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Publishing data

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Peter Desmet edited this page Apr 14, 2022 · 6 revisions

Once you are happy with the Darwin Core data you cooked together, you are ready to get them published. 👏 The easiest way to do so is by using the Integrated Publishing Toolkit (IPT).

Find an IPT

If you don't have an IPT at your institution, navigate the map of existing IPT installations and contact the person administering one near you. Many IPT installations will host datasets for other institutions.

Using the IPT

If you haven't used the IPT before, we advice to watch the introduction video or browse the IPT documentation. Once you know your way around, here is how to proceed:

Creating a resource

From Manage Resources create a new resource (= a checklist dataset in your case). Use your my_dataset_shortname as shortname and choose Type: Checklist. Don't upload any data yet.

Skip this step completely if you have created your checklist dataset on the IPT before and just want to update the data.

Linking or uploading data

  1. Go to the overview page of your resource (it will look like this).
  2. Under Source data:
  • Choose URL and provide the raw GitHub URL to your Darwin Core data file, e.g. https://raw.githubusercontent.com/trias-project/checklist-recipe/main/data/processed/taxon.csv. The Source Name will be taken automatically from the name of your file.
  • Or, choose File and upload the Darwin Core data file from your computer. Click Yes to overwrite a previously uploaded (and now outdated) file if applicable.
  1. Save the linked or uploaded file.

Repeat the process for any of the extension file(s) you have on your computer.

Mapping data

  1. Under Darwin Core Mapping select Darwin Core Taxon > Add.
  2. Select taxon from the dropdown menu.
  3. Since your data is already mapped to Darwin Core, the IPT will automap all columns for you. 👍
  4. Inspect and click Save and Back.

Repeat the process for any of the extensions you have uploaded, but make sure you select the correct extension (step 1) and file (step 2).

Note: if you overwrote existing source files on the IPT with more recent ones on your computer, be sure to verify your mapping again. E.g. a newly added column in your Darwin Core data will brake the mapping. Often it is easiest to click Edit next to Darwin Core Taxon and then click Delete to remove your whole mapping (including extensions) and start over. Since all of the mapping is automapping, redoing the mapping in the IPT shouldn't take long.

Writing metadata

Under Metadata click Edit to describe your dataset. See this section of the IPT manual for more information on metadata.

Note: with all the effort you put into documenting your mapping process, it is a good idea to refer to your repository (which contains your R Markdown file) in the Sampling Methods section, ideally as step descriptions. These will end up in the Methodology section of your dataset on GBIF. See for example the Methodology section of this checklist which followed the checklist recipe.

Publishing data

To publish your dataset:

  1. Under Visibility click Public.
  2. Under Published versions click Publish. You won't be able to do so as long as your required metadata is not complete.
  3. If this is the first time you published your dataset, register it with GBIF under Visibility Register.

For more information on publishing data using the IPT, see this section of the IPT manual.

Congrats!

Congratulations on publishing your checklist data in an open and repeatable way (and making it this far in the wiki)! 🎉

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