{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T16:21:47Z","timestamp":1774282907572,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,10,8]],"date-time":"2019-10-08T00:00:00Z","timestamp":1570492800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIH\/NCATS UW-CTSA","award":["UL1 TR002319"],"award-info":[{"award-number":["UL1 TR002319"]}]},{"name":"NIH\/NCATS CD2H","award":["U24TR002306"],"award-info":[{"award-number":["U24TR002306"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>Academic medical centers and health systems are increasingly challenged with supporting appropriate secondary use of clinical data. Enterprise data warehouses have emerged as central resources for these data, but often require an informatician to extract meaningful information, limiting direct access by end users. To overcome this challenge, we have developed Leaf, a lightweight self-service web application for querying clinical data from heterogeneous data models and sources.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and Methods<\/jats:title>\n                    <jats:p>Leaf utilizes a flexible biomedical concept system to define hierarchical concepts and ontologies. Each Leaf concept contains both textual representations and SQL query building blocks, exposed by a simple drag-and-drop user interface. Leaf generates abstract syntax trees which are compiled into dynamic SQL queries.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Leaf is a successful production-supported tool at the University of Washington, which hosts a central Leaf instance querying an enterprise data warehouse with over 300 active users. Through the support of UW Medicine (https:\/\/uwmedicine.org), the Institute of Translational Health Sciences (https:\/\/www.iths.org), and the National Center for Data to Health (https:\/\/ctsa.ncats.nih.gov\/cd2h\/), Leaf source code has been released into the public domain at https:\/\/github.com\/uwrit\/leaf.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>Leaf allows the querying of single or multiple clinical databases simultaneously, even those of different data models. This enables fast installation without costly extraction or duplication.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Leaf differs from existing cohort discovery tools because it does not specify a required data model and is designed to seamlessly leverage existing user authentication systems and clinical databases in situ. We believe Leaf to be useful for health system analytics, clinical research data warehouses, precision medicine biobanks, and clinical studies involving large patient cohorts.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jamia\/ocz165","type":"journal-article","created":{"date-parts":[[2019,8,28]],"date-time":"2019-08-28T09:59:20Z","timestamp":1566986360000},"page":"109-118","source":"Crossref","is-referenced-by-count":50,"title":["Leaf: an open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research"],"prefix":"10.1093","volume":"27","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 and Medical Education, UW Medicine Research IT, University of Washington, Seattle, Washington, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5338-6942","authenticated-orcid":false,"given":"Clifford H","family":"Spital","sequence":"additional","affiliation":[{"name":"UW Medicine Research IT, University of Washington, Seattle, Washington, USA"}]},{"given":"Robert A","family":"Black","sequence":"additional","affiliation":[{"name":"Population Health Analytics, University of Washington, Seattle, Washington, USA"}]},{"given":"Jason M","family":"Morrison","sequence":"additional","affiliation":[{"name":"Clinical Research Informatics, St. Jude\u2019s Children\u2019s Research Hospital, Memphis, Tennessee, USA"}]},{"given":"Bas","family":"de Veer","sequence":"additional","affiliation":[{"name":"UW Medicine Research IT, University of Washington, Seattle, Washington, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8233-5132","authenticated-orcid":false,"given":"Elizabeth","family":"Zampino","sequence":"additional","affiliation":[{"name":"UW Medicine Research IT, University of Washington, Seattle, Washington, USA"}]},{"given":"Robert D","family":"Harrington","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Disease, University of Washington, Seattle, Washington, USA"}]},{"given":"Bethene D","family":"Britt","sequence":"additional","affiliation":[{"name":"UW Medicine Analytics, University of Washington, Seattle, Washington, USA"}]},{"given":"Kari A","family":"Stephens","sequence":"additional","affiliation":[{"name":"Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA"}]},{"given":"Adam B","family":"Wilcox","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA"}]},{"given":"Peter","family":"Tarczy-Hornoch","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA"}]},{"given":"Sean