gms | German Medical Science

Aims: A centralized Biobank Management System Architecture (BBMS) shall be integrated in order to improve biomedical research investigations by providing ubiquitous access to a comprehensive sample research database. Sample collections of pre-existing as well as new biobank projects shall be managed by the centralized BBMS. The samples shall be annotated with prior specified, consented, and well-structured metadata, documenting the individual sample characteristics, such as the donor’s clinical history or research results. Several data privacy and security issues must be considered. Furthermore, a search interface needs to be realized, allowing complex database queries with respect to the samples’ metadata annotations.

Methods: Semantic Mediawiki serves as central communication medium allowing a consented specification of research project aspects. The biobank management system StarLIMS is deployed, meeting the local requirements of: project-specific sample storage management, configurable transaction audit trails, and a comprehensive rights management. The open source clinical trials software OpenClinica is adapted and configured to securely hold the samples’ donors medical documentation.

A data warehouse is configured to join data from different databases and to provide a complete view on the data.

Results: Biobank WiKi Aachen (BIWIKA) is an adapted Semantic Mediawiki software system extended by several interfaces allowing convenient specification of: research projects, structured documentation parameters, and their characteristics, such as definition and domain. BIWIKA allows consenting discussions on research project aspects and standard operating procedures. StarLIMS has been configured according to the local preconditions and extended by new interfaces allowing convenient sample submission and detailed audit trail documentation. OpenClinica has been adapted and configured to securely store medical data for research meeting the demands on data privacy and security. The specified and consented projects in BIWIKA are implemented in StarLIMS and OpenClinica accordingly. The StarLIMS database comprehends the pre-existing sample collections and project-specific sample collections. Complex research investigations and statistical analysis can be performed in the data warehouse.

Conclusions: Research investigations on biomaterial samples are significantly improved by a centralized BBMS providing a comprehensive view on the characteristics of in parts spatially distributed sample collections. Investigations with respect to the samples’ prior specified, consented, and structured metadata characteristics can be performed as well as statistical analysis. Hence, long, tedious, and error-prone investigations for qualified biomaterial for research are omitted.