{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:08:44Z","timestamp":1740136124750,"version":"3.37.3"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T00:00:00Z","timestamp":1722988800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24 TR004111","UL1 TR002319"],"award-info":[{"award-number":["U24 TR004111","UL1 TR002319"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>To demonstrate that 2 popular cohort discovery tools, Leaf and the Shared Health Research Information Network (SHRINE), are readily interoperable. Specifically, we adapted Leaf to interoperate and function as a node in a federated data network that uses SHRINE and dynamically generate queries for heterogeneous data models.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Materials and Methods<\/jats:title>\n                  <jats:p>SHRINE queries are designed to run on the Informatics for Integrating Biology &amp; the Bedside (i2b2) data model. We created functionality in Leaf to interoperate with a SHRINE data network and dynamically translate SHRINE queries to other data models. We randomly selected 500 past queries from the SHRINE-based national Evolve to Next-Gen Accrual to Clinical Trials (ENACT) network for evaluation, and an additional 100 queries to refine and debug Leaf\u2019s translation functionality. We created a script for Leaf to convert the terms in the SHRINE queries into equivalent structured query language (SQL) concepts, which were then executed on 2 other data models.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results and Discussion<\/jats:title>\n                  <jats:p>91.1% of the generated queries for non-i2b2 models returned counts within 5% (or \u00b15 patients for counts under 100) of i2b2, with 91.3% recall. Of the 8.9% of queries that exceeded the 5% margin, 77 of 89 (86.5%) were due to errors introduced by the Python script or the extract-transform-load process, which are easily fixed in a production deployment. The remaining errors were due to Leaf\u2019s translation function, which was later fixed.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Our results support that cohort discovery applications such as Leaf and SHRINE can interoperate in federated data networks with heterogeneous data models.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jamia\/ocae211","type":"journal-article","created":{"date-parts":[[2024,8,8]],"date-time":"2024-08-08T00:07:45Z","timestamp":1723075665000},"page":"2202-2209","source":"Crossref","is-referenced-by-count":0,"title":["Towards cross-application model-agnostic federated cohort discovery"],"prefix":"10.1093","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3598-8747","authenticated-orcid":false,"given":"Nicholas J","family":"Dobbins","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics & Medical Education, University of Washington , Seattle, WA 98195, United States"},{"name":"Biomedical Informatics & Data Science, Department of Medicine, Johns Hopkins University , Baltimore, MD 21218, United States"}]},{"given":"Michele","family":"Morris","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Pittsburgh , Pittsburgh, PA 15260, United States"}]},{"given":"Eugene","family":"Sadhu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Pittsburgh , Pittsburgh, PA 15260, United States"}]},{"given":"Douglas","family":"MacFadden","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard University , Boston, MA 02138, United States"}]},{"given":"Marc-Danie","family":"Nazaire","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard University , Boston, MA 02138, United States"}]},{"given":"William","family":"Simons","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard University , Boston, MA 02138, United States"}]},{"given":"Griffin","family":"Weber","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard University , Boston, MA 02138, United States"}]},{"given":"Shawn","family":"Murphy","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard University , Boston, MA 02138, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2079-8684","authenticated-orcid":false,"given":"Shyam","family":"Visweswaran","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Pittsburgh , Pittsburgh, PA 15260, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,8,7]]},"reference":[{"issue":"1","key":"2024092007524965400_ocae211-B1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1093\/jamia\/ocz165","article-title":"Leaf: an open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research","volume":"27","author":"Dobbins","year":"2019","journal-title":"J Am Med Inform Assoc"},{"issue":"2","key":"2024092007524965400_ocae211-B2","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1136\/jamia.2009.000893","article-title":"Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)","volume":"17","author":"Murphy","year":"2010","journal-title":"J Am Med Inform Assoc"},{"key":"2024092007524965400_ocae211-B3","doi-asserted-by":"crossref","first-page":"103253","DOI":"10.1016\/j.jbi.2019.103253","article-title":"Facilitating