{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T22:37:09Z","timestamp":1790807829911,"version":"4.1.0"},"reference-count":39,"publisher":"JMIR Publications Inc.","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JMIR Med Inform"],"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n Biomedical data warehouses (BDWs) have become an essential tool to facilitate the reuse of health data for both research and decisional applications. Beyond technical issues, the implementation of BDWs requires strong institutional data governance and operational knowledge of the European and national legal framework for the management of research data access and use.<\/jats:p>\n <\/jats:sec>\n \n Objective<\/jats:title>\n In this paper, we describe the compound process of implementation and the contents of a regional university hospital BDW.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n We present the actions and challenges regarding organizational changes, technical architecture, and shared governance that took place to develop the Nantes BDW. We describe the process to access clinical contents, give details about patient data protection, and use examples to illustrate merging clinical insights.<\/jats:p>\n <\/jats:sec>\n \n Implementation (Results)<\/jats:title>\n More than 68 million textual documents and 543 million pieces of coded information concerning approximately 1.5 million patients admitted to CHUN between 2002 and 2022 can be queried and transformed to be made available to investigators. Since its creation in 2018, 269 projects have benefited from the Nantes BDW. Access to data is organized according to data use and regulatory requirements.<\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n Data use is entirely determined by the scientific question posed. It is the vector of legitimacy of data access for secondary use. Enabling access to a BDW is a game changer for research and all operational situations in need of data. Finally, data governance must prevail over technical issues in institution data strategy vis-\u00e0-vis care professionals and patients alike.<\/jats:p>\n <\/jats:sec>","DOI":"10.2196\/50194","type":"journal-article","created":{"date-parts":[[2024,6,25]],"date-time":"2024-06-25T00:48:32Z","timestamp":1719276512000},"page":"e50194-e50194","source":"Crossref","is-referenced-by-count":16,"title":["Implementing a Biomedical Data Warehouse From Blueprint to Bedside in a Regional French University Hospital Setting: Unveiling Processes, Overcoming Challenges, and Extracting Clinical Insight"],"prefix":"10.2196","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4318-9141","authenticated-orcid":false,"given":"Matilde","family":"Karakachoff","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1019-9821","authenticated-orcid":false,"given":"Thomas","family":"Goronflot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-5095-1813","authenticated-orcid":false,"given":"Sandrine","family":"Coudol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4464-0996","authenticated-orcid":false,"given":"Delphine","family":"Toublant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9723-9688","authenticated-orcid":false,"given":"Adrien","family":"Bazoge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0466-2816","authenticated-orcid":false,"given":"Pac\u00f4me","family":"Constant Dit Beaufils","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3013-2472","authenticated-orcid":false,"given":"Emilie","family":"Varey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6398-5578","authenticated-orcid":false,"given":"Christophe","family":"Leux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8433-2815","authenticated-orcid":false,"given":"Nicolas","family":"Mauduit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6027-9486","authenticated-orcid":false,"given":"Matthieu","family":"Wargny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1131-9554","authenticated-orcid":false,"given":"Pierre-Antoine","family":"Gourraud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1010","published-online":{"date-parts":[[2024,6,24]]},"reference":[{"issue":"1","key":"R1","doi-asserted-by":"publisher","first-page":"38","DOI":"10.15265\/IY-2017-007","article-title":"Clinical data reuse or secondary use: current status and potential future progress","volume":"26","author":"Meystre","journal-title":"Yearb Med Inform"},{"issue":"1","key":"R2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1197\/jamia.M2273","article-title":"Toward a national framework for the secondary use of health data: an American Medical Informatics Association white paper","volume":"14","author":"Safran","journal-title":"J Am Med Inform Assoc"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2016.08.007","article-title":"Automated population of an i2b2 clinical data warehouse from an openEHR-based data repository","volume":"63","author":"Haarbrandt","journal-title":"J Biomed Inform"},{"issue":"8","key":"R4","doi-asserted-by":"publisher","DOI":"10.2196\/17687","article-title":"What you need to know before implementing a clinical research data warehouse: comparative review of integrated data