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DOI: 10.1055/a-2259-0008
Simplifying Multimodal Clinical Research Data Management: Introducing an Integrated and User-friendly Database Concept
Funding This work was supported by funding from the Foundation “Else Kröner-Fresenius-Stiftung” within the Else Kröner Graduate School for Medical Students “Jena School for Ageing Medicine (JSAM)” and Else Kröner Anti Age.
Abstract
Background Clinical research, particularly in scientific data, grapples with the efficient management of multimodal and longitudinal clinical data. Especially in neuroscience, the volume of heterogeneous longitudinal data challenges researchers. While current research data management systems offer rich functionality, they suffer from architectural complexity that makes them difficult to install and maintain and require extensive user training.
Objectives The focus is the development and presentation of a data management approach specifically tailored for clinical researchers involved in active patient care, especially in the neuroscientific environment of German university hospitals. Our design considers the implementation of FAIR (Findable, Accessible, Interoperable, and Reusable) principles and the secure handling of sensitive data in compliance with the General Data Protection Regulation.
Methods We introduce a streamlined database concept, featuring an intuitive graphical interface built on Hypertext Markup Language revision 5 (HTML5)/Cascading Style Sheets (CSS) technology. The system can be effortlessly deployed within local networks, that is, in Microsoft Windows 10 environments. Our design incorporates FAIR principles for effective data management. Moreover, we have streamlined data interchange through established standards like HL7 Clinical Document Architecture (CDA). To ensure data integrity, we have integrated real-time validation mechanisms that cover data type, plausibility, and Clinical Quality Language logic during data import and entry.
Results We have developed and evaluated our concept with clinicians using a sample dataset of subjects who visited our memory clinic over a 3-year period and collected several multimodal clinical parameters. A notable advantage is the unified data matrix, which simplifies data aggregation, anonymization, and export. This streamlines data exchange and enhances database integration with platforms like Konstanz Information Miner (KNIME).
Conclusion Our approach offers a significant advancement for capturing and managing clinical research data, specifically tailored for small-scale initiatives operating within limited information technology (IT) infrastructures. It is designed for immediate, hassle-free deployment by clinicians and researchers.
The database template and precompiled versions of the user interface are available at: https://github.com/stebro01/research_database_sqlite_i2b2.git.
Protection of Human and Animal Subjects
The study adhered to the World Medical Association Declaration of Helsinki's ethical guidelines for research involving human subjects and received approval from our local Ethics board (Reference: 2022-2658-Daten).
Publication History
Received: 14 July 2023
Accepted: 22 November 2023
Accepted Manuscript online:
01 February 2024
Article published online:
27 March 2024
© 2024. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/)
Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany
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References
- 1 Klingner CM, Denker M, Grün S. et al. Research data management and data sharing for reproducible research-results of a community survey of the German National Research Data Infrastructure Initiative Neuroscience. eNeuro 2023 ;10(2):ENEURO.0215-22.2023
- 2 Wachtler T, Bauer P, Denker M. et al. NFDI-Neuro: building a community for neuroscience research data management in Germany. Neuroforum 2021; 27 (01) 3-15
- 3 Denker M, Grün S, Wachtler T, Scherberger H. Reproducibility and efficiency in handling complex neurophysiological data. Neuroforum 2021; 27 (01) 27-34
