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Published January 26, 2024 | Version v1
Project deliverable Open

D2.1 - SOPs for minimal clinical, image and omics data exchange

  • 1. ROR icon European Molecular Biology Laboratory
  • 2. ROR icon Lygature
  • 3. ROR icon Barcelona Supercomputing Center
  • 4. ROR icon Erasmus MC
  • 1. University of Twente
  • 2. Netherlands Comprehensive Cancer Organisation
  • 3. Masaryk University
  • 4. ROR icon Biobanking and Biomolecular Resources Research Infrastructure Consortium
  • 5. Vall d´Hebron Institut d´Oncologia
  • 6. ROR icon Vall d'Hebron Institute of Oncology
  • 7. ROR icon European Molecular Biology Laboratory
  • 8. ROR icon Lygature

Description

In recent years, partially due to the rise of AI, the trend in cancer research is to combine data from different sources and different modalities. For combining data from different data types within one modality, the main challenges include a lack of standardisation in the data format, data model, metadata model, and data access procedures. Hence, there is a clear need for harmonisation and interoperability. When combining and integrating data from different modalities, these challenges become even more pressing.

In EOSC4Cancer, we focus on all these aspects in the context of the use cases that cover the patient journey from cancer prevention to diagnosis to treatment, laying the foundation of data trajectories and workflows for future cancer mission projects. To address the above challenges, in this deliverable, we formulate standard operating procedures (SOPs) per data type for data access, data models, and data interoperability. 

The results are SOPs for seven data types widely used in cancer research: exposome, cancer registry, screening, clinical, genomic, radiology, and pathology data. Instead of niche SOPs for the EOSC4Cancer datasets, we provide more general considerations and guidelines, so they can be used by the broader community. Lastly, we provide some insights in next steps to improve these SOPs.

Files

EOSC4Cancer_D21_zenodo.pdf

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