{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T02:41:32Z","timestamp":1780108892278,"version":"3.54.0"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T00:00:00Z","timestamp":1662076800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"MassGeneral Brigham and\u00a0National Institutes of Health","award":["R00-LM011575"],"award-info":[{"award-number":["R00-LM011575"]}]},{"name":"MassGeneral Brigham and\u00a0National Institutes of Health","award":["R01-HG009174"],"award-info":[{"award-number":["R01-HG009174"]}]},{"name":"MassGeneral Brigham and\u00a0National Institutes of Health","award":["R01HL151643"],"award-info":[{"award-number":["R01HL151643"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The i2b2 platform is used at major academic health institutions and research consortia for querying for electronic health data. However, a major obstacle for wider utilization of the platform is the complexity of data loading that entails a steep curve of learning the platform\u2019s complex data schemas. To address this problem, we have developed the i2b2-etl package that simplifies the data loading process, which will facilitate wider deployment and utilization of the platform.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have implemented i2b2-etl as a Python application that imports ontology and patient data using simplified input file schemas and provides inbuilt record number de-identification and data validation. We describe a real-world deployment of i2b2-etl for a population-management initiative at MassGeneral Brigham.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>i2b2-etl is a free, open-source application implemented in Python available under the Mozilla 2 license. The application can be downloaded as compiled docker images. A live demo is available at https:\/\/i2b2clinical.org\/demo-i2b2etl\/ (username: demo, password: Etl@2021).<\/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\/btac595","type":"journal-article","created":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T12:05:27Z","timestamp":1662033927000},"page":"4833-4836","source":"Crossref","is-referenced-by-count":5,"title":["I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6219-861X","authenticated-orcid":false,"given":"Kavishwar B","family":"Wagholikar","sequence":"first","affiliation":[{"name":"Harvard Medical School , Boston, MA 02115, USA"},{"name":"Massachusetts General Hospital , Boston, MA 02114, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Layne","family":"Ainsworth","sequence":"additional","affiliation":[{"name":"Mass General Brigham , Boston, MA 02199, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Zelle","sequence":"additional","affiliation":[{"name":"Brigham and Women\u2019s Hospital , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kira","family":"Chaney","sequence":"additional","affiliation":[{"name":"Brigham and Women\u2019s Hospital , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Mendis","sequence":"additional","affiliation":[{"name":"Mass General Brigham , Boston, MA 02199, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffery","family":"Klann","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA 02115, USA"},{"name":"Massachusetts General Hospital , Boston, MA 02114, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander J","family":"Blood","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA 02115, USA"},{"name":"Brigham and Women\u2019s Hospital , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela","family":"Miller","sequence":"additional","affiliation":[{"name":"Mass General Brigham , Boston, MA 02199, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rupendra","family":"Chulyadyo","sequence":"additional","affiliation":[{"name":"Mass General Brigham , Boston, MA 02199, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Oates","sequence":"additional","affiliation":[{"name":"Mass General Brigham , Boston, MA 02199, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William J","family":"Gordon","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA 02115, USA"},{"name":"Mass General Brigham , Boston, MA 02199, USA"},{"name":"Brigham and Women\u2019s Hospital , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel J","family":"Aronson","sequence":"additional","affiliation":[{"name":"Mass General Brigham , Boston, MA 02199, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin M","family":"Scirica","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA 02115, USA"},{"name":"Brigham and Women\u2019s Hospital , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shawn N","family":"Murphy","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA 02115, USA"},{"name":"Massachusetts General Hospital , Boston, MA 02114, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,9,2]]},"reference":[{"key":"2022101415185366600_btac595-B1","first-page":"1","article-title":"Integrating clinical data into the i2b2 repository","volume":"2009","author":"Abend","year":"2009","journal-title":"Summit Transl. Bioinform"},{"issue":"11 Supplement","key":"2022101415185366600_btac595-B2","doi-asserted-by":"crossref","first-page":"A1762","DOI":"10.1016\/S0735-1097(18)32303-9","article-title":"A remote lipid management program improves appropriate statin use and cholesterol levels across a wide population of high cardiovascular risk patients","volume":"71","author":"Benson","year":"2018","journal-title":"J. Am. Coll. Cardiol"},{"key":"2022101415185366600_btac595-B3","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1002\/clc.23291","article-title":"Rationale and design of a navigator-driven remote optimization of guideline-directed medical therapy in patients with heart failure with reduced ejection fraction","volume":"43","author":"Blood","year":"2020","journal-title":"Clin. Cardiol"},{"key":"2022101415185366600_btac595-B4","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/s41746-020-00308-0","article-title":"International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium","volume":"3","author":"Brat","year":"2020","journal-title":"NPJ Digit. Med"},{"key":"2022101415185366600_btac595-B5","first-page":"506","article-title":"i2b2 to optimize patients enrollment","volume":"281","author":"Bucalo","year":"2021","journal-title":"Stud. Health Technol. Inform"},{"key":"2022101415185366600_btac595-B6","article-title":"The mass general brigham biobank portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics","author":"Castro","year":"2021","journal-title":"J. Am. Med. Inform. Assoc"},{"key":"2022101415185366600_btac595-B7","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1055\/s-0041-1739195","article-title":"Workflow