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e-Biobanking for Inflammatory Bowel Diseases

Data2Semantics (From Data to Semantics for Scientific Data Publishers)

Objectives background and description of work in WP

In the String of Pearls project (, a joint infrastructure has been build to collect and access the patient data and biomaterials of at least eight patient categories. In this project a joint database and biobank for all patients with a specific diagnosis using uniform definitions and storage circumstances. In this workpackage we will consider the Inflammatory Bowel Disease (IBD) patient cohort.

The IBD data is collected at all UMCs and stored at the LUMC, using the regular electronic patient records to store patient data including imaging data and biobanks to store biomaterial and already completed analyses of the biomaterials. Clinicians of all UMCs have agreed on uniform definitions. The IBD disease has high degree of heterogeneity and hence the right diagnose and treatment is difficult.

The workpackage, which will be carried out in close cooperation with Daan Hommes (LUMC, Professor of Gastroenterology, IBD coordinator) consists of three parts:

  1. Transformation to e-biobank. The best representation for storing data is not necessarily the best representation for mining them. We will consider how the IBD patient cohort can be transformed to an e-biobank environment, embedded in VL-e, where the focus is on knowledge discovery from the cohort. Data preparation, linking, integration, modeling, evaluation, specific interest scans but also unbiased scans of data should be supported.
  2. Image integration. The common visualization platform for linking images of different modalities of the Cyttron project will integrated.
  3. Subgroup discovery. The discovery of (interesting) subgroups has a high practical relevance for IBD. Subgroup discovery is well suited for finding dependencies, i.e., discovering relations between a dependent and (several) independent variables, for inductive and explorative data analysis tasks.
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