Fig. 1.

Mapping the TCGA experimental workflow to S3DB entities. A Genomic Characterization element links a raw array data file containing either copy number or expression to a patient's clinical information (1–3). The filename syntax “US14702406_251584710166_S01_GE2-v5_91_0806.txt” (1) was used to link the raw data to the patient indirectly using the information in the SDRF file. In the example, the raw data is obtained from Sample “TCGA-06-0132-01A” (2), which was collected from a tumor (as indicated by “01A”) of Patient “TCGA-06-0132” (3). Each of these links was assigned to an S3DB Statement whereas the links between domain descriptors “GenomicCharacterization”, “Sample” and “Patient” were assigned to S3DB Rules.