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Part 1: Anatomy of a MagIC contribution

The Magnetics Information Consortium (MagIC), hosted at http://earthref.org/MagIC is a database that serves as a Findable, Accessible, Interoperable, Reusable (FAIR) archive for paleomagnetic and rock magnetic data. Its data model is fully described here: https://www2.earthref.org/MagIC/data-models/3.0. Each contribution is associated with a publication via the DOI.

There are nine data tables. The fields associated with these tables are detailed here: https://www2.earthref.org/MagIC/data-models/3.0

  • contribution: metadata of the associated publication.
  • locations: metadata for locations, which are groups of sites (e.g., stratigraphic section, region, etc.)
  • sites: metadata and derived data at the site level (units with a common expectation)
  • samples: metadata and derived data at the sample level.
  • specimens: metadata and derived data at the specimen level.
  • measurements: metadata and measurements at the specimen level.
  • criteria: criteria by which data are deemed acceptable
  • ages: ages and metadata for sites/samples/specimens
  • images: associated images and plots.

Let's make upload a contribution!

  1. Log-in to MagIC/Earthref (https://www2.earthref.org/MagIC)

  2. Go to upload tool (https://www2.earthref.org/MagIC/upload)

  3. Download and examine contribution

  4. Go to Data model to learn table/column names (https://www2.earthref.org/MagIC/data-models/3.0)

  5. Go back to main upload page and let's drag and drop the file to upload

  6. Upon uploading, we can examine the tables which are parsed and matched up with the table name and data model fields

  7. Click the upload button in the lower right, which will bring you to an upload page where you can click through to upload data into your private workspace

  8. Here we can add the DOI for the study which is 10.1029/93JB00024 (then click save), add the lab for the study Paleomagnetic Laboratory (USGS Menlo Park, USA), and then click to validate the contribution

  9. Once the study is validated, a contribution can be published (let's not do that here as this study is already in MagIC) or for a private contribution a private link can be shared. Sharing such a link enables data to be made available for peer review. Note that the DOI for the contribution (Future Data DOI) is already available at this stage which enables the data to be properly referenced within a manuscript when it is submitted.

Part 2: Inspecting a contribution using PmagPy

In this part of the tutorial, we are going to download and inspect a MagIC contribution using PmagPy. We will use a Jupyter notebook that is hosted on the EarthRef.org JupyterHub server:

https://jupyterhub.earthref.org/

This JupyterHub enables you to run PmagPy code without having to install anything locally. You can get to it via the MagIC website:

Once you are on JupyterHub, open the MagIC Workshop 2023 Tutorial - Setup.ipynb notebook:

By executing cells in this setup notebook, you will install the MagIC workshop materials into your JupyterHub. We will now be working in a notebook called Inspecting_a_MagIC_contribution.ipynb within the 1_MagIC_intro folder of the 2023_MagIC_Tutorial folder.

We will use this notebook to inspect a MagIC contribution using PmagPy functions.