Prepare Your Biosamples 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 biosamples associated with it.
    • It's easy to handle multiple biosamples - just create a new value column for each additional biosample.
    • For example, if I had 20 biosamples associated with my submission, I would create 19 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 Biosamples metadata file, you can download one here.

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

  • For the Biosample property, each value will look something like this: EXR-AMILO1GASTCANC1-BS.
    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 biosample. Here, my biosample 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 -BS to indicate that the file is a Biosamples file.
      • If I had a second biosample, I would write something like EXR-AMILO1GASTCANC2-BS 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 - Name property, you should write a name for your biosample that conveys some important information about that sample.
    • No two biosamples should have the same name within your submission.
  • For the - Donor ID property, you should write the ID for the donor associated with the biosample.
    • For example, if the donor EXR-AMILO1GASTCANC1-DO is associated with the current biosample, I would write EXR-AMILO1GASTCANC1-DO.
    • You should also fill in the *-- DocURL subproperty with the same ID but in the following format: coll/Donors/doc/ and then your ID.
      • I would put coll/Donors/doc/EXR-AMILO1GASTCANC1-DO.
  • You don't need to write anything for the - Biological Sample Elements property, but don't delete it from your file!
  • You don't need to write anything for the -- Species property, but don't delete it from your file!
  • For the --- Scientific Name property, you should write Homo sapiens or Mus musculus.
  • For the --- Common Name property, you should write Human or Mouse.
  • For the -- Disease Type property, your value will be enforced by ontologies.
    • Here is a list of previously used values for this property:
      • glioblastoma multiforme, colorectal cancer, Ulcerative Colitis, Healthy Control, Healthy Subject, Gastric Cancer Pathologic TNM Finding v7, Cardiovascular Disorder, Alzheimer's Disease, Subarachnoid Hemorrhage, Parkinson's Disease, Intraventricular Brain Hemorrhage, Systemic Lupus Erythematosus, Chronic Maternal Hypertension with Superimposed Preeclampsia, severe pre-eclampsia, pre-eclampsia, Fetus Small for Gestational Age, HELLP Syndrome, Nephrotic Syndrome, liver disease, Colon Carcinoma, Prostate Carcinoma, Pancreatic Carcinoma
    • If your disease type 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 Disease Type property.
      3. Begin typing the name of your disease type. 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 Biosamples metadata file.
    • If you still can't find an appropriate term for your disease type, feel free to contact William.
  • For the -- Anatomical Location property, your value will be enforced by ontologies.
    • Here is a list of previously used values for this property:
      • Cellular analyte, Entire cardiovascular system, Entire oral cavity, Colon part, Structure of nervous tissue, Entire brain, Brain ventricle structure, Entire body system, High density lipoprotein, Urinary system structure, Entire bile duct
    • If your anatomical location is not listed above, then follow the steps above for Disease Type to find a valid value.
      Just double click the pencil icon next to Anatomical Location instead of Disease Type.
  • If your biosample is biofluid-based, then you will want to leave the -- Biological Fluid property in your metadata file - you don't need to fill in a value, but don't delete it!
    • You will then want to fill in a value for the --- Biofluid Name property. Your value will be enforced by ontologies.
      • Here is a list of previously used values for this property:
        • Culture Media, Conditioned, Plasma, Saliva, Cerebrospinal fluid, Serum, Urine, Bile
      • If your anatomical location is not listed above, then follow the steps above for Disease Type to find a valid value.
        Just double click the pencil icon next to Biofluid Name instead of Disease Type.
  • If your biosample is biofluid-based, then you will want to leave the -- Biological Fluid property in your metadata file - you don't need to fill in a value, but don't delete it!
    • You will then want to fill in a value for the --- Biofluid Name property. Your value will be enforced by ontologies.
      • Here is a list of previously used values for this property:
        • Culture Media, Conditioned, Plasma, Saliva, Cerebrospinal fluid, Serum, Urine, Bile
      • If your anatomical location is not listed above, then follow the steps above for Disease Type to find a valid value.
        Just double click the pencil icon next to Biofluid Name instead of Disease Type.
  • If your biosample is cell culture supernatant-based, then you will want to leave the -- Cell Culture Supernatant property in your metadata file - you don't need to fill in a value, but don't delete it!
    • You will then want to fill in values for the --- Source, ---- Type, --- Tissue, and ---- Tissue Type properties. Your values will be enforced by ontologies.
      • Here is a list of previously used values for --- Source:
        • Tumor Tissue, Human Cell Line
      • Here is a list of previously used values for ---- Type:
        • cell culture, colorectal cancer cell
      • Here is a list of previously used values for --- Tissue:
        • brain, colon
      • Here is a list of previously used values for ---- Tissue Type:
        • Tumor tissue sample, frozen specimen
      • If your values for any of the required properties are not listed above, then follow the steps above for Disease Type to find a valid value.
        Just double click the pencil icon next to the property name (Source, Type, Tissue, Tissue Type) instead of Disease Type.
  • You don't need to write anything for the - Molecular Sample Elements property, but don't delete it from your file!
  • For the -- exRNA Source property, you should put one of the following values:
    • extracellular exosome, extracellular vesicle, HDL-containing protein-lipid-RNA complex, total cell-free biofluid RNA, ribonucleoprotein complex, protein-lipid-RNA complex, LDL-containing protein-lipid-RNA complex, apoptotic body
  • For the -- Fractionation property, you should put Yes or No.
  • Finally, you should put the value 1 for the * Related Experiments property.
    • For the *- Related Experiment subproperty, write the Experiments ID for the experiment associated with the current biosample.
    • I might put EXR-AMILO1GASTCANC1-EX, for example.
    • For the *-- DocURL subproperty, write the same ID but in the following format: coll/Experiments/doc/ and then your ID.
    • I would put coll/Experiments/doc/EXR-AMILO1GASTCANC1-EX.
  • 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 Biosample property (excluding the identifying number at the end if you have multiple documents).
    • For example, I would name my metadata file EXR-AMILO1GASTCANC-BS.metadata.tsv.
    • If you need help saving your metadata file, we have instructions available here.

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