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OpenClinica Data Uploader

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OpenClinica Data Uploader

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  1. STREAMLINING OPENCLINICA DATA UPLOADSJacob Rousseau1, Marinel Cavelaars2, Jeroen Beliën3,Jan-Willem Boiten4, Gerrit Meijer11 Dept. of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands2 The Hyve, Utrecht, The Netherlands3 VU University Medical Center, Amsterdam, The Netherlands4 Lygature, Utrecht, The Netherlands

  2. OpenClinica Data Uploader OpenClinica Data Uploader: Web-based and stand-alone tool for data uploads to OpenClinica 2

  3. CTMM-TraIT • TraIT (Translational research IT) started in October 2011 as a public / private partnership initiative to provide a national translational research infrastructure • CTMM-TraIT has 32 partners contributing to the TraIT services – all Dutch academic medical centers, charities, private partners, research institutes and OpenClinica LLC • TraIT services are used by more than 2700 users from approximately 250 institutes 3

  4. CTMM-TraIT application suite 4

  5. OpenClinica.nl environments in TraIT • OpenClinica instances • Archive – for large ‘non-active’ studies • Acceptance – for technical testing, integration development and issue solving • Sandbox – for user CRF- and study-development • Production – for clinical data storage 5

  6. OpenClinica.nl 6

  7. OpenClinica.nl user support • Large number of the TraIT applications are centrally hosted at our hosting provider • TraIT provides user support for all applications and a dedicated support officer for OpenClinica.nl • OpenClinica training 7

  8. Number of studies 2014 2015 2016 8

  9. Number of users 2014 2015 2016 9

  10. Integrated applications • Ldot →OpenClinica Ldot is the study scheduling- and workflow-tool developed for CTMM-TraIT by MEMIC, Maastricht University, Uses OpenClinica SOAP web-services • OpenClinica → ODM2I2B2 →tranSMART tranSMART is the central data-sharing and analytics datamart used by CTMM-TraIT • OpenClinica → Imaging applications. ( DICOM-viewers and tEPIS ) With parameterized links • tranSMART → Imaging applications Using URL’s • Single Sign-On using SAML 2.0 • tranSMART → Galaxy Custom tool • OpenClinica Data Uploader ( OCDU ) → OpenClinica 10

  11. Data uploading to OpenClinica • Users want to upload data to OpenClinica from various sources • Excel and csv-files • EHR-systems • Study migrations from other eCRF applications • Clinical data acquisition devices • OpenClinica extensions to upload data • OpenClinica Bulk Loader – sgranite • OpenClinica web-service client (TraIT) - Arjan van der Velde; tightly integrated with MirthConnect • OpenClinica Data Importer (TraIT) – Cuneyt Parlayan; Windows application / inserts of subjects and events with SQL-scripts • ODIN – Csaba Halmagyi, Dept. Haematology, University of Cambridge – web based, uses web-services 11

  12. Design goals • Run either in interactive or in stand-alone mode to allow unattended uploads • Web-based • Easy integration in different types of data-pipelines • Usable for users mixed levels of OpenClinica know-how • User-interface with step-by-step wizard-flow • Complete client-side validation with clear error-messages in order to avoid user confusion and subsequent errors generated by OpenClinica web-services • Mapping functionality from source-data to OpenClinica CRF-items • Connect to multiple OpenClinica instances • Handle different initial situations (subject and/or events can be present or absent) 12

  13. High-level design • Input: text-files with tab-separated values • Separate input files for subjects, events and CRF-data • Column names should match item-names in the CRF but custom mapping is possible • Reuse mappings previously made for unattended uploads • Clear feedback on errors in the input files • Use OpenClinica SOAP-Webservice API 13

  14. Development partnership • The Hyve, Utrecht, The Netherlands • NIHR Rare Diseases Translational Research Collaboration, Department of Haematology, University of Cambridge, United Kingdom 14

  15. Functional sketch – interactive mode 15

  16. Functional sketch – unattended mode 16

  17. Technology stack • Java 1.8 with lambda-expressions • Spring-Boot • Spring-MVC and Thymeleaf • Postgres (8.4) • Unit-testing with JUnit 4 • Continuous integration • GitHub • OpenClinica Data Importer: https://github.com/CTMM-TraIT/Open-Clinica-Data-Uploader • OpenClinica: https://github.com/CTMM-TraIT/OpenClinica 17

  18. Changes to OpenClinica web-services code • Addition of extra information to the web-services • Study → getMetadata, required status of an item per CRF-version • StudySubject → listAllByStudy, study-subject information to include studySubjectOID • StudySubject → listAllByStudy, changes of the Event element in to include: • Repeat occurrence • Event status • List of eventCRF’s with CRF-name, CRF-OID, status and version-information … <OpenClinica:ItemPresentInForm FormOID="F_MUSTFOR_NON__020" PageNumber="1" PHI="No“ ShowItem="Yes" OrderInForm= "2" Required="Yes"> <OpenClinica:LeftItemText>male0_female1</OpenClinica:LeftItemText> …. 18

  19. User Interface – wizard flow

  20. User Interface – Column mapping to CRF-items

  21. Application configuration • Customization of log-in page, welcome message, logo and application name • Selection of OpenClinica instances to connect to in application.yml file • Scheduling and error reporting for unattended mode 21

  22. Demonstration • Interactive mode • Definition of mapping • Registration of subjects and scheduling of events • Upload of data • Validation errors 22

  23. Future plans Future development on OpenClinica Data Uploader • Convert to REST-API • Integrate with more types of pipe-lines OpenClinca web-services enhancements • Addition of web-service dry-run / test-only mode • Introduce single validation module for both manual and web-service channels 23

  24. Acknowledgements • Csaba Halmagyi - Dept. Haematology, Cambridge University, Great Britain • Piotr Zakrzewski - The Hyve, Utrecht, the Netherlands • Bo Gao - The Hyve, Utrecht, the Netherlands • Ilona Pinter - The Hyve, Utrecht, the Netherlands • Jolanda Strubel - The Hyve, Utrecht, the Netherlands • Rene Breet - Free University, Medical faculty, Amsterdam,  the Netherlands • Marieke Vianen - Utrecht University Medical Center, Utrecht, the Netherlands • Cuneyt Parlayan - Free University, Medical faculty, Amsterdam,  the Netherlands • Remond Fijneman - The Netherlands Cancer Institute, Amsterdam, the Netherlands 24

  25. Questions & Comments 25

  26. REVISIONS • Revision history: • 0.2 processed comments • 0.3 addition more integrated applications

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