Loading the data
These datasets can be loaded using transmart-data (available on github: https://github.com/tranSMART-Foundation/transmart-data/tree/release-16.3).
From the top level transmart-data directory on your system (on Oracle, replace 'samples/postgres' with 'samples/oracle'):
Select a dataset from the library server and install each datatype in turn, starting with the clinical data (if any) and any platform annotation. Loading the ref_annotation target(s) identifies any platform annotation and installs if it is not already in the database. Finally load the remaining available datatypes(s) by specifying the Load Target shown in the table for each dataset.
For example, to load the complete set of data for study GSE13168 (load target RanchoGSE13168):
The files are available to download as tar.xz files from the tranSMART Foundation library server. Each .tar.xz file contains all the required datafiles plus a file with a .params type which defines all the parameters needed by the loading scripts. In general you need several of these files (e.g. clinical, annotation, expression) in order to load the complete study, and must load the clinical data first. This information should be sufficient to load the datasets using any other loader of your choice.
Scripts are also provided to load all targets for a given study from the top level transmart-data directory. The scripts will check they are running from the top-level transmart-data directory, check for an Oracle or PostgreSQL database defined by the ./vars file, and will load all targets for the selected study. See the Script column in the tables below. The individual datatypes will be downloaded automatically by the script.