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Introduction

These pages provide instructions on how to load data into a tranSMART installation.  They also provide guidance on how to curate and organize your data prior to loading.

For a brief video tutorial on how to load data into tranSMART using transmart-batch, click here. Video for tMDataLoader is coming.

 

ContentDescription
Curated Data RepositoryThis page contains curated data sets that are ready to load into tranSMART. Check back often to see what's been added.
Supported Data TypesAn overview of the types of data that tranSMART supports, and details of how to load each.

TranSMART ETL Guide (Kettle)

A guide to clinical and expression ETL from JnJ (May 2015)
eTRIKS Standards Starter Packthe eTRIKS project has developed a comprehensive approach to data standards for use with tranSMART. Data harmonisation begins with standards.
Integrated Curation Environment (ICE) GuideThe ICE is a GUI-based data loading framework developed by Sanofi (v1.4, Jan 2015).

Loading data using tMDataLoader

tMDataLoader Wiki

tMDataLoader is a command-line data loading interface developed by Clarivate Analytics (Formerly IP&Sciences, Thomson Reuters) (v2.1, May 2015).
Tutorial: How to load the Cell Line Use Case dataset with transmart-batchThis page describes how to load a very complete set of example cell line data from multiple platforms, using the transmart-batch ETL mechanism. Data are provided by the CTMM TraIT project.
CTMM TraIT OpenClinica-to-tranSMART ConverterFor those who use OpenClinica to acquire eCRF data, the CTMM TraIT project has developed tools to help transfer data from OpenClinica to tranSMART. This GitHub repository contains the tools and complete documentation.
Loading VCF files with transmart-dataHow to load Variant Call Format (VCF) files into tranSMART
TranSMART Guide for Manual Data DeletingSometimes you may want to delete data.

For details on the data loading with the Clarivate Analytics ETL tool, please see tMDataLoader Wiki. The wiki is updated regularly to document ETL updates and new options. 

 

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