gms | German Medical Science

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

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie

02. - 06.09.2018, Osnabrück

Integration of biological networks into healthcare systems with FHIRgraph

Meeting Abstract

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  • Florian Auer - Universitätsmedizin Göttingen, Göttingen, Deutschland
  • Frank Kramer - Universitätsmedizin Göttingen, Göttingen, Deutschland
  • Tim Beißbarth - Universitätsmedizin Göttingen, Göttingen, Deutschland

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie. 63. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS). Osnabrück, 02.-06.09.2018. Düsseldorf: German Medical Science GMS Publishing House; 2018. DocAbstr. 260

doi: 10.3205/18gmds084, urn:nbn:de:0183-18gmds0849

Veröffentlicht: 27. August 2018

© 2018 Auer 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



In modern Systems Medicine approaches, as well as in bioinformatics analyses, biological networks are commonly used as abstract representation to capture increasingly complex aspects and associations. Albeit its benefits, the sharing of networks, the collaboration on network curation, keeping track of changes between different network versions, and detecting different versions itself, still is a major problem in network biology. Reproducibility and a standardized interface with existing healthcare systems are essential for research and application in a clinical setting.

To integrate network models into established infrastructure we combine two major technologies: The Network Data Exchange (NDEx) to manipulate, store and exchange networks of various types and formats, and Fast Healthcare Interoperability Resources (FHIR®) as next generation communication standard for healthcare systems and applications.

NDEx is an open-source software framework for the exchange of network data, available as public or private installation. For sharing and communication the Cytoscape Cyberinfrastructure Network Interchange Format (CX format) is used to define networks and its descriptive aspects. Inspired by the concept, we define FHIR resources, a set of modular reusable components, resembling the NDEx and CX core aspects. To demonstrate the interoperability with public and private NDEx server installations, we implemented these resources in FHIRgraph.

Currently, there's no complex data type available to represent networks within the FHIR framework, despite its increasing application in research. With FHIRgraph we not only facilitate the usage of biological networks, but also provide a standardized interface for exchange and collaboration.

The authors declare that they have no competing interests.

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