phenotype transfer using a common data model","volume":"96","author":"Hripcsak","year":"2019","journal-title":"J Biomed Inform"},{"issue":"Suppl 3","key":"2024092007524965400_ocae211-B4","doi-asserted-by":"crossref","first-page":"S739","DOI":"10.1007\/s11606-014-2894-x","article-title":"The Rare Diseases Clinical Research Network\u2019s organization and approach to observational research and health outcomes research","volume":"29","author":"Krischer","year":"2014","journal-title":"J Gen Intern Med"},{"key":"2024092007524965400_ocae211-B5","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/978-3-319-67144-4_6","article-title":"Facilitating clinical studies in rare diseases","author":"Gopal-Srivastava","year":"2017","journal-title":"Rare Diseases Epidemiology: Update and Overview. Advances in Experimental Medicine and Biology."},{"issue":"2","key":"2024092007524965400_ocae211-B6","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1093\/jamiaopen\/ooy033","article-title":"Accrual to Clinical Trials (ACT): a clinical and translational science award consortium network","volume":"1","author":"Visweswaran","year":"2018","journal-title":"JAMIA Open"},{"issue":"5","key":"2024092007524965400_ocae211-B7","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1197\/jamia.M3191","article-title":"The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories","volume":"16","author":"Weber","year":"2009","journal-title":"J Am Med Inform Assoc"},{"issue":"5","key":"2024092007524965400_ocae211-B8","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1007\/s10916-011-9720-3","article-title":"Federated querying architecture with clinical & translational health IT application","volume":"35","author":"Livne","year":"2011","journal-title":"J Med Syst"},{"key":"2024092007524965400_ocae211-B9","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.jbi.2015.04.012","article-title":"Federated queries of clinical data repositories: scaling to a national network","volume":"55","author":"Weber","year":"2015","journal-title":"J Biomed Inform"},{"key":"2024092007524965400_ocae211-B10","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.jbi.2013.11.009","article-title":"Federated Aggregate Cohort Estimator (FACE): an easy to deploy, vendor neutral, multi-institutional cohort query architecture","volume":"52","author":"Wyatt","year":"2014","journal-title":"J Biomed Inform"},{"key":"2024092007524965400_ocae211-B11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1200\/CCI.17.00067","article-title":"Using a federated network of real-world data to optimize clinical trials operations","volume":"2","author":"Topaloglu","year":"2018","journal-title":"JCO Clin Cancer Inform"},{"issue":"3","key":"2024092007524965400_ocae211-B12","doi-asserted-by":"crossref","first-page":"204","DOI":"10.18043\/ncm.75.3.204","article-title":"The Patient-Centered Outcomes Research Network: a national infrastructure for comparative effectiveness research","volume":"75","author":"Califf","year":"2014","journal-title":"North Carolina Med J"},{"issue":"4","key":"2024092007524965400_ocae211-B13","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1136\/amiajnl-2014-002746","article-title":"Developing a data infrastructure for a learning health system: the PORTAL network","volume":"21","author":"McGlynn","year":"2014","journal-title":"J Am Med Inform Assoc"},{"issue":"4","key":"2024092007524965400_ocae211-B14","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1136\/amiajnl-2014-002751","article-title":"pSCANNER: patient-centered scalable national network for effectiveness research","volume":"21","author":"Ohno-Machado","year":"2014","journal-title":"J Am Med Inform Assoc"},{"issue":"4","key":"2024092007524965400_ocae211-B15","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1136\/amiajnl-2014-002756","article-title":"The greater plains collaborative: a PCORnet clinical research data network","volume":"21","author":"Waitman","year":"2014","journal-title":"J Am Med Inform Assoc"},{"issue":"11","key":"2024092007524965400_ocae211-B16","doi-asserted-by":"crossref","first-page":"e18735","DOI":"10.2196\/18735","article-title":"Balancing accuracy and privacy in federated queries of clinical data repositories: algorithm development and validation","volume":"22","author":"Yu","year":"2020","journal-title":"J Med Internet Res"},{"issue":"4","key":"2024092007524965400_ocae211-B17","doi-asserted-by":"crossref","first-page":"e35789","DOI":"10.2196\/35789","article-title":"Generation of a fast healthcare interoperability resources (FHIR)-based ontology for federated feasibility queries in the context of COVID-19: feasibility study","volume":"10","author":"Rosenau","year":"2022","journal-title":"JMIR Med Inform"},{"issue":"2","key":"2024092007524965400_ocae211-B18","doi-asserted-by":"crossref","first-page":"ooad035","DOI":"10.1093\/jamiaopen\/ooad035","article-title":"A global federated real-world data and analytics platform for