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Data Management I

learning-objectives

  • Describe the components of FAIR data

  • Describe the Data Lifecycle

  • Download data from the Data Store

  • Create a README file and upload it to the Data Store

Description:

In this module, we introduce the concepts of FAIR data and the Data Lifecycle and demonstrate how to move data between your computer and the CyVerse Data Store.

Here is a link to the FAIR Data assessment tool mentioned in the video: Fair Data Assessment Tool

Downloading data from the Discovery Environment

  1. If necessary, log into the CyVerse Discovery Environment.

  2. Click the Data icon (Data Icon) to browse your collection of files in the CyVerse Data Store.

  3. In the top left of the page, you should see your username with a dropdown arrow next to it; Click on your username, then click Community Data in the dropdown menu.

    Tip

    This dropdown menu allows you to navigate between your home directory in the Data Store (i.e. your username), and other CyVerse data collections such as files shared with you (i.e. “Shared with Me”), and files shared by the CyVerse community (i.e. “Community Data”). You may also access files located in your “Trash” folder.

  4. From the Community Data directory, scroll down until you find the cyverse_training folder, and click on it. Then navigate to the cyverse_mooc folder, then muscle_3_8_31, then to 01_muscle_input, which will contain our example data. This is the full file path, which should show up as part of your URL:

    /iplant/home/shared/cyverse_training/cyverse_mooc/muscle_3_8_31/01_muscle_input

  5. Click (Select) the checkbox next to the DE_sample_plants.fas file to select it.

  6. Click on the More Actions button on the upper right and select the Download option to download the file to your local computer.

    Tip

    We don’t recommend downloading many (more than 10) or large (more than 2GB) files directly from the Discovery Environment since files transferred in this way will make use of HTML protocols which are slow and subject to failure for very large data sets. Cyberduck or iCommands (discussed below and in the Data Store Guide) are recommended for these uses.

Uploading a File to the Discovery Environment

  1. On your computer, use any text editor to create a file called README.txt. You may wish to save it in the same place you have the DE_sample_plants.fas file (i.e. your Desktop, Downloads, etc.).

  2. In the README.txt file, add several pieces of information about the DE_sample_plants.fas file you just downloaded:

    • Name of file: DE_sample_plants.fas

    • Type of file: FASTA file containing DNA sequences

    • Type of organism: plants

    Adding a simple README with this sort of information can quickly make your data more FAIR.

    Note

    Make sure you save this as a plain text file (“.txt”), other file formats (e.g. “.docx”) may not be rendered in the Discovery Environment.

  3. In the Discovery Environment, click the Data icon (Data Icon) to access your home folder; you can access this from the same dropdown menu where you previously selected Community Data.

  4. Navigate to the tutorial_folder directory you created earlier.

  5. Click the Upload icon in the upper right, then select Browse Local. Then navigate to your README.txt file and select it.

  6. It may take a moment, but your README.txt file should now be uploaded to your tutorial_folder on the Data Store; you may need to refresh your web browser to see the update.

Output/Results

Output

Description

Example
  • On CyVerse

    README.txt

  • On your Computer

    DE_sample_plants.fas

The README file is a simple but useful way to describe folder contents. The fasta file contains data we will use in future steps.

View the example tutorial folder.

Self Assessment Questions

Question

Q1. What do the letters in FAIR refer to?

  1. Fixable, Assessable, Interpretable, Recyclable

  2. Fast Access In Repetition

  3. Findable, Accessible, Interoperable, Reusable

  4. Fixable, Automated, Intersectional, Reducible

Answer

The correct answer is C.

Question

Q2. True or False, is FAIR data is the same as Open data?

Answer

False. Open data must be free for use and distribution by anyone, whereas data can be limited in access while still being FAIR. Likewise, Open data are not necessarily easily findable, interoperable, or reusable.

Question

Q3. Which of the following are NOT true of the process of making your data FAIR?

  1. It will be the same regardless of discipline

  2. It may require some technical skills

  3. It can be easier with CyVerse

  4. It happens on a continuum, not a binary FAIR/not FAIR

Answer

The correct answer is A. Making your data FAIR can vary widely by discipline. For example, human health data may be subject to stricter security and more limited sharing, which must be accounted for when attempting to make data FAIR.

Question

Q4. True or false, is adding a README file a quick way to make your data more FAIR?

Answer

True, a README can provide quick access to metadata and is easily discovered within a given directory.

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