{"doi":"10.1093/jamia/ocac063","title":"Design and validation of a FHIR-based EHR-driven phenotyping toolbox","abstract":"OBJECTIVES: 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. MATERIALS AND METHODS: 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. RESULTS: 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%). CONCLUSIONS: 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.","journal":"Journal of the American Medical Informatics Association","year":2022,"id":264267,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":12,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9212,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":251749,"name":"Jennifer A. Pacheco","orcid":"0000-0001-8021-5818","position":1,"is_corresponding":false},{"id":394671,"name":"Prakash Adekkanattu","orcid":"0000-0003-1125-1449","position":2,"is_corresponding":false},{"id":394672,"name":"Evan Sholle","orcid":"0000-0001-9518-4399","position":3,"is_corresponding":false},{"id":807068,"name":"Sajjad Abedian","orcid":"0000-0002-0411-5185","position":4,"is_corresponding":false},{"id":492393,"name":"Daniel J. Stone","orcid":"0000-0003-4506-0712","position":5,"is_corresponding":false},{"id":889897,"name":"David Knaack","orcid":null,"position":6,"is_corresponding":false},{"id":921879,"name":"Jie Xu","orcid":"0000-0001-7682-4776","position":7,"is_corresponding":false},{"id":394674,"name":"Zhenxing Xu","orcid":"0000-0001-9515-523X","position":8,"is_corresponding":false},{"id":85506,"name":"Yifan Peng","orcid":"0000-0001-9309-8331","position":9,"is_corresponding":false},{"id":921880,"name":"Natalie C. Benda","orcid":"0000-0002-3256-0243","position":10,"is_corresponding":false},{"id":875219,"name":"Fei Wang","orcid":"0000-0001-5768-7323","position":11,"is_corresponding":false},{"id":58247,"name":"Yuan Luo","orcid":"0000-0003-0195-7456","position":12,"is_corresponding":false},{"id":444276,"name":"Guoqian Jiang","orcid":"0000-0003-2940-0019","position":13,"is_corresponding":false},{"id":255218,"name":"Jyotishman Pathak","orcid":"0000-0002-4856-410X","position":14,"is_corresponding":false},{"id":394676,"name":"Luke V. Rasmussen","orcid":"0000-0002-4497-8049","position":15,"is_corresponding":false},{"id":394669,"name":"Pascal Brandt","orcid":"0000-0001-5116-0555","position":0,"is_corresponding":true}],"reference_count":55,"raw_metadata":null,"created_at":"2026-07-19T00:26:37.567338Z","pmid":"35799370","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}