3.7. Genotype, Phenotype, and Environment

The fourth set of fields in TPPS is the Genotype, Phenotype, and Environment section, where users upload Genotypic, Phenotypic, and Environmental data and metadata about each organism. In multi-species submissions, users can reuse data from the previous species by checking the ‘<Genotype/Phenotype/Environmental> information for <organism i> is the same as <genotype/phenotype/environmental> information for <organism i-1>.’ box, which is only available after the first organism. The form fields and their properties are as follows:

  • Tree Species x: fieldset

3.7.1. Phenotype

  • Phenotype Information: fieldset - only visible if the user selects ‘Genotype x Phenotype’, ‘Genotype x Phenotype x Environment’, or ‘Phenotype x Environment’ from ‘Data Type’ in Study Design

    • Phenotype x: fieldset

      • Phenotype Name: textfield - autocomplete options from chado.phenotype table
      • Phenotype Attribute: textfield - autocomplete options from chado.phenotype table
      • Phenotype Description: textarea
      • Phenotype Units: textfield - autocomplete options from chado.phenotypeprop table
      • Phenotype Structure: textfield - autocomplete options from chado.phenotype table - only visible if the ‘Phenotype x has a structure descriptor’ checkbox is checked
      • Phenotype Value Range : textfield - autocomplete options from chado.phenotypeprop table - only visible if the ‘Phenotype x has a value range’ checkbox is checked
    • Phenotype Metadata file: managed_file - spreadsheet of metadata about each phenotype - only visible if the ‘I would like to upload a phenotype metadata file’ checkbox is checked

    • Phenotype Metadata File Columns: fieldset of select elements - user will define which of their columns contain the Phenotype Name/Identifier, Phenotype Attribute, Phenotype Description, Phenotype Units, Phenotype Structure, Max/Min Phenotype Values - only visible if the ‘I would like to upload a phenotype metadata file’ checkbox is checked

    • Phenotype File: managed_file - spreadsheet of phenotypes

    • Phenotype File Columns: fieldset of select elements - user will define which of their columns contain the Tree ID, Phenotype Name/Identifier, and Phenotype value

A screenshot of the manual phenotype information fields can be seen below:

../_images/TPPS_phenotype_manual.png

A screenshot of the phenotype metadata file field can be seen below:

../_images/TPPS_phenotype_meta.png

A screenshot of the phenotype data file field can be seen below:

../_images/TPPS_phenotype_data.png

3.7.2. Genotype

  • Genotype Information: fieldset - only visible if the user selects ‘Genotype’, ‘Genotype x Phenotype’, ‘Genotype x Environment’, or ‘Genotype x Phenotype x Environment’ from ‘Data Type’ in Study Design

    • Genotype Marker Type: checkboxes - options ‘SNPs’, ‘SSRs/cpSSRs’, ‘Other’

    • Genotype SNPs: fieldset - only visible if the user selects ‘SNPs’ from ‘Genotype Marker Type’

      • SNPs Genotyping Design: select - options ‘GBS’, ‘Targeted Capture’, ‘Whole Genome Resequencing’, ‘RNS-Seq’, ‘Genotyping Array’
      • GBS Type: select - options ‘RADSeq’, ‘ddRAD-Seq’, ‘NextRAD’, ‘RAPTURE’, ‘Other’ - only visible if the user selects ‘GBS’ from ‘SNPs Genotyping Design’
      • GBS Custom Type: textfield - only visible if the user selects ‘Other’ from ‘GBS Type’
      • Targeted Capture Type: select - options ‘Exome Capture’, ‘Other’ - only visible if the user selects ‘Targeted Capture’ from ‘SNPs Genotyping Design’
      • Targeted Capture Custom Type: textfield - only visible if the user selects ‘Other’ from ‘Targeted Capture Type’
    • Genotype SSRs/cpSSRs Type: textfield - only visible if the user selects ‘SSRs/cpSSRs’ from ‘Genotype Marker Type’

    • Genotype Other Marker Type: textfield - only visible if the user selects ‘Other’ from ‘Genotype Marker Type’

    • Reference Genome: select - stored reference genomes, as well as ‘I can provide a URL to the website of my reference file(s)’, ‘I can provide a GenBank accession number (BioProject, WGS, TSA) and select assembly file(s) from a list’, ‘I can upload my own reference genome file’, ‘I can upload my own reference transcriptome file’, ‘I am unable to provide a reference assembly’

    • BioProject Accession: textfield - only visible if the user selects ‘I can provide a GenBank accession number (BioProject, WGS, TSA) and select assembly file(s) from a list’ from ‘Reference Genome’

      • NCBI Assembly Accessions: checkboxes - options pulled directly from NCBI
    • URL or Manual Assembly File: fieldset - Tripal FASTA Loader fields - only visible if the user selects ‘I can provide a URL to the website of my reference file(s)’, ‘I can upload my own reference genome file’, or ‘I can upload my own reference transcriptome file’ from ‘Reference Genome’

    • Genotype File Type: checkboxes - options ‘Genotype Spreadsheet/Assay’, ‘Assay Design’, ‘VCF’. ‘Assay Design’ only visible if the user selects ‘SNPs’ from ‘Genotype Marker Type’.

    • Genotype VCF File: managed_file - .VCF file of genotypes - only visible if the user selects ‘VCF’ from ‘Genotype File Type’

    • Genotype File: managed_file - spreadsheet of genotypes - only visible if the user selects ‘Genotype Spreadsheet/Assay’ from ‘Genotype File Type’

    • Genotype File Columns: fieldset of select elements - user will define which of their columns contain the Tree ID and Genotype Data

    • Assay Design File: managed_file - Assay design file - only visible if the user selects ‘Assay Design’ from ‘Genotype File Type’

A screenshot of the genotype marker type fields can be seen below:

../_images/TPPS_genotype_marker.png

A screenshot of the genotype reference fields can be seen below:

../_images/TPPS_genotype_ref.png

A screenshot of the genotype file fields can be seen below:

../_images/TPPS_genotype_file.png

3.7.3. Environment

  • Environment Information: fieldset - only visible if the user selects ‘Environment’, ‘Phenotype x Environment’, ‘Genotype x Environment’, or ‘Genotype x Phenotype x Environment’ from ‘Data Type’ in Study Design

    • CartograTree Environmental Layers: fieldset - only visible if CartograTree Layers are enabled in TPPS admin configuration and the ‘I used environmental layers in my study that are indexed by CartograTree.’ checkbox is checked.

      • CartograTree Environmental Layer x: checkbox - Indicates if the CartograTree Environmental Layer x was used.
    • CartograTree Environmental Layer Parameters: fieldset - only visible if CartograTree Layers are enabled in TPPS admin configuration and the ‘I used environmental layers in my study that are indexed by CartograTree.’ checkbox is checked.

      • CartograTree Environmental Layer x Parameters: checkboxes - options of possible parameter types for the selected CartograTree Environmental Layer. Each CartograTree Environmental Layer x Parameters checkboxes set is only visible if that layer was selected in ‘CartograTree Environmental Layers’.
    • Custom Environmental Data: fieldset - only visible if the ‘I have environmental data that I collected myself.’ checkbox was checked.

      • Environmental Data x: fieldset

        • Environmental Data Name: textfield
        • Environmental Data Description: textfield
        • Environmental Data Units: textfield
        • Environmental Data Value: textifled