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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 typeSymbolExampleAbbreviation
Numerical / Continuous

AgeLDD (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 typeLDDHDDHDD-Datatables
ClinicalX

aCGH / CNV
Xdeapp.de_subject_acgh_data
cDNAX

Metabolomics
Xdeapp.de_subject_metabolomics_data
MethylationX

miRNA
Xdeapp.de_subject_mirna_data
mRNA
Xdeapp.de_subject_microarray_data
Proteomics
Xdeapp.de_subject_protein_data
RBM
Xdeapp.de_subject_rbm_data
RNASeq
Xdeapp.de_subject_rnaseq_data
SNP
X

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
X

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

An overview of the capabilities of the different existing ETL-tools can be found here: Data loading tools

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