The main goal of the clinical infrastructure work package is the creation and utilization of unfied research data respositories which allow easy access of project relevant research data by all MyPathSem members. This goal is archived by the combination of (1) the establisment of a data store module, (2) the data acquisition of all relevant data from the clinical system to omics data from preceding research projects, (3) data harmonization, (4) data enrichment with local as well as world knowledge and the data integration into the data store module. For the data store module a two-layered approach with FAIRDOM/SEEK for the data file level and i2b2/tranSMART for the patient data level was chosen.
i2b2/tranSMART docker-compose implementation: https://gitlab.gwdg.de/medinfpub/tm_umg
Talend Open Studio i2b2/tranSmart-API connector: