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  T3/Oat Sandbox

Data Submission

  • Data templates are Excel, .txt, or .csv worksheets with column headers for the data T3 requires or accepts.
  • The example values can be replaced with your own. Notes about the restrictions for valid data are included in the templates.
  • Once populated, the files can be loaded into T3 using the Curate menu, which is available to registered Sandbox users.
  • To make updates or corrections, edit your file and reload.
  • Please use the oat Sandbox for test-loading your files. When they're ready, click here to submit them to the T3 Curator for loading into the official database.

Instructions - Rules for filling in the templates, and sequence of submission
Tutorial1 Register Login
Tutorial1 Uploading germplasm information
Tutorial2 Creating line panels in T3 Oat
Tutorial2 Line Submission
Tutorial3 Creating line panels
Tutorial3 Uploading phenotype trial descriptions and data
Tutorial4 Phenotype data
Tutorial4 Uploading marker information
Tutorial5 Creating marker panels
Tutorial5 Uploading Marker information
Tutorial6 Creating Marker Panels
Tutorial6 Uploading genotype experiment descriptions and data
Tutorial7 Genotype Experiments and Data
Tutorial7 T3 and the Android FieldBook
Tutorial8 T3 and Android FieldBook

Data Templates

Topic Link Modified Contents
Germplasm Lines Oat06Nov17 Name, synonyms, pedigree for oat
Genetic Characters12Dec13 Genes, QTLs, trait-linked markers, market class
Name conversion macros24Sep11 Excel spreadsheet to convert germplasm names to T3 formatted names.
Phenotyping Traits16Sep11 Please discuss with the curators before adding a new trait.
Trial description02Nov16 Location, planting date, experimental design...
Trial means02Nov16 Values for all traits for test lines and checks, summary statistics
Plot-Level Results30Jul13 Trait values for each plot
Fieldbook07Apr14 Field map
Canopy Spectral
CSR System29Mar13 Instrument annotation
CSR description27Feb13 Description of the CSR experiment
CSR results03Jan13 Data file format
Genotyping Experiment description30Sep13 Platform, software, manifest file, experiment details...
Line translation04Nov11 Line Name and Trial Code
Illumina data03Jan13 alleles for lines and markers (coded as A or B)
GBS data11Apr14 alleles for lines and markers (coded as ACTG, N = missing, H = heterozygous)
GBS data, over 100K markers07Nov14 instructions for loading large GBS data sets using the command line
DArT data17Jul13 alleles for lines and markers (coded as 1 = present, 0 = absent)
Experiment results (1D)16Sep11 1D table of alleles for lines and markers
Markers Sequence Generic24Feb14 Marker sequences and allele definitions
Sequence Illumina OPA16Sep11 Markers from Illumina Manifest, Golden Gate OPA format
Sequence Illumina Infinium21Aug12 Markers from Illumina Manifest, Infinium HD format
Markers from DArT19Jun13 Markers from Diversity Array Technologies
Gene function04Nov11 Sequence annotations and name synonyms
Genetic Character markers15Feb13 Trait-linked markers named for their associated gene or QTL
Map location16Sep11 Genetic maps

In 2009 the Toronto International Data Release Workshop agreed on a policy statement about prepublication data sharing. Accordingly, the data producers are making many of the datasets in T3 available prior to publication of a global analysis. Guidelines for appropriate sharing of these data are given in the excerpt from the Toronto Statement

I agree to the Data Usage Policy as specified in Toronto Statement.