D","family":"Mooney","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,10,8]]},"reference":[{"issue":"6","key":"2020110613103388800_ocz165-B1","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1197\/jamia.M1873","article-title":"Informatics challenges for the impending patient information explosion","volume":"12","author":"Berner","year":"2005","journal-title":"J Am Med Inform Assoc"},{"issue":"1","key":"2020110613103388800_ocz165-B2","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1093\/bib\/bbv118","article-title":"Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams","volume":"18","author":"Shameer","year":"2017","journal-title":"Brief Bioinform"},{"issue":"1","key":"2020110613103388800_ocz165-B3","doi-asserted-by":"crossref","first-page":"13.","DOI":"10.1186\/1755-8794-4-13","article-title":"The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies","volume":"4","author":"McCarty","year":"2011","journal-title":"BMC Med Genomics"},{"issue":"2","key":"2020110613103388800_ocz165-B4","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/j.jbi.2008.08.010","article-title":"Research electronic data capture (REDCap)\u2014a metadata-driven methodology and workflow process for providing translational research informatics support","volume":"42","author":"Harris","year":"2009","journal-title":"J Biomed Inform"},{"key":"2020110613103388800_ocz165-B5","doi-asserted-by":"crossref","DOI":"10.1201\/b15703","volume-title":"User Centered System Design|New Perspectives on Human-Computer Interaction","author":"Norman","year":"1986"},{"issue":"2","key":"2020110613103388800_ocz165-B6","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"},{"issue":"e1","key":"2020110613103388800_ocz165-B7","doi-asserted-by":"crossref","first-page":"e68","DOI":"10.1136\/amiajnl-2011-000115","article-title":"The design and implementation of an open-source, data-driven cohort recruitment system: the Duke integrated subject cohort and enrollment research network (DISCERN)","volume":"19","author":"Ferranti","year":"2012","journal-title":"J Am Med Inform Assoc"},{"issue":"3","key":"2020110613103388800_ocz165-B8","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.cct.2010.03.005","article-title":"Automated matching software for clinical trials eligibility: measuring efficiency and flexibility","volume":"31","author":"Penberthy","year":"2010","journal-title":"Contemp Clin Trials"},{"issue":"e1","key":"2020110613103388800_ocz165-B9","doi-asserted-by":"crossref","first-page":"e60","DOI":"10.1136\/amiajnl-2011-000133","article-title":"Implementation of a deidentified federated data network for population-based cohort discovery","volume":"19","author":"Anderson","year":"2012","journal-title":"J Am Med Inform Assoc"},{"key":"2020110613103388800_ocz165-B10","year":"2019"},{"issue":"9\u201310","key":"2020110613103388800_ocz165-B11","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1016\/j.infsof.2008.01.006","article-title":"Empirical studies of agile software development: a systematic review","volume":"50","author":"Dyb\u00e5","year":"2008","journal-title":"Inform Softw Technol"},{"issue":"1","key":"2020110613103388800_ocz165-B12","first-page":"14","article-title":"Improving patient identification data on the patient master index","volume":"29","author":"Carine","year":"1999","journal-title":"Health Inf Manage"},{"key":"2020110613103388800_ocz165-B13","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/978-1-4614-7518-7_2","volume-title":"Web Services Foundations","author":"Pautasso","year":"2014"},{"key":"2020110613103388800_ocz165-B14","year":"2019"},{"key":"2020110613103388800_ocz165-B15"},{"key":"2020110613103388800_ocz165-B16"},{"issue":"1","key":"2020110613103388800_ocz165-B17","doi-asserted-by":"crossref","first-page":"160035","DOI":"10.1038\/sdata.2016.35","article-title":"MIMIC-III, a freely accessible critical care database","volume":"3","author":"Johnson","year":"2016","journal-title":"Sci Data"},{"issue":"Database issue","key":"2020110613103388800_ocz165-B18","doi-asserted-by":"crossref","first-page":"D267","DOI":"10.1093\/nar\/gkh061","article-title":"The unified medical language system (UMLS): integrating biomedical terminology","volume":"32","author":"Bodenreider","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2020110613103388800_ocz165-B19","doi-asserted-by":"crossref","first-page":"909.","DOI":"10.1093\/jamia\/ocv188","article-title":"Data interchange using i2b2","volume":"23","author":"Klann","year":"2016","journal-title":"J Am Med Inform Assoc"},{"key":"2020110613103388800_ocz165-B20","author":"Klensin"},{"key":"2020110613103388800_ocz165-B21","author":"Bender"},{"issue":"9","key":"2020110613103388800_ocz165-B22","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.3899\/jrheum.180771","article-title":"Demographic, clinical and immunologic correlates among a