Prepare Your Analyses Metadata File

  • First, download the template linked here.
  • After you've opened the template, you will provide values in the value column.
  • At this point, if you haven't created a metadata file before, you should read through the Understanding the Nested Tabbed Format page to better understand how your file is formatted.
  • You are only required to provide values for those properties which have TRUE in the required column.
    • Even if a property has TRUE in the required column, if its parent property does NOT have TRUE in the required column, then you are not required to fill in the (sub) property.
  • If you want to see a completed Analyses metadata file, you can download one here.
    • WE HIGHLY RECOMMEND YOU DOWNLOAD THE EXAMPLE, AS IT WILL MAKE UNDERSTANDING THE DIRECTIONS BELOW MUCH EASIER!
  • Here are some specific instructions for filling out an Analyses metadata file:
  • For the Analysis property, the value will look something like this: EXR-AMILO1GASTCANC-AN.
    1. The ID will always start with EXR- (this stands for exRNA).
    2. Next, I wrote AMILO1 because my PI is Aleksandar MILOsavljevic (AMILO). The 1 indicates that he is the first PI with this particular ID. If you're not sure about your PI ID, feel free to contact William.
    3. Third, I wrote GASTCANC to give some information about my study. Here, my study is studying gastric cancer, so I wrote GASTCANC.
    4. Finally, the value ends with -AN to indicate that the file is a Analyses file.
  • For the - Status property, you can write either "Add" or "Protect".
    • Write "Add" if you want to add your files to the public Atlas immediately.
    • Write "Protect" if you want to keep your files in the consortium-only Atlas until the embargo period ends on your submission.
  • For the - Date of Analysis property, you should write the date you're submitting your files to the DCC.
    • Write the date in the format YYYY/MM/DD. For example, if I was submitting my files on September 21st, 2017, I would write 2017/09/21.
  • For the * Conditions Associated with Analysis property, you don't need to write anything, but don't delete it!
  • Underneath the * Conditions Associated with Analysis property, you should write one *- Condition property for each condition mentioned in your Biosamples file.
    • For example, if I had three different conditions ("Healthy Control", "glioblastoma multiforme", and "Alzheimer's Disease") mentioned in my Biosamples file, I would list these conditions like the following:
      • *- Condition Healthy Control
      • *- Condition glioblastoma multiforme
      • *- Condition Alzheimer's Disease
  • For the - Data Analysis Level property, you don't need to write anything, but don't delete it!
  • For the -- Type property, you should write "qPCR Data Analysis".
  • For the --- qPCR Data Analysis Level property, you don't need to write anything, but don't delete it!
  • You should then fill out all relevant subproperties underneath the --- qPCR Data Analysis Level property.
  • In particular, you should fill out the ---* Biosamples property and its subproperties.
    • For the ---* Biosamples property, you don't need to write anything, but don't delete it!
    • Underneath the ---* Biosamples property, you should write one ---*- Biosample ID property for each biosample in your submission. The value for each line should be a different biosample in your submission.
    • Underneath each ---*- Biosample ID property, you should write one ---*-- DocURL property. The value for each line should be "coll/Biosamples/doc/" and then your biosample ID. For example, you could write "coll/Biosamples/doc/EXR-AMILO1GASTCANC1-BS" if that was a valid biosample ID for your submission.
    • Underneath each ---*- Biosample ID property, you should write one ---*-- qPCR Target Doc ID property. The value for each line should be the qPCR Target ID associated with the relevant biosample ID. For example, if my EXR-AMILO1GASTCANC1-BS biosample had an associated qPCR Targets ID of EXR-AMILO1GASTCANC1-QT, I would write "EXR-AMILO1GASTCANC1-QT".
    • Underneath each ---*-- qPCR Target Doc ID property, you should write one ---*--- DocURL property. The value for each line should be "/coll/qPCR%20Targets/doc/" and then your qPCR Targets ID. For example, you could write "coll/qPCR%20Targets/doc/EXR-AMILO1GASTCANC1-QT".
  • If you're confused by the directions above related to the ---* Biosamples property and its subproperties, you should look at the COMPLETED ANALYSES EXAMPLE FILE.
  • If you didn't fill out a value for a property, then please delete the row containing that property from your file. Make sure that you actually remove the row entirely and don't leave a blank row!
    However, if the domain for the property is [valueless] and you filled out values for any subproperties, then don't delete the row.
  • Finally, save your metadata file in tab-delimited format with a file name that ends in .metadata.tsv.
    • I recommend you name your metadata file after the value given for your Analysis property.
    • For example, I would name my metadata file EXR-AMILO1GASTCANC-AN.metadata.tsv.
    • If you need help saving your metadata file, we have instructions available here.

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