{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:08:18Z","timestamp":1740136098357,"version":"3.37.3"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,7,7]],"date-time":"2022-07-07T00:00:00Z","timestamp":1657152000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01GM105688"],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fulbright Foreign Student Program"},{"name":"South African National Research Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,16]]},"abstract":"Abstract<\/jats:title>\n \n Objectives<\/jats:title>\n To develop and validate a standards-based phenotyping tool to author electronic health record (EHR)-based phenotype definitions and demonstrate execution of the definitions against heterogeneous clinical research data platforms.<\/jats:p>\n <\/jats:sec>\n \n Materials and Methods<\/jats:title>\n We developed an open-source, standards-compliant phenotyping tool known as the PhEMA Workbench that enables a phenotype representation using the Fast Healthcare Interoperability Resources (FHIR) and Clinical Quality Language (CQL) standards. We then demonstrated how this tool can be used to conduct EHR-based phenotyping, including phenotype authoring, execution, and validation. We validated the performance of the tool by executing a thrombotic event phenotype definition at 3 sites, Mayo Clinic (MC), Northwestern Medicine (NM), and Weill Cornell Medicine (WCM), and used manual review to determine precision and recall.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n An initial version of the PhEMA Workbench has been released, which supports phenotype authoring, execution, and publishing to a shared phenotype definition repository. The resulting thrombotic event phenotype definition consisted of 11 CQL statements, and 24 value sets containing a total of 834 codes. Technical validation showed satisfactory performance (both NM and MC had 100% precision and recall and WCM had a precision of 95% and a recall of 84%).<\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n We demonstrate that the PhEMA Workbench can facilitate EHR-driven phenotype definition, execution, and phenotype sharing in heterogeneous clinical research data environments. A phenotype definition that integrates with existing standards-compliant systems, and the use of a formal representation facilitates automation and can decrease potential for human error.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/jamia\/ocac063","type":"journal-article","created":{"date-parts":[[2022,7,8]],"date-time":"2022-07-08T04:57:12Z","timestamp":1657256232000},"page":"1449-1460","source":"Crossref","is-referenced-by-count":6,"title":["Design and validation of a FHIR-based EHR-driven phenotyping toolbox"],"prefix":"10.1093","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5116-0555","authenticated-orcid":false,"given":"Pascal S","family":"Brandt","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics and Medical Education, University of Washington , Seattle, Washington, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8021-5818","authenticated-orcid":false,"given":"Jennifer 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