repositories in health care institutions","volume":"4","author":"Gagalova","journal-title":"JMIR Form Res"},{"issue":"2","key":"R5","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1136\/jamia.2009.002691","article-title":"The enterprise data trust at Mayo Clinic: a semantically integrated warehouse of biomedical data","volume":"17","author":"Chute","journal-title":"J Am Med Inform Assoc"},{"issue":"1","key":"R6","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1186\/s12911-020-01177-z","article-title":"Implementation of data access and use procedures in clinical data warehouses. A systematic review of literature and publicly available policies","volume":"20","author":"Pavlenko","journal-title":"BMC Med Inform Decis Mak"},{"issue":"4","key":"R7","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1136\/amiajnl-2013-002370","article-title":"Clinical research data warehouse governance for distributed research networks in the USA: a systematic review of the literature","volume":"21","author":"Holmes","journal-title":"J Am Med Inform Assoc"},{"issue":"6","key":"R8","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1197\/jamia.M2905","article-title":"Advancing the framework: use of health data--a report of a working conference of the American Medical Informatics Association","volume":"15","author":"Bloomrosen","journal-title":"J Am Med Inform Assoc"},{"issue":"5 Pt 2","key":"R9","doi-asserted-by":"publisher","first-page":"1442","DOI":"10.1111\/j.1475-6773.2010.01140.x","article-title":"Data governance and stewardship: designing data stewardship entities and advancing data access","volume":"45","author":"Rosenbaum","journal-title":"Health Serv Res"},{"issue":"6","key":"R10","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1038\/nrg3208","article-title":"Mining electronic health records: towards better research applications and clinical care","volume":"13","author":"Jensen","journal-title":"Nat Rev Genet"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmedinf.2020.104281","article-title":"Successfully implementing a national electronic health record: a rapid umbrella review","volume":"144","author":"Fennelly","journal-title":"Int J Med Inform"},{"issue":"2","key":"R12","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/j.neurad.2023.01.156","article-title":"Management of unruptured intracranial aneurysms: how real-world evidence can help to lift off barriers","volume":"50","author":"Constant Dit Beaufils","journal-title":"J Neuroradiol"},{"issue":"1","key":"R13","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1002\/cncr.28395","article-title":"Breast cancer treatment across health care systems: linking electronic medical records and state registry data to enable outcomes research","volume":"120","author":"Kurian","journal-title":"Cancer"},{"issue":"3","key":"R14","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1093\/jamia\/ocv176","article-title":"Development of a large urban longitudinal HIV clinical cohort using a web-based platform to merge electronically and manually abstracted data from disparate medical record systems: technical challenges and innovative solutions","volume":"23","author":"Greenberg","journal-title":"J Am Med Inform Assoc"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmedinf.2019.05.018","article-title":"Automatic trial eligibility surveillance based on unstructured clinical data","volume":"129","author":"Meystre","journal-title":"Int J Med Inform"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.3233\/SHTI190464","article-title":"PREDIMED: clinical data warehouse of Grenoble Alpes University Hospital","volume":"264","author":"Artemova","journal-title":"Stud Health Technol Inform"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmedinf.2017.02.006","article-title":"The Georges Pompidou University Hospital Clinical Data Warehouse: a 8-years follow-up experience","volume":"102","author":"Jannot","journal-title":"Int J Med Inform"},{"key":"R18","unstructured":"Wack M . Installation d\u2019un entrep\u00f4t de donn\u00e9es cliniques pour la recherche au CHRU de Nancy: d\u00e9ploiement technique, int\u00e9gration et gouvernance des donn\u00e9es [Doctoral thesis]. Universit\u00e9 de Lorraine; Oct7, 2017. URL: http:\/\/docnum.univ-lorraine.fr\/public\/BUMED_T_2017_WACK_MAXIME.pdf [Accessed 17-06-2024]"},{"issue":"1","key":"R19","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/s12911-022-01762-4","article-title":"Evaluation of Doc'EDS: a French semantic search tool to query health documents from a clinical data warehouse","volume":"22","author":"Pressat-Laffouilh\u00e8re","journal-title":"BMC Med Inform Decis Mak"},{"key":"R20","unstructured":"Entrep\u00f4ts de donn\u00e9es de sant\u00e9 hospitaliers en France. Haute Autorit\u00e9 de Sant\u00e9. Nov17, 2022. URL: https:\/\/www.has-sante.fr\/jcms\/p_3386123\/fr\/entrepots-de-donnees-de-sante-hospitaliers-en-france [Accessed 03-01-2023]"},{"issue":"7","key":"R21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pdig.0000298","article-title":"Good practices for clinical data warehouse implementation: a case study in France","volume":"2","author":"Doutreligne","journal-title":"PLOS