- 4 Amorim RC, Castro JA, Rocha da Silva J, Ribeiro C. A comparison of research data management platforms: architecture, flexible metadata and interoperability. Univers Access Inf Soc 2017; 16 (04) 851-862
- 5 Wilkinson MD, Dumontier M, Aalbersberg IJJ. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 2016; 3: 160018
- 6 Roche DG, Kruuk LEB, Lanfear R, Binning SA. Public data archiving in ecology and evolution: how well are we doing?. PLoS Biol 2015; 13 (11) e1002295
- 7 Sarica A, Cerasa A, Quattrone A. Random forest algorithm for the classification of neuroimaging data in Alzheimer's disease: a systematic review. Front Aging Neurosci 2017; 9: 329
- 8 Das S, Zijdenbos AP, Harlap J, Vins D, Evans AC. LORIS: a web-based data management system for multi-center studies. Front Neuroinform 2012; 5: 37
- 9 Hussein R, Wurhofer D, Strumegger EM. et al. General Data Protection Regulation (GDPR) toolkit for digital health. Stud Health Technol Inform 2022; 290: 222-226
- 10 Deutsche Forschungsgemeinschaft. Handling of Research Data. Accessed July 7, 2023 at: https://www.dfg.de/en/research_funding/principles_dfg_funding/research_data/index.html
- 11 Schelter JS, Abiteboul S, Howe B, Jagadish HV, Sebastian S. Responsible Data Management. Accessed July 7, 2023 at: https://cacm.acm.org/magazines/2022/6/261173-responsible-data-management/fulltext
- 12 Duda SN, Kennedy N, Conway D. et al. HL7 FHIR-based tools and initiatives to support clinical research: a scoping review. J Am Med Inform Assoc 2022; 29 (09) 1642-1653
- 13 Moher D, Liberati A, Tetzlaff J, Altman DG. PRISMA Group. Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS Med 2009; 6 (07) e1000097
- 14 Halchenko YO, Meyer K, Poldrack B. et al. DataLad: distributed system for joint management of code, data, and their relationship. J Open Source Softw 2021; 6 (63) 3262
- 15 Harris PA, Taylor R, Thielke R, Payne J, Gonzalez N, Conde JG. Research electronic data capture (REDCap)–a metadata-driven methodology and workflow process for providing translational research informatics support. J Biomed Inform 2009; 42 (02) 377-381
- 16 Database Trends and Applications. The Role of ACID in the Integrity of Your Database Data. Published November 1, 2017. Accessed July 7, 2023 at: https://www.dbta.com/Authors/Craig-S.-Mullins-3535.aspx ; https://www.dbta.com/Columns/DBA-Corner/The-Role-of-ACID-in-the-Integrity-of-Your-Database-Data-121440.aspx
- 17 Bhosale S, Patil P. SQLite: Light Database System. Int J Comput Sci Mobile Comput 2015; 44: 882-885
- 18 i2b2 Community Wiki. 2. Quick Start Guide - Bundles and CDM. Accessed March 30, 2023 at: https://community.i2b2.org/wiki/display/BUN/2.+Quick+Start+Guide
- 19 HL7 Consortium. CQL - Clinical Quality Language Release 1. Accessed April 2, 2023 at: https://cql.hl7.org/01-introduction.html
- 20 Cavelaars M, Rousseau J, Parlayan C. et al. OpenClinica. J Clin Bioinforma 2015; 5 (01) S2
- 21 Bodenreider O, Cornet R, Vreeman DJ. Recent developments in clinical terminologies - SNOMED CT, LOINC, and RxNorm. Yearb Med Inform 2018; 27 (01) 129-139
- 22 Berthold MR, Cebron N, Dill F. et al. KNIME - the Konstanz information miner: version 2.0 and beyond. SIGKDD Explor 2009; 11 (01) 26-31
- 23 Lyon L. Dealing with data: roles, rights, responsibilities and relationships consultancy report. Published online January 1, 2007
- 24 Hruby GW, McKiernan J, Bakken S, Weng C. A centralized research data repository enhances retrospective outcomes research capacity: a case report. J Am Med Inform Assoc 2013; 20 (03) 563-567
- 25 Checklists work to improve science. Nature 2018; 556 (7701) 273-274
- 26 Donner EK. Research data management systems and the organization of universities and research institutes: a systematic literature review. J Librarian Inform Sci 2022 ;09610006211070282
- 27 Perrier L, Blondal E, Ayala AP. et al. Research data management in academic institutions: a scoping review. PLoS ONE 2017; 12 (05) e0178261
- 28 Springer Publishing Connect. Introduction to Healthcare Data and the Role of Excel®. 2022 . Accessed April 30, 2023 at: https://connect.springerpub.com/content/book/978-0-8261-5028-8/chapter/ch01
