gms | German Medical Science

64. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS)

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie

08. - 11.09.2019, Dortmund

Implementing ETL-processes for a Medical Data Integration Center - First experiences from the Heidelberg University Hospital

Meeting Abstract

  • Nilay Yüksekogul - Universitätsklinikum Heidelberg, Heidelberg, Germany
  • Nikita Meyer - Universitätsklinikum Heidelberg, Heidelberg, Germany
  • Lakshmi Shilpa Aguduri - UniversitätsKlinikum Heidelberg, Heidelberg, Germany
  • Angela Merzweiler - Universitätsklinikum Heidelberg, Heidelberg, Germany
  • Oliver Heinze - Universitätsklinikum Heidelberg, Heidelberg, Germany

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie. 64. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS). Dortmund, 08.-11.09.2019. Düsseldorf: German Medical Science GMS Publishing House; 2019. DocAbstr. 112

doi: 10.3205/19gmds169, urn:nbn:de:0183-19gmds1697

Published: September 6, 2019

© 2019 Yüksekogul 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

Introduction: The Heidelberg University Hospital is part of the HIGHmed [1] consortium and has the task to set up a Medical Data Integration Center in Heidelberg and collect the data using an openEHR [2] based data warehouse to ensure and improve semantic interoperability [3] between the members of the consortium. The common data model is based on openEHR archetypes. For this purpose, the data from the source systems were transformed into the openEHR data model and transported to the openEHR-based data warehouse using Extract, Transform and Load (ETL) routes. The objective of this work is to describe the experiences from the implementation of ETL processes for a Medical Data Integration Center in the Heidelberg University Hospital.

Methods: As a development method, Design and Creation [4] was used in conjunction with the agile project development method SCRUM using 14 day sprints. The requirements for the implementation of the ETL processes were determined together with the clinical stakeholders. In order to be able to collect the data from the individual source systems in a data warehouse, the data was enriched over several intermediate steps. Talend was used for the implementation of ETL routes.

Results: All administration and observational HL7 v2 messages were converted to XML in a preliminary step by the HL7 consumer, which was developed using the JAVA library HAPI [5], and further processed by Talend in ETL processes. The ETL process includes extraction from the relevant clinical source systems, mapping to the target data model, enrichment with additional data, and logging. Test cases were used to develop the process in an agile environment.

Discussion: The ETL tool Talend provides many benefits, even if it is not always easy to understand the functionalities immediately. Changes can be incorporated into the routes in an iterative process. The introduced methods and tools seem to be adequate not only to process data in a research setting, but also to use it in a live operation systems environment.

The authors declare that they have no competing interests.

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


References

1.
HiGHmed. [Accessed 2019 Mar 21]. Available from: http://www.highmed.org/ External link
2.
openEHR. [Accessed 2019 Mar 21]. Available from: https://www.openehr.org/ External link
3.
Haarbrandt B, Schreiweis B, et al. HiGHmed - An Open Platform Approach to Enhance Care and Research across Institutional Boundaries. Methods of information in medicine. 2018;57:e66-e81.
4.
Oates BJ. Researching Information Systems and Computing. London: SAGE Publications; 2006.
5.
HAPI The Open Source HL7 API for Java. [Accessed 2019 July 16]. Available from: https://hapifhir.github.io/hapi-hl7v2/ External link