Digit Health"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.3233\/SHTI190522","article-title":"eHOP clinical data warehouse: from a prototype to the creation of an inter-regional clinical data centers network","volume":"264","author":"Madec","journal-title":"Stud Health Technol Inform"},{"issue":"2","key":"R23","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph20021645","article-title":"Opportunities and obstacles to the development of health data warehouses in hospitals in France: the recent experience of comprehensive cancer centers","volume":"20","author":"Bocquet","journal-title":"Int J Environ Res Public Health"},{"issue":"1","key":"R24","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1055\/s-0039-1677917","article-title":"The French Health Data Hub and the German Medical Informatics initiatives: two national projects to promote data sharing in healthcare","volume":"28","author":"Cuggia","journal-title":"Yearb Med Inform"},{"issue":"3","key":"R25","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1051\/medsci\/2021016","article-title":"Health data hub: why and how?","volume":"37","author":"Goldberg","journal-title":"Med Sci (Paris)"},{"issue":"1","key":"R26","doi-asserted-by":"publisher","DOI":"10.2196\/46694","article-title":"iCHECK-DH: Guidelines and Checklist for the Reporting on Digital Health Implementations","volume":"25","author":"Perrin Franck","journal-title":"J Med Internet Res"},{"key":"R27","unstructured":"Liste de recherches sur donn\u00e9es et\/ou \u00e9chantillons men\u00e9es au CHU de Nantes, notamment \u00e0 partir de l\u2019entrep\u00f4t. Centre Hospitalier Universitaire de Nantes. URL: https:\/\/www.chu-nantes.fr\/liste-des-etudes-menees-au-chu-de-nantes-utilisant-des-donnees-de-l-entrepot-de-recherche [Accessed 26-01-2024]"},{"key":"R28","volume":"210","author":"Delamarre","journal-title":"Stud Health Technol Inform"},{"key":"R29","doi-asserted-by":"crossref","unstructured":"Labrak Y Bazoge A Dufour R et al. DrBERT: a robust pre-trained model in French for biomedical and clinical domains. In: Rogers A Boyd-Graber J Okazaki N , editors. Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). Association for Computational Linguistics; 2023:16207-16221. [doi: 10.18653\/v1\/2023.acl-long.896]","DOI":"10.18653\/v1\/2023.acl-long.896"},{"issue":"11","key":"R30","doi-asserted-by":"publisher","DOI":"10.2196\/36711","article-title":"Linking biomedical data warehouse records with the national mortality database in France: large-scale matching algorithm","volume":"10","author":"Guardiolle","journal-title":"JMIR Med Inform"},{"key":"R31","unstructured":"General Data Protection Regulation (GDPR). URL: https:\/\/gdpr-info.eu\/ [Accessed 06-06-2023]"},{"key":"R32","unstructured":"D\u00e9lib\u00e9ration 2018-295 Du 19 Juillet 2018. L\u00e9gifrance. Oct23, 2018. URL: https:\/\/www.legifrance.gouv.fr\/cnil\/id\/CNILTEXT000037509951 [Accessed 11-06-2024]"},{"key":"R33","unstructured":"Bases statistiques SAE. Donn\u00e9es statistiques publiques en sant\u00e9 et social. Jan6, 2015. URL: https:\/\/data.drees.solidarites-sante.gouv.fr\/explore\/dataset\/708_bases-statistiques-sae\/ [Accessed 28-12-2021]"},{"key":"R34","unstructured":"En chiffres. Centre Hospitalier Universitaire de Nantes. URL: https:\/\/www.chu-nantes.fr\/activite-et-chiffres-cles [Accessed 03-01-2023]"},{"issue":"4","key":"R35","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1093\/neuros\/nyw135","article-title":"Understanding the pathophysiology of intracranial aneurysm: the ICAN Project","volume":"80","author":"Bourcier","journal-title":"Neurosurgery"},{"issue":"3","key":"R36","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.neurad.2014.12.001","article-title":"OFSEP, a nationwide cohort of people with multiple sclerosis: consensus minimal MRI protocol","volume":"42","author":"Cotton","journal-title":"J Neuroradiol"},{"issue":"7","key":"R37","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1177\/014107680009300703","article-title":"Urgency of caesarean section: a new classification","volume":"93","author":"Lucas","journal-title":"J R Soc Med"},{"key":"R38","volume":"247","author":"Jantzen","journal-title":"Stud Health Technol Inform"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmpb.2018.12.030","article-title":"What can millions of laboratory test results tell us about the temporal aspect of data quality? Study of data spanning 17 years in a clinical data warehouse","volume":"181","author":"Looten","journal-title":"Comput Methods Programs Biomed"}],"container-title":["JMIR Medical Informatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/medinform.jmir.org\/2024\/1\/e50194","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T17:32:41Z","timestamp":1782840761000},"score":1,"resource":{"primary":{"URL":"https:\/\/medinform.jmir.org\/2024\/1\/e50194"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,24]]},"references-count":39,"URL":"https:\/\/doi.org\/10.2196\/50194","relation":{},"ISSN":["2291-9694"],"issn-type":[{"value":"2291-9694","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,24]]},"article-number":"v12i1e50194"}}