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Associate Data with Metadata

The Data Store supports a variety of solutions that allow you to associate your raw data with metadata. Metadata is of critical importance to a quality research (see this article on FAIR Principles), yet it is often given less consideration until the time of publication and sharing. Here are a few metadata features that you can adopt and be aware of at the outset, see more of CyVerse’s capabilities on the Data Commons Wiki page.

Some things to remember about the platform

  • You can add metadata to a single file/folder, or in bulk to large collections of data. You can use your own metadata schema, or apply one of our metadata templates.
  • The Discovery Environment supports several metadata templates that can be used for submission of metadata. Additional templates you may wish to use can be found at resources like FairSharing.org.
  • Metadata can be managed through a graphical interface in the Discovery Environment or using iCommands at the command line. We will only cover the Discovery Environment in this guide. See instructions for iCommands metadata on the CyVerse wiki.

Viewing and Editing Metadata for a Single File/folder in the Discovery Environment

Note

You must have write or own permission to edit an object’s metadata.

  1. Log into the Discovery Environment.

  2. Click on the data icon (Data Icon) to view to browse for data. Select (checkbox) a single file/folder to add metadata to.

  3. Under the More Actions menu, click on the `Metadata` choice. You will see existing metadata for the file/folder in the Attribute, Value, Unit (AVU) format.

    edit_view_metadata

    Tip

    A single piece of metadata, or an AVU, is made up of attributes, values, and units. An attribute is a changeable property or characteristic of the file or folder you have selected that can be set to a value. For example, “time point” might be an attribute of a file, while ‘7’ could be its value, and hour a unit of time.

Adding metadata

  1. Click the “+ Add Metadata” button to add a new entry. Then follow the directions for editing metadata below.

Editing or deleting metadata

  1. You may use the “pencil” icon to edit an existing entry or the “trash can” icon to delete an entry.
  2. After you have made any edits or deletion, click ‘Save’ (on the top right of the screen) to save all entries and apply the metadata.

Adding Metadata to Multiple Files/folder in the Discovery Environment

Adding Metadata using a CyVerse Template

  1. Log into the Discovery Environment.

  2. Click on the data icon (Data Icon) to open a Data window. Select (checkbox) a single file/folder to add metadata to. Next,

  3. Under the More Actions menu, click on the Metadata. Click on the subsequent More Actions menu and select View in Template. You have two choices in using the template:

    1. Choose a template and clicking Select will allow you to apply the template and edit the metadata manually in the DE interface.
    2. Clicking the download icon (Download icon) will download a .csv file you can edit and upload (See applying Bulk metadata below).

    click OK to download. (In this example, we will use the DOI Request - DataCite Metadata) template.

Editing metadata template in DE

  1. Follow the steps in the “Editing or deleting metadata” from the previous section above

Editing a downloaded metadata template

  1. Unzip the downloaded template; it will contain two files blank.csv and guide.csv. Open these files using the spreadsheet editor of your choice.

    Tip

    • blank.csv is the metadata template that you will complete for your data.
    • gude.csv contains instructions for your template, and will usually include controlled vocabulary terms for metadata descriptors.

  2. Edit the template in one of two ways:

  • If all data will be in a single folder

    1. In the blank.csv spreadsheet, in the ‘file name or path’ column, enter the file names of all the files/folder in that folder you wish to annotate with metadata.

      Tip

      Finding the file path in the DE

      In any data window click the kebab icon (kebab menu or 3-dots menu) next to any file or folder; choose copy path to get the path to that item in the Data Store.

    2. In the remaining columns of the template, enter the values for each file/attribute combination that apply.

    3. If desired, add additional columns to the end of the template. The metadata in the additional columns will be saved in the Data Store but will not be stored as part of the template.

    4. Save the file in CSV format. Make sure none of the names of the files or the parent folder includes spaces or special characters. You may name this metadata file anything you wish, but keep it in CSV format.

  • If data will be in multiple folders

    1. In the blank.csv spreadsheet, in the ‘file name or path’ column, enter the full path of the top-level folder (e.g. /iplant/home/YOURUSERNAME/FOLDERNAME)
    2. In the remaining columns in the first row, enter the values for each file/attribute combinations
    3. Repeat for each file, but make sure to add the full file path (e.g. / iplant/home/YOURUSERNAME/FOLDERNAME) for each file.
    4. If desired, add additional columns to the end of the template. The metadata in the columns will be saved in the Data Store but will not be stored as part of the template.
    5. Save the file in CSV format. Make sure none of the names of the files or the parent folder includes spaces or special characters. You may name this metadata file anything you wish, but keep it in CSV format.

  1. In an open ‘Data’ window in the Discovery Environment, navigate to appropriate location for uploading the template:

    • If the first column of your metadata file contains only file names (that is, all data files are in the same folder), navigate to the folder and use the Upload button (Browse local) or your choice of upload tool to upload the metadata (csv file) to that folder.

    • If the first column of your metadata file contains the full path to each file (that is, the data files are in different folders), it does not matter where the metadata file is located on the Data Store. Use he Upload button (Browse local) or your choice of upload tool to upload the metadata (csv file) to an appropriate location on the Data Store.

      Tip

      If you commit to using absolute file paths (e.g. /iplant/home/your_file_location) you can keep all of your metadata spreadsheets in one location on the Data Store for convenient management and editing.

  1. To apply the metadata, in the Data window, select (checkbox) the name of the folder containing the data files to which you want to apply the metadata in bulk.
  2. Click the More Actions menu select ‘Apply Bulk Metadata’; brows to the uploaded metadata spreadsheet and select it.

Your metadata should now be applied to your files. You should receive a notification in the Discovery Environment and you can confirm the metadata has been correctly applied by following the steps in the preceding section to view metadata.

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