Jochem studied Biomedical Sciences and Bioinformatics. As an intern at The Hyve he finished his master’s degree with a focus on technical requirements for the integration of diverse molecular data types (e.g. from genomics, transcriptomics, proteomics). He later joined The Hyve as a data scientist and project manager
Title: The TraIT-The Hyve Data Team: The process, tools and the FAIR data principle
The CTMM-TraIT Data Team, part of the Translational IT project of the Dutch public-private partnership Center for Translational Molecular Medicine, is a collaboration between hospital data managers and The Hyve. We provide data services for projects that are interested in the open source translational research tools in the TraIT portfolio. In addition to tranSMART, this includes cBioPortal, EGA and tEPIS. Over the past two years more than 20 projects have been accommodated in tranSMART by the TraIT Data Team. In this talk I will share the process and the tools we use in the Data Team workflow.
Our process involves the study representative at different stages, namely in (1) creating an understanding of the project, (2) modeling the project data to the tranSMART data model in the best way possible, and (3) organising the tranSMART concept tree. Due to our collaborative method, and the complexity of tranSMART input files, we spent a large proportion of our time communicating about the concept tree. To facilitate this we developed a graphical editor, The Arborist, giving the non-technical user easy control of the concept tree. This collaboration greatly reduces time spent on inefficient communication and increases satisfaction of the Study representative.
In our data curation we focus on the reusability of datasets. We are therefore working with research partners to make data FAIR, by following the principles of making data Findable, Accessible, Interoperable, and Reusable. By this we hope to make tranSMART a central piece in rich workflows where data is sent through many specialised tools.