Users perspectice
From a users perspective tranSMART only differs three differend data types, which are visualised in the hierarchical i2b2 tree through different symbols:
Data type | Symbol | Example | Abbreviation |
---|---|---|---|
Numerical / Continuous | Age | LDD (lowdimensional data) | |
Categorical / Discreet | Gender | ||
Highdimensional data | Omics (mRNA, SNP, ...) | HDD (highdimensional data) |
Data perspective
In tranSMART exist two important database schema for storing the imported data:
Database schema | |
---|---|
i2b2demodata.* | Storage of lowdimensional data as EAV. |
deapp.* | Storage of highdimensional data in datatype-specific tables |
Import perspective
An adminstrator can import multiple datatypes into tranSMART:
Data type | LDD | HDD | HDD-Datatables |
---|---|---|---|
Clinical | X | ||
aCGH / CNV | X | deapp.de_subject_acgh_data | |
cDNA | X | ||
Metabolomics | X | deapp.de_subject_metabolomics_data | |
Methylation | X | ||
miRNA | X | deapp.de_subject_mirna_data | |
mRNA | X | deapp.de_subject_microarray_data | |
Proteomics | X | deapp.de_subject_protein_data | |
RBM | X | deapp.de_subject_rbm_data | |
RNASeq | X | deapp.de_subject_rnaseq_data | |
SNP | X | deapp.de_snp_calls_by_gsm | |
VCF | X | deapp.de_variant_dataset |
An overview of the capabilities of the different existing ETL-tools can be found here: Data loading tools