research","volume":"6","author":"Palchuk","year":"2023","journal-title":"JAMIA Open"},{"issue":"12","key":"2024092007524965400_ocae211-B19","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.1093\/jamia\/ocad166","article-title":"A broadly applicable approach to enrich electronic-health-record cohorts by identifying patients with complete data: a multisite evaluation","volume":"30","author":"Klann","year":"2023","journal-title":"J Am Med Inform Assoc"},{"issue":"4","key":"2024092007524965400_ocae211-B20","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1136\/amiajnl-2014-002764","article-title":"Changing the research landscape: the New York City clinical data research network","volume":"21","author":"Kaushal","year":"2014","journal-title":"J Am Med Inform Assoc"},{"issue":"3","key":"2024092007524965400_ocae211-B21","doi-asserted-by":"crossref","first-page":"e31684","DOI":"10.2196\/31684","article-title":"A national network of safe havens: Scottish perspective","volume":"24","author":"Gao","year":"2022","journal-title":"J Med Internet Res"},{"issue":"2","key":"2024092007524965400_ocae211-B22","doi-asserted-by":"crossref","first-page":"100033","DOI":"10.1016\/j.xgen.2021.100033","article-title":"CanDIG: federated network across Canada for multi-omic and health data discovery and analysis","volume":"1","author":"Dursi","year":"2021","journal-title":"Cell Genom"},{"issue":"7","key":"2024092007524965400_ocae211-B23","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1007\/s40264-023-01296-2","article-title":"Development and application of an active pharmacovigilance framework based on electronic healthcare records from multiple centers in Korea","volume":"46","author":"Choe","year":"2023","journal-title":"Drug Saf"},{"issue":"4","key":"2024092007524965400_ocae211-B24","doi-asserted-by":"crossref","first-page":"e10233","DOI":"10.1002\/lrh2.10233","article-title":"Toward cross-platform electronic health record-driven phenotyping using Clinical Quality Language","volume":"4","author":"Brandt","year":"2020","journal-title":"Learn Health Syst"},{"key":"2024092007524965400_ocae211-B25","first-page":"85","volume-title":"Machine Learning, Image Processing, Network Security and Data Sciences - 2nd International Conference, MIND 2020, Proceedings","author":"Choudhury","year":"2020"},{"issue":"5","key":"2024092007524965400_ocae211-B26","doi-asserted-by":"crossref","first-page":"e36709","DOI":"10.2196\/36709","article-title":"The architecture of a feasibility query portal for distributed COVID-19 Fast Healthcare Interoperability Resources (FHIR) patient data repositories: design and implementation study","volume":"10","author":"Gruendner","year":"2022","journal-title":"JMIR Med Inform"},{"issue":"8","key":"2024092007524965400_ocae211-B27","doi-asserted-by":"crossref","first-page":"1638","DOI":"10.1093\/jamia\/ocae130","article-title":"Cumulus: a federated electronic health record-based learning system powered by Fast Healthcare Interoperability Resources and artificial intelligence","volume":"31","author":"McMurry","journal-title":"J Am Med Inform Assoc"},{"issue":"4","key":"2024092007524965400_ocae211-B28","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1136\/amiajnl-2014-002747","article-title":"Launching PCORnet, a national patient-centered clinical research network","volume":"21","author":"Fleurence","year":"2014","journal-title":"J Am Med Inform Assoc"},{"key":"2024092007524965400_ocae211-B29","first-page":"574","article-title":"Observational Health Data Sciences and Informatics (OHDSI): opportunities for observational researchers","volume":"216","author":"Hripcsak","year":"2015","journal-title":"Stud Health Technol Inform"},{"issue":"3","key":"2024092007524965400_ocae211-B30","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1093\/jamia\/ocaa196","article-title":"The National COVID Cohort Collaborative (N3C): rationale, design, infrastructure, and deployment","volume":"28","author":"Haendel","year":"2021","journal-title":"J Am Med Inform Assoc"}],"container-title":["Journal of the American Medical Informatics Association"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jamia\/article-pdf\/31\/10\/2202\/59206329\/ocae211.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jamia\/article-pdf\/31\/10\/2202\/59206329\/ocae211.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,20]],"date-time":"2024-09-20T07:53:23Z","timestamp":1726818803000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jamia\/article\/31\/10\/2202\/7729230"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,7]]},"references-count":30,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2024,8,7]]},"published-print":{"date-parts":[[2024,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/jamia\/ocae211","relation":{},"ISSN":["1067-5027","1527-974X"],"issn-type":[{"type":"print","value":"1067-5027"},{"type":"electronic","value":"1527-974X"}],"subject":[],"published-other":{"date-parts":[[2024,10]]},"published":{"date-parts":[[2024,8,7]]}}}