{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,23]],"date-time":"2025-04-23T00:54:42Z","timestamp":1745369682065,"version":"3.37.3"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000092","name":"National Library of Medicine","doi-asserted-by":"publisher","award":["R01LM010685"],"id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["R01HG012657"],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Phecodes are widely used and easily adapted phenotypes based on International Classification of Diseases codes. The current version of phecodes (v1.2) was designed primarily to study common\/complex diseases diagnosed in adults; however, there are numerous limitations in the codes and their structure.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Here, we present phecodeX, an expanded version of phecodes with a revised structure and 1,761 new codes. PhecodeX adds granularity to phenotypes in key disease domains that are under-represented in the current phecode structure\u2014including infectious disease, pregnancy, congenital anomalies, and neonatology\u2014and is a more robust representation of the medical phenome for global use in discovery research.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n phecodeX is available at https:\/\/github.com\/PheWAS\/phecodeX.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad655","type":"journal-article","created":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T17:27:01Z","timestamp":1699291621000},"source":"Crossref","is-referenced-by-count":15,"title":["Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2866-3562","authenticated-orcid":false,"given":"Megan M","family":"Shuey","sequence":"first","affiliation":[{"name":"Department of Medicine, Vanderbilt University Medical Center , Nashville, TN 37203, United States"},{"name":"Vanderbilt Genetics Institute, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5048-9540","authenticated-orcid":false,"given":"William W","family":"Stead","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Ida","family":"Aka","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"April L","family":"Barnado","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Julie A","family":"Bastarache","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Elly","family":"Brokamp","sequence":"additional","affiliation":[{"name":"Vanderbilt Genetics Institute, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Meredith","family":"Campbell","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Virginia Commonwealth University , Richmond, VA 23219, United States"}]},{"given":"Robert J","family":"Carroll","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Jeffrey A","family":"Goldstein","sequence":"additional","affiliation":[{"name":"Department of Pathology, Northwestern Feinberg School of Medicine , Chicago, IL 60611, United States"}]},{"given":"Adam","family":"Lewis","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Beth A","family":"Malow","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Jonathan D","family":"Mosley","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University Medical Center , Nashville, TN 37203, United States"},{"name":"Vanderbilt Genetics Institute, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Travis","family":"Osterman","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Dolly A","family":"Padovani-Claudio","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Vanderbilt University Medical Center , Nashville, TN 37232, United States"}]},{"given":"Andrea","family":"Ramirez","sequence":"additional","affiliation":[{"name":"All of Us Research Program, National Institutes of Health , Bethesda, MD 20892, United States"}]},{"given":"Dan M","family":"Roden","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University Medical Center , Nashville, TN 37203, United States"},{"name":"Vanderbilt Genetics Institute, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Bryce A","family":"Schuler","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Edward","family":"Siew","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Jennifer","family":"Sucre","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Isaac","family":"Thomsen","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Rory J","family":"Tinker","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Sara","family":"Van Driest","sequence":"additional","affiliation":[{"name":"All of Us Research Program, National Institutes of Health , Bethesda, MD 20892, United States"},{"name":"Department of Pediatrics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Colin","family":"Walsh","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Jeremy L","family":"Warner","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Quinn S","family":"Wells","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Lee","family":"Wheless","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University Medical Center , Nashville, TN 37203, United States"}]},{"given":"Lisa","family":"Bastarache","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203, United 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