ICE, the Sanofi curation & loading framework for tranSMART, is a tool developed by Sanofi starting from 2012.
- 0 released in Github in July 2012
- 1 released in Github in September 2012
- 4 built in 2014 to support Sanofi new tranSMART release
ICE aims to provide a user-friendly interface to load data into tranSMART, from already created mapping files, or by helping users to create these mapping files. The tool helps curators to:
- Create the study tree
- Map labels (column heads) with reference terminology
- Link with Bioportal website
- Map values
- Define visit names and time points
- Trigger tranSMART ETL pipelines and load data in a click
- Monitor loading success
- Perform quality controls
Different data types can be loaded into tranSMART using ICE:
- Clinical data
- Gene expression data
- RNAseq data
- miRNA QPCR data
- miRNAseq data
- Proteomics (mass spectrometry) data
- RBM data
- Metabolomics data
- SNP Data
- Gene expression analysis
Tables in the “Additional information” section at the end of this guide describe the data and annotation file formats required for each high dimensional data type.
ICE can also be used to transfer files for the Browse part of tranSMART, in case the files are stored in tranSMART application server (and not in a MongoDB database).
This application is provided under license GPL v.3 by Sanofi-Aventis Recherche et Développement.
This application has been tested with tranSMART Sanofi RC2 version. It should theoretically work with tranSMART version 1.2 (Oracle), but has not been tested.
Tested Java Runtime Environments are JRE 1.6 and JRE 1.7
This application has been implemented in Java, with Eclipse Rich Client Platform (RCP). It uses java libraries “Kettle API” and “JDBC” (database connection) and Kettle jobs developed by Recombinant. ETL procedures originally created by Recombinant were further developed by Cognizant as part of tranSMART RC2 development.
- ICE User Guide v1.4 https://drive.google.com/file/d/0B8lizkKDeaKhMWZBWnlnODVEQW8/view