusetts, USA"},{"name":"Division of Rheumatology, Inflammation, and Immunity, Brigham and Women\u2019s Hospital , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J Michael","family":"Gaziano","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"},{"name":"Department of Medicine, Harvard Medical School , Boston, Massachusetts, USA"},{"name":"Division of Aging, Department of Medicine, Brigham and Women's Hospital , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sumitra","family":"Muralidhar","sequence":"additional","affiliation":[{"name":"Office of Research and Development, Veterans Health Administration , Washington, District of Columbia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1727-7076","authenticated-orcid":false,"given":"Kelly","family":"Cho","sequence":"additional","affiliation":[{"name":"Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System , Boston, Massachusetts, USA"},{"name":"Department of Medicine, Harvard Medical School , Boston, Massachusetts, USA"},{"name":"Division of Aging, Department of Medicine, Brigham and Women's Hospital , Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,3,7]]},"reference":[{"key":"2023041909005172400_ocad030-B1","author":"Veterans Administration","year":"2022"},{"issue":"4","key":"2023041909005172400_ocad030-B2","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1097\/NAQ.0000000000000118","article-title":"The veterans affairs's corporate data warehouse: uses and implications for nursing research and practice","volume":"39","author":"Price","year":"2015","journal-title":"Nurs Adm Q"},{"issue":"2","key":"2023041909005172400_ocad030-B3","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1002\/jts.22399","article-title":"Validation of an electronic medical record-based algorithm for identifying posttraumatic stress disorder in U.S. veterans","volume":"32","author":"Harrington","year":"2019","journal-title":"J Trauma Stress"},{"issue":"12","key":"2023041909005172400_ocad030-B4","doi-asserted-by":"crossref","first-page":"e033962","DOI":"10.1136\/bmjopen-2019-033962","article-title":"Do oncology researchers adhere to reproducible and transparent principles? 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