{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T08:43:24Z","timestamp":1748594604116,"version":"3.37.3"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2022,10,12]],"date-time":"2022-10-12T00:00:00Z","timestamp":1665532800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"Mayo Clinic Center for Individualized Medicine, Mayo Clinic Division of Digital Health Sciences","award":["5000821-5500001377","75N97019P00280","776-01280-000-107"],"award-info":[{"award-number":["5000821-5500001377","75N97019P00280","776-01280-000-107"]}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35HG011899"],"award-info":[{"award-number":["R35HG011899"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Departments of Pediatrics and Biomedical Informatics of the Ohio State University College of Medicine"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Despite the increasing evidence of utility of genomic medicine in clinical practice, systematically integrating genomic medicine information and knowledge into clinical systems with a high-level of consistency, scalability and computability remains challenging. A comprehensive terminology is required for relevant concepts and the associated knowledge model for representing relationships. In this study, we leveraged PharmGKB, a comprehensive pharmacogenomics (PGx) knowledgebase, to formulate a terminology for drug response phenotypes that can represent relationships between genetic variants and treatments. We evaluated coverage of the terminology through manual review of a randomly selected subset of 200 sentences extracted from genetic reports that contained concepts for \u2018Genes and Gene Products\u2019 and \u2018Treatments\u2019.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Results showed that our proposed drug response phenotype terminology could cover 96% of the drug response phenotypes in genetic reports. Among 18\u200a653 sentences that contained both \u2018Genes and Gene Products\u2019 and \u2018Treatments\u2019, 3011 sentences were able to be mapped to a drug response phenotype in our proposed terminology, among which the most discussed drug response phenotypes were response (994), sensitivity (829) and survival (332). In addition, we were able to re-analyze genetic report context incorporating the proposed terminology and enrich our previously proposed PGx knowledge model to reveal relationships between genetic variants and treatments. In conclusion, we proposed a drug response phenotype terminology that enhanced structured knowledge representation of genomic medicine.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac646","type":"journal-article","created":{"date-parts":[[2022,10,10]],"date-time":"2022-10-10T21:31:20Z","timestamp":1665437480000},"page":"5279-5287","source":"Crossref","is-referenced-by-count":1,"title":["Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2874-8136","authenticated-orcid":false,"given":"Yiqing","family":"Zhao","sequence":"first","affiliation":[{"name":"Department of Artificial Intelligence and Informatics, Mayo Clinic , Rochester, MN 55905, USA"}]},{"given":"Matthew","family":"Brush","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO 80045, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2638-3081","authenticated-orcid":false,"given":"Chen","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Mayo Clinic , Rochester, MN 55905, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2502-8961","authenticated-orcid":false,"given":"Alex H","family":"Wagner","sequence":"additional","affiliation":[{"name":"The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children\u2019s Hospital , Columbus, OH 43205, USA"},{"name":"Department of Pediatrics, The Ohio State University College of Medicine , Columbus, OH 43210, USA"},{"name":"Department of Biomedical Informatics, The Ohio State University College of Medicine , Columbus, OH 43210, USA"}]},{"given":"Hongfang","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Artificial Intelligence and Informatics, Mayo Clinic , Rochester, MN 55905, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9673-5612","authenticated-orcid":false,"given":"Robert R","family":"Freimuth","sequence":"additional","affiliation":[{"name":"Department of Artificial Intelligence and Informatics, Mayo Clinic , Rochester, MN 55905, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,10,12]]},"reference":[{"key":"2022113016210904000_btac646-B1","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/ng0407-426","article-title":"PharmGKB: a logical home for knowledge relating genotype to drug response phenotype","volume":"39","author":"Altman","year":"2007","journal-title":"Nat. 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