- 29 Dobell E, Herold S, Buckley J. Spreadsheet error types and their prevalence in a healthcare context. J Organ End User Comput 2018; 30 (02) 20-42
- 30 Rajalingham K, Chadwick DR, Knight B. Classification of spreadsheet errors. 2008 ; eprint no.0805.4224:2-5
- 31 Kush R, Goldman M. Fostering responsible data sharing through standards. N Engl J Med 2014; 370 (23) 2163-2165
- 32 Solbrig HR, Prud'hommeaux E, Grieve G. et al. Modeling and validating HL7 FHIR profiles using semantic web Shape Expressions (ShEx). J Biomed Inform 2017; 67: 90-100
- 33 Payne P, Ervin D, Dhaval R, Borlawsky T, Lai A. TRIAD: The Translational Research Informatics and Data Management Grid. Appl Clin Inform 2011; 2 (03) 331-344
- 34 ClinCapture. Captivate® Electronic Data Capture (EDC). Accessed October 23, 2023 at: https://www.clincapture.com/captivate-electronic-data-capture-edc/
- 35 eNNOV Software for Life. MACRO. Accessed October 27, 2023 at: https://en.ennov.com/solutions/clinical/macro/
- 36 Gao QB, Kong Y, Fu Z. et al. EZ-Entry: a clinical data management system. Comput Biol Med 2008; 38 (09) 1042-1044
- 37 Oracle Help Center. Oracle Clinical and Oracle Clinical Remote Data Capture Release 5.4. Accessed October 23, 2023 at: https://docs.oracle.com/en/industries/health-sciences/clinical-remote-capture/5.4/index.html
- 38 Brandt CA, Deshpande AM, Lu C. et al; Center for Medical Informatics. TrialDB: a web-based clinical study data management system. AMIA Annu Symp Proc 2003; 2003: 794
- 39 Hurtado S, García-Nieto J, Navas-Delgado I, Aldana-Montes JF. FIMED: Flexible management of biomedical data. Comput Methods Programs Biomed 2021; 212: 106496
- 40 Nguyen L, Shah A, Harker M. et al. DADOS-Prospective: an open source application for web-based prospective data collection. Source Code Biol Med 2006; 1 (01) 7
- 41 Ärzteblatt DÄG Redaktion Deutsches. PhOSCo (Pharma Open Source Community): Open Source für klinische Studien. Deutsches Ärzteblatt. Published May 7, 2004. Accessed October 22, 2023 at: https://www.aerzteblatt.de/archiv/41737/PhOSCo-(Pharma-Open-Source-Community)-Open-Source-fuer-klinische-Studien
- 42 Lee H, Chapiro J, Schernthaner R. et al. How I do it: a practical database management system to assist clinical research teams with data collection, organization, and reporting. Acad Radiol 2015; 22 (04) 527-533
- 43 Egbring M, Kullak-Ublick GA, Russmann S. Phynx: an open source software solution supporting data management and web-based patient-level data review for drug safety studies in the general practice research database and other health care databases. Pharmacoepidemiol Drug Saf 2010; 19 (01) 38-44
- 44 Wolstencroft K, Owen S, Krebs O. et al. SEEK: a systems biology data and model management platform. BMC Syst Biol 2015; 9 (01) 33
- 45 Bauch A, Adamczyk I, Buczek P. et al. openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics 2011; 12 (01) 468
- 46 Sansone SA, Rocca-Serra P, Field D. et al. Toward interoperable bioscience data. Nat Genet 2012; 44 (02) 121-126
- 47 Ferretti Y, Miyoshi NSB, Silva Jr WA, Felipe JC. BioBankWarden: a web-based system to support translational cancer research by managing clinical and biomaterial data. Comput Biol Med 2017; 84: 254-261
- 48 Rossi E, Rosa M, Rossi L, Priori A, Marceglia S. WebBioBank: a new platform for integrating clinical forms and shared neurosignal analyses to support multi-centre studies in Parkinson's Disease. J Biomed Inform 2014; 52: 92-104
- 49 LabArchives. All Your Research in One Place. Accessed October 27, 2023 at: https://www.labarchives.com/
- 50 Labguru. Lab Management Software | Laboratory System. Accessed October 27, 2023 at: https://www.labguru.com
- 51 SciNote. Electronic Lab Notebook (ELN Software). Published July 18, 2023. Accessed October 27, 2023 at: https://www.scinote.net/
- 52 eLabNext. eLabJournal. Accessed October 27, 2023 at: https://www.elabnext.com/products/elabjournal/
- 53 RSpace. ELN & Inventory. Accessed October 27, 2023 at: https://www.researchspace.com/
- 54 eLabFTW. Open Source Laboratory Notebook. Accessed October 27, 2023 at: https://www.elabftw.net