gms | German Medical Science

66. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS), 12. Jahreskongress der Technologie- und Methodenplattform für die vernetzte medizinische Forschung e. V. (TMF)

26. - 30.09.2021, online

Article

Send article

GECCO on FHIR – Towards Interoperable Data on COVID-19

Meeting Abstract

Search Medline for

  • Cornelius Erbelding - Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany; Medical Data Integration Center (meDIC), University Hospital Tübingen, Tübingen, Germany
  • Benjamin Sailer - Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany; Medical Data Integration Center (meDIC), University Hospital Tübingen, Tübingen, Germany
  • Holger Stenzhorn - Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany; Medical Data Integration Center (meDIC), University Hospital Tübingen, Tübingen, Germany; Institute for Medical Biometry, Epidemiology and Medical Informatics, Saarland University Medical Center, Homburg, Germany
  • Stephanie Biergans - Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany; Medical Data Integration Center (meDIC), University Hospital Tübingen, Tübingen, Germany
  • Florian Kohlmayer - Institute of Medical Informatics, Statistics and Epidemiology, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany
  • Eva-Maria Kobak - Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany; Medical Data Integration Center (meDIC), University Hospital Tübingen, Tübingen, Germany
  • Anna-Antonia Pape - Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany; Medical Data Integration Center (meDIC), University Hospital Tübingen, Tübingen, Germany
  • Raphael Verbücheln - Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany; Medical Data Integration Center (meDIC), University Hospital Tübingen, Tübingen, Germany; Dept. of Computer Science, University of Tübingen, Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
  • Oliver Kohlbacher - Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany; Medical Data Integration Center (meDIC), University Hospital Tübingen, Tübingen, Germany

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie. 66. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS), 12. Jahreskongress der Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V. (TMF). sine loco [digital], 26.-30.09.2021. Düsseldorf: German Medical Science GMS Publishing House; 2021. DocAbstr. 38

doi: 10.3205/21gmds012, urn:nbn:de:0183-21gmds0128

Published: September 24, 2021

© 2021 Erbelding et al.
This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 License. See license information at http://creativecommons.org/licenses/by/4.0/.

Outline

Text

As part of the NUM CODEX project, we have developed a workflow for data collection and transformation of patients suffering from COVID-19. Based on the GECCO dataset, electronic Case Report Forms (eCRFs) were designed for the electronic data capture (EDC)-Systems REDCap and DIS. Their standard CDISC ODM output was subsequently mapped and transformed into FHIR resources. These adhere to the FHIR profiles, value sets, and code systems outlined in the GECCO FHIR implementation guide. In the following, we first provide an overview of the NUM CODEX project and the GECCO dataset. We then depict how our workflow fits within the overarching project architecture: As a basis for the REDCap and DIS eCRFs, we created a data dictionary from the (logical) GECCO definitions in ART-DECOR. We present how individual data items have been implemented in the data dictionary, show the generated eCRF as well as the resulting CDISC ODM export. Finally, we show a dedicated mapping tool to transform the CDISC ODM into FHIR resources. We describe our approach to map single data items onto respective FHIR resources and how this mapping was actually implemented in the tool. Our approach allows for the combination of different strategies (e.g. manual vs automatic) and different EDC systems (REDCap vs DIS) for data collection of COVID-19 patients and the possibility of merging the data with other FHIR resources. This strategy offers flexibility and is easy to implement for all university clinics as part of NUM CODEX.

The authors declare that they have no competing interests.

The authors declare that an ethics committee vote is not required.

