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Tool in the Spotlight - tranSMART

Data integration in tranSMART data warehouse

tranSMART logo

 

 

 

 

tranSMART is an open-source data platform for translational research used by academic researchers and pharmaceutical companies around the world. Next to TraIT, it has been successfully deployed by a large number of publicly funded and public-private consortia, such as IMI eTRIKS, IMI EMIF, and IMI Translocation and in a number of large pharma companies, such as Janssen, Sanofi and Pfizer.

The platform enables scientists to develop and refine research hypotheses by investigating correlations between diverse data modalities ranging from demographics, lab results, and questionnaires, to high-throughput “omics” sources (copy number variations, gene expression, protein and metabolite abundance, and small genomic variants). It allows for the assessment of the researcher’s analytical results in the context of published literature and other work. Its audience includes principal investigators of biomedical research projects as well as clinical and basic biomedical researchers.

Because of its data integration capabilities tranSMART plays a pivotal role within the TraIT infrastructure. Data from other tools in the TraIT portfolio (OpenClinica, XNAT, Catalogue, and PhenotypeDB) are made available and integrated within tranSMART. It is therefore a convenient tool for biologists and clinicians, who can use the web interface to explore data in order to quickly form and test hypotheses, and bioinformaticians, who can use the REST API and an R package to programmatically access the data. Additionally, data can be exported to the Galaxy pipelining tool for further downstream analysis.

Over the past four years TraIT has been a key contributor to the international tranSMART community which is jointly responsible for the maturation of the platform. TraIT developers have built new functionality and added support for various molecular data types needed by translational research projects in The Netherlands. They have fixed numerous bugs in the software to bring the software to production level quality, and have built interfaces to other TraIT solutions (such as OpenClinica and XNAT).

Learn more on tranSMART at http://www.ctmm-trait.nl/trait-tools/transmart

cBioPortal

For specialized data visualization in the cancer disease areas the cBioPortal data warehouse (a private instance of the well known and loved cbioportal.org) is used in TraIT, providing a clear view of the genomic and proteomic aberrations across datasets and among different cancer data types. The tool will soon be available in the TraIT toolset linked to tranSMART for patient (sub)cohort selection.

If this sparks your interest, please contact servicedesk@health-ri.nl to explore the options to see your data along public datasets in tranSMART or cBioPortal.

 

Back to newsletter December 2016