Overview over all known ETL tools and there capabilities for loading data into the tranSMART database.

Overview of the ETL tools

The tranSMART Project Management Committee has decided to focus our efforts on transmart-batch and tmDataLoader going forward.

ETL toolOpen
Source
tranSMART version
(Development Roadmap)
DownloadManual
transmart-data(Haken)17.1 and earlier
(for data dictionaries and database management)

16.2 and earlier: https://github.com/tranSMART-Foundation/transmart-data

17.1: https://github.com/tranSMART-Foundation/transmart-core/tree/master/transmart-data

Loading data with transmart-data
tMDataLoader(Haken)16.2 and earlierhttps://github.com/Clarivate-LSPS/tMDataLoaderhttps://github.com/Clarivate-LSPS/tMDataLoader/wiki
https://drive.google.com/file/d/0ByehpOFIhEbadDZiT1VvYW5ERnM/view
transmart-batch(Haken)17.1 and earlier

16.2 and earlier: https://github.com/tranSMART-Foundation/transmart-batch

17.1: https://github.com/tranSMART-Foundation/transmart-core/blob/master/transmart-batch

16.2 and earlier: https://github.com/tranSMART-Foundation/transmart-batch/tree/master/docs

17.1: https://github.com/tranSMART-Foundation/transmart-core/blob/master/transmart-batch/docs/

Integrated Curation Environment (ICE)(Haken)16.2 and earlierhttps://github.com/transmart/transmart-ICEhttps://drive.google.com/file/d/0B8lizkKDeaKhMWZBWnlnODVEQW8/view
Kettle(Haken)16.2 and earlierhttps://github.com/transmart/tranSMART-ETLLoading data with Kettle (Step by step tranSMART ETL Guide)

Overview of the loading capabilities (state of 18.10.2016)

Data type / ETL tooltransmart-datatMDataLoadertransmart-batchIntegrated Curation Environment (ICE)

SupportHDDSupportHDDSupportHDDSupportHDD
Clinical

Y

- - -

Y

- - -

Y

- - -

Y

- - -

DictionaryY- - -N- - -N- - -N- - -
aCGH / CNV *

Y

Y

Y

Y

Y

Y

N

N

Metabolomics

Y

Y

Y

Y

Y

Y

Y

Y

miRNA

Y

Y

Y

Y

Y

Y

Y

Y

mRNA

Y

Y

Y

Y

Y

Y

Y

Y

Proteomics

Y

Y

Y

Y

Y

Y

Y

Y

RNASeq

Y

Y

Y

Y

Y

Y

Y

Y

SNP

N

N

Y

Y

N

N

Y

Y

VCF

Y

Y

Y

Y

N

N

N

N

* aCGH data is called CNV data in the ETL tool transmart-batch

Columns:

  • Support: The column tells if an import is generally possible
  • HDD: The column tells if an import as an highdimensional data is possible (for explanation of HDD see here: Supported Data Types)

Values:

  • Y: the ETL tool is able to load the specified data
  • N: the ETL tool is NOT able to load the specified data


Further information