Outline

References

1.
Netzwerk Universitätsmedizin. Organisation. [cited 2021 March 31]. Available from: https://www.netzwerk-universitaetsmedizin.de/organisation External link
2.
Bundesministerium für Bildung und Forschung. Karliczek: Netzwerk Universitätsmedizin startet vertiefte Forschungsarbeit zu Covid-19 [Pressemitteilung]. 01.10.2020. Available from: https://www.bmbf.de/bmbf/shareddocs/downloads/files/2020-10-01_141-pm-pk-netzwerk-uni-medizin-covid-19.pdf External link
3.
Gehring S, Eulenfeld R; German Medical Informatics Initiative. Unlocking Data for Research and Health Care. Methods of Information in Medicine. 2018;57:e46-e49. DOI: 10.3414/ME18-13-0001 External link
4.
Haux R. Health Information Systems - from Present to Future? Methods of Information in Medicine. 2018;57:e43-e45. DOI: 10.3414/ME18-03-0004 External link
5.
Medizininformatik Initiative. CODEX COVID-19 Data Exchange Platform. [cited 2021 March 31]. Available from: https://www.medizininformatik-initiative.de/de/use-cases/codex-covid-19-data-exchange-platform External link
6.
Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, Da Silva Santos LB, Bourne PE, et al. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 2016;3:160018. DOI: 10.1038/sdata.2016.18 External link
7.
European Union (EU). Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC: GDPR. 2016.
8.
Medizininformatik Initiative. Medizininformatik-Initiative liefert Datenbasis für COVID-19-Forschung. 2021 January 15 [cited 2021 March 31]. Available from: https://www.medizininformatik-initiative.de/de/medizininformatik-initiative-liefert-datenbasis-fuer-covid-19-forschung External link
9.
Bundesministerium für Bildung und Forschung. CODEX bündelt Daten für die Covid-19-Forschung. 2021 January 20 [cited 2021 March 31]. Available from: https://www.gesundheitsforschung-bmbf.de/de/codex-bundelt-daten-fur-die-covid-19-forschung-12743.php External link
10.
Netzwerk Universitätsmedizin. Aufgaben und Ziele. [cited 2021 March 31]. Available from: https://www.netzwerk-universitaetsmedizin.de/aufgaben-und-ziele External link
11.
Sass J, Bartschke A, Lehne M, Essenwanger A, Rinaldi E, Rudolph S, Heitmann KU, Vehreschild JJ, von Kalle C, Thun S. The German Corona Consensus Dataset (GECCO): a standardized dataset for COVID-19 research in university medicine and beyond. BMC Medical Informatics and Decision Making. 2020;20:341. DOI: 10.1186/s12911-020-01374-w External link
12.
Covid-19 Research-Dataset GECCO: JSON Representation. [cited 2021 March 31]. Available from: http://art-decor.org/decor/services/RetrieveDataSet?id=2.16.840.1.113883.3.1937.777.53.1.1&effectiveDate=2020-04-08T13:04:13&language=de-DE&ui=en-US&format=json External link
13.
ART-DECOR. [cited 2021 March 31]. Available from: https://www.art-decor.org External link
14.
GECCO FHIR Profiles. [cited 2021 March 31]. Available from: https://simplifier.net/ForschungsnetzCovid-19 External link
15.
Bundesinstitut für Arzneimittel und Medizinprodukte (BfArM). ICD-10-GM. [cited 2021 March 31]. Available from: https://www.dimdi.de/dynamic/en/classifications/icd/icd-10-gm External link
16.
McDonald CJ, Huff SM, Suico JG, Hill G, Leavelle D, Aller R, Forrey A, Mercer K, DeMoor G, Hook J, Williams W, Case J, Maloney P. LOINC, a universal standard for identifying laboratory observations: a 5-year update. Clinical chemistry. 2003;49:624–633. DOI: 10.1373/49.4.624 External link
17.
SNOMED International. SNOMED-CT. [cited 2021 March 31]. Available from: https://www.snomed.org/snomed-ct External link
18.
Harris PA, Taylor R, Minor BL, Elliott V, Fernandez M, O'Neal L, McLeod L, Delacqua G, Delacqua F, Kirby J, Duda SN. The REDCap consortium: Building an international community of software platform partners. Journal of Biomedical Informatics. 2019;95:103208. DOI: 10.1016/j.jbi.2019.103208 External link
19.
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. Journal of Biomedical Informatics. 2009;42:377–381. DOI: 10.1016/j.jbi.2008.08.010 External link
20.
Lautenschläger R, Kohlmayer F, Prasser F, Kuhn KA. A generic solution for web-based management of pseudonymized data. BMC Medical Informatics and Decision Making. 2015;15:100. DOI: 10.1186/s12911-015-0222-y External link
21.
HL7 International. HL7 FHIR. [cited 2021 March 31]. Available from: https://www.hl7.org/fhir/ External link
22.
IBM. IBM FHIR Server. [cited 2021 March 31]. Available from: https://ibm.github.io/FHIR External link
23.
Medizininformatik Initiative. Mustertext zur Patienteneinwilligung. [cited 2021 March 31]. Available from: https://www.medizininformatik-initiative.de/de/mustertext-zur-patienteneinwilligung External link
24.
CDISC. ODM-XML. [cited 2021 March 31]. Available from: https://www.cdisc.org/standards/data-exchange/odm External link
25.
Spring. Spring Boot. [cited 2021 March 31]. Available from: https://spring.io/projects/spring-boot External link
26.
Spring. Spring Framework. [cited 2021 March 31]. Available from: https://spring.io/projects/spring-framework External link
27.
FasterXML. jackson. [cited 2021 March 31]. Available from: https://github.com/FasterXML/jackson External link
28.
FasterXML. jackson-dataformat-xml. [cited 2021 March 31]. Available from: https://github.com/FasterXML/jackson-dataformat-xml External link
29.
HAPI. Package 'org.hl7.fhir.r4.model'. [cited 2021 March 31]. Available from: https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-r4/org/hl7/fhir/r4/model/package-summary.html External link
30.
Oracle. Package 'java.util.stream'. [cited 2021 March 31]. Available from: https://docs.oracle.com/en/java/javase/16/docs/api/java.base/java/util/stream/package-summary.html External link
31.
HAPI. HAPI FHIR. [cited 2021 March 31]. Available from: https://hapifhir.io/ External link
32.
Hund H, Wettstein R, Heidt CM, Fegeler C. Executing Distributed Healthcare and Research Processes – the HiGHmed Data Sharing Framework. Studies in Health Technology and Informatics. 2021;278:126-133. DOI: 10.3233/shti210060 External link
33.
HiGHmed. Data Sharing Framework. [cited 2021 March 31]. Available from: https://github.com/highmed/highmed-dsf/ External link
34.
Bild R, Bialke M, Buckow K, Ganslandt T, Ihrig K, Jahns R, Merzweiler A, Roschka S, Schreiweis B, Stäubert S, Zenker S, Prasser F. Towards a comprehensive and interoperable representation of consent-based data usage permissions in the German medical informatics initiative. BMC Medical Informatics and Decision Making. 2020;20:103. DOI: 10.1186/s12911-020-01138-6 External link
35.
HL7 Deutschland e.V. Einwilligungsmanagement. [cited 2021 March 31]. Available from: https://simplifier.net/Einwilligungsmanagement/ External link