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University of Basel


A rack of biological samples being retrieved from a liquid nitrogen tank.
© Universit√§tsspital Basel

Many excellent resources exist at the various institutes and research laboratories, and the university hospital stores patient-derived biological samples and large amounts of clinically valuable data every day. The data is acquired by the core clinical information system and many expert systems, including pathology, radiology and biobank systems.

For optimal research utilization, data needs to be extracted from the original clinical or expert systems and transformed and integrated into one consolidation system, which provides a holistic and analyzable view on anonymized or coded patient information to the scientist. Furthermore, data standardization and harmonization is required as basis for data interoperability and hence sharing of scientific data between research institutions.

The goal of PHB is to evaluate the existing infrastructure and to identify and implement required components needed for optimal research utilization, interoperability and sharing.

The Ethical, Legal, and Societal Implications surrounding the sharing of biospecimens and clinical data are addressed by its own PHB project team. This work will be done in synchronization with the national ELSI advisory group of the Swiss Personalized Health Network (SPHN).

Clinical Data Warehouse (CDW)
Clinical Data Warehouse (CDW)

Clinical Data Warehouse

97% of patients treated at the University Hospital Basel are not enrolled in a clinical trial but receive standard care. To optimally support research and personalized health, it must be ensured that valuable clinical routine information about their diagnosis, treatment, and outcome is easily accessible for the scientists. The challenge is to consolidate the information, stored in the clinical information system and many expert systems, and to present the data to scientists in a technically analyzable form and compliant to legal regulations.


The Clinical Data Warehouse (CDW) denominates an IT platform to merge the vast riches of clinical data from routine clinical practice and make them available for research projects. This will greatly increase the data pool required for personalized health research and reach also those patients not enrolled in a clinical trial. Embedding “omics” and other research data derived from patients’ biological specimens adds even more scientific value to the accessible research data pool.


An interface for data sharing and collaborative research with national and international partners is a key factor. PHB is working towards interoperability within the PH Alliance Zurich-Basel and the Swiss Personalized Health Network (SPHN). The ELSI groups of both PHB and SPHN play instrumental roles in ensuring that the ethical, legal, and societal implications are adequately addressed, e.g. that the patient’s consent information is always linked to all clinical data and biological material.


Tasks of the PHB Clinical Data Warehouse Project Team:

  • Contribute to the strategy of the University Hospital Basel to adapt its IT infrastructure to the new challenges.
  • Define requirements and recommend platforms, standards, and procedures ensuring the Clinical Data Warehouse will be functional and serves its purpose.
  • Specify the data set to be made accessible for personalized health-focused research through the Clinical Data Warehouse. This data set should comprise various sources, including diagnostic imaging, pathology, clinical, and demographic data
  • Embed with the clinical information data generated from research projects, including “omics” data from patient-derived specimens.
  • Liaise with the PHB Biobanking Project Team to integrate the biospecimen catalog and biosample-derived data into the Clinical Data Warehouse.
  • Work with the ELSI Project Teams of PHB and SPHN to ensure the technical framework complies with the ethical, legal, and societal implications of data processing.
  • Ensure the Clinical Data Warehouse is interoperable with the systems of our partners of the PH Alliance Zurich-Basel and the Swiss Personalized Health Network.


Biobanks are collections of biological materials, e.g. blood and tissue samples, linked with personal data from the donor. Using such collections in combination with “omics” technologies and other sources of data allows finding associations between the genome, environment and the appearance, course, and treatment success of diseases. Biobanks are therefore an important cornerstone of Personalized Health.


Many excellent biobanks with high quality biospecimens and data exist at the various institutes and the University Hospital. While the size, nature of the biological material, and the purpose of collection largely differ between different biobanks, they all have in common the need for suitable infrastructure and standards for collecting, processing, storing, and using the biospecimens while honoring the increasingly complex ethical, legal, and societal challenges.

An IT solution is needed that enables a harmonized administration and linkage of the existing biospecimens with various data sources (e.g. clinical history, demographics, “omics” data) as a prerequisite for making the collected samples available for research and healthcare.


Tasks of the PHB Biobanking Project Team:

  • Implement the biobanking strategy of the University Hospital Basel to create and maintain a sustainable biobanking infrastructure.
  • Integrate our local partner institutions, especially the University Children's Hospital, University Psychiatric Clinic and the Swiss Tropical and Publich Health Institute  in harmonizing and interconnecting the different institutional biobanks.
  • Synchronize the local biobanking strategy and its implementation with that of SPHN and the Swiss Biobanking Platform (SBP) to enable accessibility of the biobank catalogue.
  • Create an interface with the Clinical Data Warehouse to link clinical and research data with the respective biospecimens.
  • Work with the ELSI Project Teams of PHB and SPHN to ensure the technical framework complies with the ethical, legal, and societal implications of biobanking.
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