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Working with External Data

Whole Tale allows you to work with and publish references to externally managed data instead of copying the data into your tale.

Questions:

  • What is "external data"?
  • How do I register and cite external data?

Objectives:

  • Learn about automatic data citation in Whole Tale
  • Learn which repositories are currently supported

Use case

A researcher is publishing the results of an analysis that relies on part of a previously published publicly accessible dataset. Instead of publishing a copy of the source data, they want to reference it in their published tale. The original researchers get proper attribution/credit for their published dataset.

External Data in Whole Tale

Whole Tale allows you to register data from external repositories for use in your tales. This serves two purposes: 1) to create an explicit link (citation) between your tale and data used and 2) to prevent making multiple copies of published research datasets. Currently, Whole Tale supports Zenodo, DataONE Network member nodes, Dataverse Network members, and the Materials Data Facility.

Activity: Register an external dataset

  • Create a new tale called Water usage example using JupyterLab
  • Select the Files tab then External Data
  • Select the blue + button

  • Select Web (DOI or URL)
  • Enter the DOI 10.5065/D6862DM8
  • Select Search to find the Humans and Hydrology... dataset then Register

What's happening?

  • Whole Tale registers the dataset if it doesn't already exist and adds it to your list of registered datasets
  • This is a "metadata only" operation -- the files (bytes) aren't transferred until they are accessed

Activity: Add the data to your tale

  • Select the Files tab then External Data
  • Select the blue + button then then WT Data Catalog
  • In the catalog window, double-click the "Humans and Hydrology..." dataset
  • Single click the usco2005.xls file then Add Selected then Save

  • Select the Metadata tab
  • Note that the dataset is cited as part of the tale metadata. The citation remains during export and publish.

What's happening?

  • The selected file is added to your tale's external data folder (../data) and cited in tale metadata

Activity: Using the data

  • Download and extract quickstart.zip example.
  • Select Files > Tale Workspace > + > Upload File to upload the extracted files to the workspace
  • Select Run Tale to start the JupyterLab environment
  • Open your JupyterLab instance
  • Open the wt_quickstart.ipynb notebook then Run > Run All Cells in JupyterLab
  • A map of water usage by county in Texas should display

What's happening?

  • The notebook reads the file from ../data

Key points:

  • Whole Tale allows you to register and add external data to your tales to prevent duplication of data and ensure proper attribution.
  • Whole Tale has an extensible data registration framework and we regularly add providers for new communities. Currently, data can be registered from Zenodo, Dataverse, DataONE member nodes, Materials Data Facility and soon DERIVA systems.

Next

Working with MATLAB