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Fig. 7 | BMC Genomics

Fig. 7

From: The biorepository portal toolkit: an honest brokered, modular service oriented software tool set for biospecimen-driven translational research

Fig. 7

CbioPortal – harvest integration architecture. The integrated query tool allows for a back and forth search between genes of interest and visualization in CBioPortal, and the tool for phenotype and specimen requests. We perform this integration in a similar fashion to the other tools in the tool-kit. We utilize a combination of constructing web endpoints and traditional ETL. The cancer genomics integration starts with a scripted pull of mutation data via a secure database connection utilizing elements of CBioPortal’s relational data structure to store this large set of data. Specimens known to the repository are loaded into the CBioPortal by the bioinformatics team with known specimen identifiers from the LIMS. This creates a natural link between any granular genomic data, the specimen and ultimately the subject. URLs are constructed in the query platform that allow for researchers to move from clinical and specimen driven queries directly to CBioPortal to visualize mutation data of interest

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