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Update Existing Metadata

Now you’d like to update your metadata in order to:

  • Correct mistake(s)
  • Provide further/change metadata to comply with a new iteration of the DCC data model affecting your datasets’ metadata
  • Provide metadata for files that have been added to your dataset

Pre-requisites

Step-by-Step

In this how-to, we’ll be using an example Assay: Bulk RNA-seq dataset named CohortN - DatasetX located in a Synapse Project called CenterA. This is a dataset that’s been annotated according to these instructions.

  1. Access the Data Curator.
    • If you are prompted to login to Synapse, please use your Synapse account (or associated Google account).

  2. Navigate to the “Select your Dataset” section in the left-hand menu of the Data Curator. From that page, select your Synapse project from the dropdown (here, CenterA).

    Data Curator Select Project

  3. Select your dataset, which corresponds to the folder name in your bucket (here, CohortN - DatasetX).

    Data Curator Select Folder

  4. Select the metadata template you would like to use (here, Assay: Bulk RNA-seq). If you don’t see the correct template for your dataset, you can select the Minimal Metadata template and contact your DCC liaison.

    Data Curator Select Data Type

  5. Navigate to the “Get Metadata Template” section in the left-hand menu, and select the “Click to Generate Google Sheets Template” button.
    • This can take awhile depending on how many files are in your folder, so please be patient!

    Data Curator Google Sheets Link Button

  6. Click on the generated link to open the metadata template in Google Sheets.

    Data Curator Google Sheets Link Generated

  7. All previously validated metadata are available.

    Google Sheets Manifest Template Prefilled

  8. Update the metadata accordingly (here, by adding a new row/file for a new sample).
    • Note: You can also download the spreadsheet as a CSV file and use a method of your choice to fill it out. The metadata CSV file will be validated by the Data Curator before submission regardless of the method used to update the template.

    Google Sheets Manifest Template Expanded

  9. If completed in Google Sheets, download the manifest template as a CSV file once it’s been updated (File -> Download -> Comma-separated values).

    Google Sheets Manifest Template Export

  10. Back in the Data Curator, navigate to the “Submit & Validate Metadata” section in the left-hand menu.

    Data Curator Validation Page

  11. Click on the “Browse” button to upload your CSV file, and check the preview of your file to make sure everything looks correct.

    Data Curator Validation Upload

  12. Validate your CSV file by clicking the “Validate Metadata” button. If the CSV file is validated successfully, you will see a “Your metadata is valid!” message, and a “Submit to Synapse” button will appear at the bottom of the page. If you encountered validation errors, address them first before re-validating and submitting the metadata (an example).

  13. Submit the metadata by clicking on the “Submit to Synapse” button.

    Data Curator Validation Success

  14. Success!

    Data Curator Submitted

  15. Check your metadata CSV file on Synapse by using the link that appears in the “Success!” pop-up. Alternatively, navigate to the dataset folder in your Synapse project where you will find the updated metadata CSV file.

Please contact your DCC liaison if you cannot resolve a metadata error or have questions regarding metadata updates and submission.