Alexander Schmitz

Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisReviewForskningpeer review


  • Charles Vesteghem, Aalborg Universitet
  • ,
  • Rasmus Froberg Brøndum, Aalborg Universitet
  • ,
  • Mads Sønderkær, Aalborg Universitet
  • ,
  • Mia Sommer, Aalborg Universitet
  • ,
  • Alexander Schmitz
  • Julie Støve Bødker, Aalborg Universitet
  • ,
  • Karen Dybkær, Aalborg Universitet
  • ,
  • Tarec Christoffer El-Galaly, Aalborg Universitet
  • ,
  • Martin Bøgsted

Compelling research has recently shown that cancer is so heterogeneous that single research centres cannot produce enough data to fit prognostic and predictive models of sufficient accuracy. Data sharing in precision oncology is therefore of utmost importance. The Findable, Accessible, Interoperable and Reusable (FAIR) Data Principles have been developed to define good practices in data sharing. Motivated by the ambition of applying the FAIR Data Principles to our own clinical precision oncology implementations and research, we have performed a systematic literature review of potentially relevant initiatives. For clinical data, we suggest using the Genomic Data Commons model as a reference as it provides a field-tested and well-documented solution. Regarding classification of diagnosis, morphology and topography and drugs, we chose to follow the World Health Organization standards, i.e. ICD10, ICD-O-3 and Anatomical Therapeutic Chemical classifications, respectively. For the bioinformatics pipeline, the Genome Analysis ToolKit Best Practices using Docker containers offer a coherent solution and have therefore been selected. Regarding the naming of variants, we follow the Human Genome Variation Society's standard. For the IT infrastructure, we have built a centralized solution to participate in data sharing through federated solutions such as the Beacon Networks.

TidsskriftBriefings in bioinformatics
Sider (fra-til)936-945
Antal sider10
StatusUdgivet - 21 maj 2020
Eksternt udgivetJa

Bibliografisk note

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