cohort of 50 cocaine users demonstrating anti-neutrophil cytoplasmic antibodies","volume":"46","author":"Morcos","year":"2019","journal-title":"J Rheumatol"},{"key":"2020110613103388800_ocz165-B23","article-title":"The interferon gamma release assay is a novel predictor of disease activity in systemic Lupus erythematosus","volume":"69 (suppl 10)","author":"Thomason","year":"2017","journal-title":"Arthritis Rheumatol"},{"key":"2020110613103388800_ocz165-B24","doi-asserted-by":"crossref","DOI":"10.1016\/j.jvs.2018.12.040","article-title":"Washington State abdominal aortic aneurysm mortality shows a steady decline between 1996 and 2016","author":"Bartek","year":"2019","journal-title":"J Vasc Surg"},{"issue":"6","key":"2020110613103388800_ocz165-B25","doi-asserted-by":"crossref","first-page":"e183","DOI":"10.1016\/j.jvs.2018.03.265","article-title":"PC040. disease-based observational cohort study of patients with thoracoabdominal aortic aneurysm","volume":"67","author":"Kang","year":"2018","journal-title":"J Vasc Surg"},{"issue":"6","key":"2020110613103388800_ocz165-B26","doi-asserted-by":"crossref","first-page":"1710","DOI":"10.1016\/j.jvs.2018.09.050","article-title":"Left ventricular hypertrophy is a possible biomarker for early mortality after type B aortic dissection","volume":"69","author":"Taylor","year":"2019","journal-title":"J Vasc Surg"},{"issue":"6","key":"2020110613103388800_ocz165-B27","doi-asserted-by":"crossref","first-page":"e89","DOI":"10.1016\/j.jvs.2018.03.090","article-title":"IP003. Aortic dissection-related mortality in Washington State remains unchanged from 1996 to 2016","volume":"67","author":"Bartek","year":"2018","journal-title":"J Vasc Surg"},{"issue":"3","key":"2020110613103388800_ocz165-B28","doi-asserted-by":"crossref","first-page":"e35","DOI":"10.1016\/j.jvs.2018.06.081","article-title":"Disease-based observation cohort study of patients with thoracoabdominal aortic aneurysm","volume":"68","author":"Kang","year":"2018","journal-title":"J Vasc Surg"},{"issue":"3","key":"2020110613103388800_ocz165-B29","doi-asserted-by":"crossref","first-page":"e54.","DOI":"10.1016\/j.jvs.2017.05.069","article-title":"Trends in Washington state aortic-related deaths over a 21-year period, 1996-2016","volume":"66","author":"Bartek","year":"2017","journal-title":"J Vasc Surg"},{"issue":"4","key":"2020110613103388800_ocz165-B30","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1007\/s11605-018-4017-1","article-title":"The safety of expectant management for adhesive small bowel obstruction: a systematic review","volume":"23","author":"Thornblade","year":"2019","journal-title":"J Gastrointest Surg"},{"issue":"9","key":"2020110613103388800_ocz165-B31","first-page":"1637","article-title":"A pharmacist managed titration of urate-lowering therapy to streamline gout management","volume":"39","author":"Huang","year":"2019","journal-title":"Arthritis Rheumatol"},{"key":"2020110613103388800_ocz165-B32","author":"Yang","year":"2019"},{"key":"2020110613103388800_ocz165-B33","author":"Mills","year":"2019"},{"key":"2020110613103388800_ocz165-B34","author":"Powelson","year":"2018"},{"key":"2020110613103388800_ocz165-B35","author":"Amin","year":"2018"},{"key":"2020110613103388800_ocz165-B36"},{"key":"2020110613103388800_ocz165-B37"},{"key":"2020110613103388800_ocz165-B38","author":"Malcolm"},{"issue":"5","key":"2020110613103388800_ocz165-B39","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1142\/S0218488502001648","article-title":"K-anonymity: a model for protecting privacy","volume":"10","author":"Sweeney","year":"2002","journal-title":"Int J Uncertain Fuzz Knowl Based Syst"},{"issue":"4","key":"2020110613103388800_ocz165-B40","doi-asserted-by":"crossref","first-page":"e0126772","DOI":"10.1371\/journal.pone.0126772","article-title":"A systematic review of re-identification attacks on health data","volume":"10","author":"El Elam","journal-title":"PLoS One"}],"container-title":["Journal of the American Medical Informatics Association"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/27\/1\/109\/34152506\/ocz165.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/27\/1\/109\/34152506\/ocz165.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,6]],"date-time":"2020-11-06T14:34:18Z","timestamp":1604673258000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jamia\/article\/27\/1\/109\/5583724"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,8]]},"references-count":40,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,10,8]]},"published-print":{"date-parts":[[2020,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/jamia\/ocz165","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/632471","asserted-by":"object"}]},"ISSN":["1527-974X"],"issn-type":[{"value":"1527-974X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,1]]},"published":{"date-parts":[[2019,10,8]]}}}