data_formats

Loading tranSMART data

For all data types

• Parameters for all data types
  • study-params.md - Study level parameters regarding security, study ID and top node.
• Metadata
  • tags.md - Loading study, concept, patient metadata and links to source data per concept.

Low-dimensional data

• Clinical data
  • clinical.md - Loading numerical and categorical low-dimensional data from clinical, non-high throughput molecular profiling, derived imaging data, biobanking data or links to source data per patient.
    • word-mapping.md - Redefine categorical values, without changing the source data.
    • ontology-mapping.md - Map variables to ontology codes to create standardized cross-study concepts.
    • trial-visit-mapping.md not yet implemented - Provide a time unit and value for your trial visit labels.
    • patient-visit-mapping.md not yet implemented - Provide start and end dates for your patient visits.
    • templates.md - Using templates in the clinical data paths.
    • xtrial.md - Uploading across trial clinical data for pre-2017 versions of tranSMART.

High-dimensional data

• General high-dimensional data processing
  • hd-params.md - Parameters that are supported for all high-dimensional data types.
  • chromosomal_region.md - Tabular file structure for loading chromosomal regions.
  • subject-sample-mapping.md - Tabular file structure for loading subject sample mappings for HD data.
• mRNA gene expression data
  • expression.md - Loading microarray gene expression data.
  • rnaseq.md - Loading gene-level RNA-Seq data as read counts and normalized read counts.
  • under development - Loading transcript-level RNA-Seq data as read counts and normalized read counts.
• Copy Number Variation data
  • cnv.md - Loading CNV data from Array CGH (comparative genomic hybridisation), SNP Array, DNA-Seq, etc.
• Small Genomic Variants
  • not yet implemented - Loading small genomic variants (SNP, indel in VCF format) from RNAseq or DNAseq.
• Proteomics data
  • proteomics.md - Loading protein mass spectrometry data as peptide or protein quantities.
• Metabolomics data
  • metabolomics.md - Loading metabolite quantities.
• GWAS data
  • gwas.md - Loading Genome Wide Association Study data.

Other

• Unloading tranSMART data
  • backout.md - Deleting data from tranSMART.
• Loading I2B2 data
  • i2b2.md - Loading data to I2B2 with transmart-batch.