Prepare Your Donors Metadata File

  • First, download the template linked here.
  • After you've opened the template, you will provide values in the value column.
  • Note that your submission will likely have multiple donors associated with it.
    • It's easy to handle multiple donors - just create a new value column for each additional donor.
    • For example, if I had 3 donors associated with my submission, I would create two additional value columns to the right of the one currently present in the template.
  • 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 Donors metadata file, you can download one here.

Here are some specific instructions for filling out a Donors metadata file:

  • For the Donor property, each value will look something like this: EXR-AMILO1GASTCANC1-DO.
    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 GASTCANC1 to give some information about my donor. Here, my donor is connected with a gastric cancer study, so I wrote GASTCANC and then 1 (because we're discussing the first value currently).
    4. Finally, the value ends with -DO to indicate that the file is a Donors file.
      • If I had a second donor, I would write something like EXR-AMILO1GASTCANC2-DO in my second value column.
  • 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 - Sex property, your value will be enforced by ontologies.
    • The following are commonly used values for this property:
      • Male, Female, Gender unknown
    • If your sex is not listed above, then follow these steps:
      1. Visit the GenboreeKB UI template for Donors (you will need to log into your GenboreeKB account if not already logged in) here.
      2. Double click the pencil icon next to the Sex property.
      3. Begin typing the name of your sex. After you type at least 3 characters, our look-ahead search will attempt to find matching terms in the ontology.
      4. Any term that pops up will be a valid value for your property. You can copy paste it into your Donors metadata file.
    • If you still can't find an appropriate term for your sex, feel free to contact William.
  • For the - Donor Type property, you should write either Experimental, Control, or Healthy Subject.
  • For the - Age property, you should write the age of your donor (with appropriate unit at the end).
    • Valid examples include 18 years, 20 months, etc.
    • Write 0 years if you don't know the age of your donor.
  • We also recommend that you fill out values for - Ethnic Group and - Racial Category if known.
    • The values for these properties are ontology-enforced.
    • Commonly used values for - Ethnic Group include:
      • Not Hispanic or Latino, Hispanic or Latino,
    • Commonly used values for - Racial Category include:
      • White, Asian, African American, Multiracial, Native Hawaiian or Other Pacific Islander
    • If your ethnic group / racial category are not listed above, then follow the steps above for Sex to find valid values for these properties.
      Just double click the pencil icon next to Ethnic Group and/or Racial Category instead of Sex.
  • 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 Donor property (excluding the identifying number at the end if you have multiple documents).
    • For example, I would name my metadata file EXR-AMILO1GASTCANC-DO.metadata.tsv.
    • If you need help saving your metadata file, we have instructions available here.

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