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

Implementing a FHIR-based interface between cBioPortal for Cancer Genomics and Hospital Information Systems

Meeting Abstract

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  • Niklas Reimer - Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, Universität zu Lübeck, Lübeck, Germany
  • Philipp Unberath - Department of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
  • Hauke Busch - Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, Universität zu Lübeck, Lübeck, Germany
  • Josef Ingenerf - IT Center for Clinical Research, Universität zu Lübeck, Lübeck, Germany; Institute of Medical Informatics, Universität zu Lübeck, Lübeck, 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. 227

doi: 10.3205/21gmds033, urn:nbn:de:0183-21gmds0339

Veröffentlicht: 24. September 2021

© 2021 Reimer et al.
Dieser Artikel ist ein Open-Access-Artikel und steht unter den Lizenzbedingungen der Creative Commons Attribution 4.0 License (Namensnennung). Lizenz-Angaben siehe



Introduction: Over the last years, precision oncology has significantly grown in popularity. Cancer treatment based on molecular markers offers new treatment options. This approach is implemented within molecular tumor boards (MTBs), consisting of an interdisciplinary team involving oncologists, pathologists, and bioinformaticians. The MIRACUM consortium [1], as part of the Medical Informatics Initiative Germany [2], is developing an IT solution for the needs of such MTBs. One of the tasks in this context is the integration of cBioPortal, an open-source data warehouse application for cancer genomics [3], [4]. To use this software in a clinical setting, additional features, such as message interfaces to the hospital information system, are required [5], [6]. Here we present an approach to exchange therapy recommendations from the MTB using the exchange standards HL7 FHIR and HL7 Version 2, enabling semantic interoperability as far as possible.

Methods: A front-end prototype tool for a form-based documentation of detailed therapy recommendations following the requirements by Buechner et al. [5] has been implemented before and is now extended to exchange JavaScript objects (JSON) through a RESTful interface. With FHIR being the intended data store, a bijective projection between JSON and FHIR is required to avoid redundancies and unnecessary additional data mappings. The representation of genomic findings in FHIR is supported by the implementation guide Genomics Reporting [7]. Another challenge in implementing a mediation layer is its integration with cBioPortal where data access is granted based on users and groups. Access to the therapy recommendations should follow the same principle. To ensure that all components correctly interact with each other, test cases are set up to guarantee a bijective projection between FHIR resources and JSON format. In addition, the validity of FHIR resources and HL7 Version 2 messages is evaluated using the validators that are integrated in their client libraries.

Results: FhirSpark is realized as a Web server with a RESTful interface that allows PUT and GET requests to save and query therapy recommendations. Internally the JSON objects exchanged through the RESTful interface are translated to FHIR resources and stored on a FHIR server. For queries, on the other hand, corresponding FHIR Search requests are generated to retrieve relevant data from the FHIR server and subsequently translated to the JSON format. To ease the integration with hospital information systems without support for HL7 FHIR, the option for HL7 Version 2 message streams is integrated as well.

Conclusion: The approach presented in this work provides a workflow to communicate MTB therapy recommendations from cBioPortal to the hospital information system through FhirSpark using FHIR and Version 2 of the HL7 standard family.

The proposed application FhirSpark offers tight integration with cBioPortal without the need for modifications to its source code. Acting as a mediation layer FhirSpark provides a bijective projection between the JSON format for cBioPortal and FHIR resources.

The authors declare that they have no competing interests.

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

This contribution has already been published [8].


Prokosch HU, Acker T, Bernarding J, Binder H, Boeker M, Boerries M, et al. MIRACUM: Medical Informatics in Research and Care in University Medicine. Methods of Information in Medicine. 2018 Jul;57(S 01):82–91.
Semler S, Wissing F, Heyder R. German Medical Informatics Initiative. Methods of Information in Medicine. 2018 Jul;57(S01):50–56.
Gao J, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013 Apr;6(269):l1.
Cerami E, et al. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer Discovery. 2012;2(5):401–404.
Buechner P, et al. Requirements Analysis and Specification for a Molecular Tumor Board Platform Based on cBioPortal. Diagnostics. 2020;10(2):93.
Unberath P, Knell C, Prokosch HU, Christoph J. Developing New Analysis Functions for a Translational Research Platform: Extending the cBioPortal for Cancer Genomics. Stud Health Technol Inform. 2019;258:46-50.
HL7 International Clinical Genomics Work Group. Genomics Reporting Implementation Guide. [Accessed 7 May 2021]. Available from: Externer Link
Reimer N, Unberath P, Busch H, Ingenerf J. FhirSpark - Implementing a Mediation Layer to Bring FHIR to the cBioPortal for Cancer Genomics [ [Proceedings Medical Informatics Europe MIE 2021 - Public Health and Informatics]. Stud Health Technol Inform. 2021 May 27;281:303-307. DOI: 10.3233/SHTI210169 Externer Link