PI's: Prof. Dr. Hans-Werner Mewes, Prof. Dr. Klaus A. Kuhn     
PhD Candidate: Frederick Kleine, Dipl.-Bioinf.

The aim of the Thesis work proposed within the framework of the GSISH cross-faculty projects is the utilization of semantic data integration technologies in the context of clinical research and omics (genomics, proteomics, ...) related experimental data with a special emphasis of the knowledge integration from genetic studies and complex molecular phenotypes. As such the project is of highest relevance for the practical integration of clinical study data within the context of biomedical knowledge. The project is based at the Chair of Medical Informatics, TUM medical center rechts der Isar, in cooperation with the Institute of Bioinformatics and Systems Biology at Helmholtz Center München.

Utilization of generic semantic technologies and data integration solutions will lead to a prototype capable to achieve a context oriented knowledge discovery system for the foundation of decision support systems (e.g. study of phenotypic data in patients with markers for disease). The project aims to develop a prototype for a domain specific workspace in a clinical trial environment.

The thesis work will evaluate, develop and (as a prototype) implement a generic solution integrating three major components (Wurst et al., 2008): (1) access to clinical research data together with selective access to clinical repositories, based on legal requirements and combined with pseudonymization concepts (2) molecular data such as genotype, metabotype, expression profiles (3) biological network information as deduced from databases, literature, annotation, computational approaches.

Since these goals are far reaching, the project is based on existing or developing technologies in close collaboration with the Kuhn and Mewes groups. (1) will employ the architectural concepts developed and further elaborated in cooperation with the Chair of Database Systems (Vaz Salles et al., 2007) (2) will start with the development of use cases based on BioXM/Viscovery tools, and (3) will interface to the knowledge system as developed by the Stümpflen group (current version of GeKnowMe). The project is based at the Chair of Medical Informatics, TUM Medical Center "Rechts der Isar", in cooperation with the Institute of Bioinformatics and Systems Biology at Helmholtz Center Munich.