In this tutorial we will make use of the sandbox of the general purpose repository Zenodo and it's integration with GitHub to assign persistent identifiers to your software/code.

Get a DOI using the Zenodo-GitHub integration

To issue a DOI for your software, you can make use of the Zenodo-GitHub integration. Zenodo archives your repository and issues a new DOI each time you create a new GitHub release which allows you to create permanent, citable versions of your lesson.

1. Connect your GitHub repository to Zenodo

Go to Zenodo Sandbox (important to try this out in the sandox first) and create an account using the email or Github option if you don't have one already.

Remember that this is a test environment, so nothing you upload here will be available on the main Zenodo platform and the DOI created is not real and will not resolve.

By using the GitHub option so signup/sign in your Zenodo account will be connected to your GitHub account automatically.

Click the down arrow next to your username in the top right corner to expand the menu, select GitHub

If you have not used your GitHub account to sign in to Zenodo sandbox select Linked Accounts first to connect your accounts

Once connected, you can selet the repository you want to issue a DOI for. You can use the repository you created for the git tutorial.

zenodo_github_dashboard (1).webp

Find your repository in the list, toggle the switch to ON

If your repository does not show up in the list, check when it was last synced in the title row of the first box and click sync now if needed

Reload the page > your repository should now be added to the list of Enabled Repositories

2. Create a release

To issue a DOI for your software/code, you need to create a release in your GitHub repository. This will trigger Zenodo to archive your repository and issue a DOI.

Go to your GitHub repository and click on the Releases on the right side menu of the codetab.
Click the Draft a new release button.
Click the Choose a tag button in the top left part of the page. Enter a version name (e.g., initial-release )in the text field and click `+ Create new tag: on publish``
Fill in the Release title field with a short title (e.g., First release of the software name).
Fill in the Description field with a description of the release (e.g., This is the first release of <Title of your software name>.).
Click the Publish release button.
Return to your Zenodo > GitHub settings (see above) and inspect the list of Enabled Repositories. A black and blue DOI badge should now be available next to your repository name.

3. Add the DOI badge to the repository

Click the DOI badge next to your repository name in the Zenodo > GitHub settings.
A popup window will open with the DOI badge
Copy the Markdown formatted text.
Go to your GitHub repository and select the README.md file in the left side menu.
Click the pen in the top right corner to edit the file > paste the copied markdown text at the top of the file and commit the changes.

4. Add metadata to your Zenodo record

During the course we have emphasized the importance of rich and curated metadata. When using the integration between Zenodo and GitHub, some of the metadata have been extracted automatically from the GitHub API. For example, the authors are determined from the repository’s contributor statistics and the description is determined from the release notes. This will usually not be rich enough and you should improve the metadata of the Zenodo record.

This can be done manually by following this step-by-step guide. but this will need to be repeated for each new release. If you anticipate that you will have several versions of the software/code we recommend including a .zenodo.json file and a license.md file at the root of your GitHub repository.

Inspect the Zenodo record for your repository to see what metadata was automatically added.
Create a .zenodo.json file at the root of your repository and copy-paste the content below or download the example .zenodo.json and add it to the root of the repository. (note the initial period "." in the file name)
Update the fields with the relevant information for your software and remove the fields that are not relevant for you. Commit the changes.
{
"title": "Title of your software",
"description" : "Put a brief description of your software here.",
"creators": [
{
"name": "Kronander, Elin",
"orcid": "0000-0003-0280-6318",
"affiliation": "NBIS",
"type": "Author"
},
{
"name": "Family Name, First Name",
"orcid": "0000-0003-0280-6318",
"affiliation": "Your institution",
"type": "Author"
}
],
"related_identifiers": [
{ "scheme": "doi",
"identifier": "10.1234/software.paper.5678",
"relation": "isDocumentedBy",
"resource_type": "publication-article"
}
],
"keywords": [
"FAIR",
"DDLS",
"Research Area"
],
"grants": [{"id":"871075"}]
}

In the example shown above , we add metadata regarding:
- - - software authorship and ORCiDs, via the creators field
    - a custom title, via the title field
    - a custom description, via the title field
    - a related identifier to the software paper, via the related_identifiers field
    - keywords, via the keywords field
    - funding information, via the grants field
If desired, add additional fields to the .zenodo.json file. You can find more information about these fields in the Zenodo documentation.

NB! Don't add a license field to the .zenodo.json file. A license will automatically be added to the Zenodo record based on the LICENSE.md file in the root of the repository
Add a MIT license file named LICENSE.md to your repository by following the steps in the GitHub documentation.

Next steps and suggestions

Apply to your own software

If you have a repository used in your own research that you want to add a DOI for you can follow the same steps as above but using the "real" Zenodo.

It is also possible to create an integration between GitHub and SciLifeLab data repository for assigning a DOI to your repository. Read more here: https://info.figshare.com/user-guide/how-to-connect-figshare-with-your-github-account/

Integrating ORCID iDs

ORCID has integrations with Zenodo which allows your works to be automatically added to your ORCID record. This means that when you create a Zenodo record for your lesson, it will also be added to your ORCID record if you have linked your Zenodo and ORCID accounts.

Go to Zenodo and log in to your account.

Click the down arrow next to your username in the top right corner to expand the menu, select Linked Accounts.

Click the Connect button next to the ORCID logo.

You will be redirected to the ORCID website to sign in and authorize Zenodo to access your ORCID profile.

Inform all the creators and contributors of your lesson that they can connect their ORCID accounts to Zenodo as well.

For each creator or contributor in your .zenodo.json file that has an ORCID id and set up this connection, Zenodo will automatically add the work to their ORCID record when you create a new release in your GitHub repository.