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User perspective

From a users perspective tranSMART only differs three differend data types, which are visualised in the hierarchical i2b2 tree through different symbols.

High Level Data TypeSymbol in transmartAppExampleAbbreviation
Numeric / Continous

Age

LDD (low dimensional data)

Categoric / Discrete

Gender
High Dimensional

Omics (mRNA, SNP, ...)HDD (high dimensional data)

ETL expert perspective

TranSMART supports a various number of data types.

Low Level Data TypeHigh Level Data TypeVisualised in the tree
Clinical DataCategoric / Numeric data(Haken)
DictionaryCategoric data(Fehler)
aCGH / CNVHigh dimensional data(Haken)
MetabolomicsHigh dimensional data(Haken)
miRNA (qPCR & Seq)High dimensional data(Haken)
mRNAHigh dimensional data(Haken)
ProteomicsHigh dimensional data(Haken)
RBMHigh dimensional data(Haken)
RNASeqHigh dimensional data(Haken)
SNPHigh dimensional data(Haken)
VCFHigh dimensional data(Haken)

By using the plugins XNAT Import Plugin and XNAT Viewer Plugin tranSMART can be extended for supporting imaging data (derived imaging data and links to images).

Database perspective

In tranSMART exist two import database schemas for storing the imported data:

Database schemaMeaning
i2b2demodata.*Storing the low dimensional data as entity-attribute-value.
deapp.*

Storing the high dimensional data as relational data.

For an import as high dimensional data, there are pre-defined database tables needed!

The high dimensional data is stored in the following database tables:

High dimensional data typeDatabase table
aCGH / CNVdeapp.de_subject_acgh_data
Metabolomicsdeapp.de_subject_metabolomics_data
miRNAdeapp.de_subject_mirna_data
mRNAdeapp.de_subject_microarray_data
Proteomicsdeapp.de_subject_protein_data
RBMdeapp.de_subject_rbm_data
RNASeqdeapp.de_subject_rnaseq_data
SNP

deapp.de_snp_calls_by_gsm
deapp.de_snp_copy_number
deapp.de_snp_data_by_patient
deapp.de_snp_data_by_probe
deapp.de_snp_data_dataset_loc
deapp.de_snp_info
deapp.de_snp_probe
deapp.de_snp_probe_sorted_def
deapp.de_snp_subject_sorted_def
deapp.de_subject_snp_dataset
deapp.de_subject_haploview_data

VCF

deapp.de_variant_dataset
deapp.de_variant_population_data
deapp.de_variant_subject_detail
deapp.de_variant_subject_id
deapp.de_variant_subject_summary

Old overview

 Have a look

Dictionaries

Below are the various data types that can be loaded into tranSMART.

  • Metadata
    • Study, concept, patient metadata
    • Hyperlinks to source data
  • Categorical/numerical data
    • Clinical / NHTMP
    • Derived imaging data / Biobanking data
  • High dimensional data
    • Gene expression: Micro array / mRNAseq, miRNAseq / qPCR miRNA
    • Copy Number Variation data / Array CGH
    • Small Genomic Variants: SNP, indel – VCF format
    • Peptide or protein quantities
    • Metabolite quantities
  • No labels