automation for a virtual hypertension management program","volume":"12","author":"Gordon","year":"2021","journal-title":"Appl. Clin. Inform"},{"key":"2022101415185366600_btac595-B8","doi-asserted-by":"crossref","first-page":"e0212463","DOI":"10.1371\/journal.pone.0212463","article-title":"Data model harmonization for the all of Us research program: transforming i2b2 data into the OMOP common data model","volume":"14","author":"Klann","year":"2019","journal-title":"PLoS One"},{"key":"2022101415185366600_btac595-B9","first-page":"124","article-title":"Supporting the health quality measures format in i2b2","volume":"2013","author":"Klann","year":"2013","journal-title":"AMIA Jt. Summits Transl. Sci. Proc"},{"key":"2022101415185366600_btac595-B10","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1093\/jamia\/ocy093","article-title":"Web services for data warehouses: OMOP and PCORnet on i2b2","volume":"25","author":"Klann","year":"2018","journal-title":"J. Am. Med. Inform. Assoc"},{"key":"2022101415185366600_btac595-B11","first-page":"251","article-title":"Accessing OMOP common data model repositories with the i2b2 Webclient - algorithm for automatic query translation","volume":"278","author":"Majeed","year":"2021","journal-title":"Stud. Health Technol. Inform"},{"key":"2022101415185366600_btac595-B12","first-page":"42","article-title":"On-the-fly query translation between i2b2 and samply in the German Biobank Node (GBN) prototypes","volume":"243","author":"Mate","year":"2017","journal-title":"Stud. Health Technol. Inform"},{"key":"2022101415185366600_btac595-B13","doi-asserted-by":"crossref","first-page":"543","DOI":"10.3233\/JAD-200796","article-title":"Racial differences in Alzheimer's disease specialist encounters are associated with usage of molecular imaging and dementia medications: an Enterprise-Wide analysis using i2b2","volume":"79","author":"Murchison","year":"2021","journal-title":"J. Alzheimers Dis"},{"key":"2022101415185366600_btac595-B14","first-page":"548","article-title":"Architecture of the open-source clinical research chart from informatics for integrating biology and the bedside","author":"Murphy","year":"2007","journal-title":"AMIA Annu. Symp. Proc"},{"key":"2022101415185366600_btac595-B15","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":"2022101415185366600_btac595-B16","doi-asserted-by":"crossref","first-page":"e0152722","DOI":"10.1371\/journal.pone.0152722","article-title":"C3-PRO: connecting ResearchKit to the health system using i2b2 and FHIR","volume":"11","author":"Pfiffner","year":"2016","journal-title":"PLoS One"},{"key":"2022101415185366600_btac595-B17","first-page":"203","article-title":"Semantic ETL into i2b2 with eureka!","volume":"2013","author":"Post","year":"2013","journal-title":"AMIA Jt. Summits Transl. Sci. Proc"},{"key":"2022101415185366600_btac595-B18","first-page":"1160","article-title":"Temporal abstraction-based clinical phenotyping with eureka!","volume":"2013","author":"Post","year":"2013","journal-title":"AMIA Annu. Symp. Proc"},{"key":"2022101415185366600_btac595-B19","first-page":"184","article-title":"Metadata-driven clinical data loading into i2b2 for clinical and translational science institutes","volume":"2016","author":"Post","year":"2016","journal-title":"AMIA Jt. Summits Transl. Sci. Proc"},{"key":"2022101415185366600_btac595-B20","first-page":"94","article-title":"A clinical data warehouse based on OMOP and i2b2 for Austrian health claims data","volume":"248","author":"Rinner","year":"2018","journal-title":"Stud. Health Technol. Inform"},{"key":"2022101415185366600_btac595-B21","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1161\/CIRCULATIONAHA.120.051913","article-title":"Digital care transformation: interim report from the first 5000 patients enrolled in a remote algorithm-based cardiovascular risk management program to improve lipid and hypertension control","volume":"143","author":"Scirica","year":"2021","journal-title":"Circulation"},{"key":"2022101415185366600_btac595-B22","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1136\/jamia.2010.007914","article-title":"R engine cell: integrating R into the i2b2 software infrastructure","volume":"18","author":"Segagni","year":"2011","journal-title":"J. Am. Med. Inform. Assoc"},{"key":"2022101415185366600_btac595-B23","first-page":"887","article-title":"The ONCO-I2b2 project: integrating biobank information and clinical data to support translational research in oncology","volume":"169","author":"Segagni","year":"2011","journal-title":"Stud. Health Technol. Inform"},{"key":"2022101415185366600_btac595-B24","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"},{"key":"2022101415185366600_btac595-B25","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s12911-018-0646-2","article-title":"Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers","volume":"18","author":"Wagholikar","year":"2018","journal-title":"BMC Med. Inform. Decis. Mak"},{"key":"2022101415185366600_btac595-B26","doi-asserted-by":"crossref","first-page":"458","DOI":"10.14740\/jocmr3830","article-title":"Phenotyping to facilitate accrual for a cardiovascular intervention","volume":"11","author":"Wagholikar","year":"2019","journal-title":"J. Clin. Med. Res"},{"key":"2022101415185366600_btac595-B27","first-page":"302","article-title":"Evolving research data sharing networks to clinical app sharing networks","volume":"2017","author":"Wagholikar","year":"2017","journal-title":"AMIA Jt. Summits Transl. Sci. Proc"},{"key":"2022101415185366600_btac595-B28","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1093\/jamia\/ocw079","article-title":"SMART-on-FHIR implemented over i2b2","volume":"24","author":"Wagholikar","year":"2017","journal-title":"J. Am. Med. Inform. Assoc"},{"key":"2022101415185366600_btac595-B29","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"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac595\/45813042\/btac595.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/20\/4833\/46535010\/btac595.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/20\/4833\/46535010\/btac595.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,14]],"date-time":"2022-10-14T21:21:34Z","timestamp":1665782494000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/20\/4833\/6687125"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,9,2]]},"references-count":29,"journal-issue":{"issue":"20","published-online":{"date-parts":[[2022,9,2]]},"published-print":{"date-parts":[[2022,10,14]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac595","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,10,15]]},"published":{"date-parts":[[2022,9,2]]}}}