How To: Upload to Zenodo - QMSKI/TransparentQMSKI GitHub Wiki

A tutorial video is here

Basic:

Advanced:

What is Zenodo?

Zenodo is an open-access data repository developed under the European OpenAIRE program and maintained by CERN in Geneva, Switzerland. In Zenodo, researchers can deposit data, software, reports, presentation, and other outputs of their work [1].

Pros of Zenodo:

  • It is free
  • It allows you to upload 50GB of data, but you can request for more
  • It provides DOIs (Digital Object Identifiers), which make your data citable and persistently available
  • It allows creating communities

Alternatives to Zenodo:

How does Zenodo look like?

The Zenodo home page is composed of three parts:

  • Top bar (red): It contains buttons to:
    • Search for data in the repository
    • Upload data
    • Search communities
    • Log in
    • Sing up (only the first time)
  • Recent uploads panel (purple): It contains a list (like a blog) of the latest data uploaded. For each dataset, you can see:
    • Date, data type (e.g. dataset, software, presentation), data openness
    • Title, authors, short description, last upload date, and number of upload versions
    • View (button on the right) to access the dataset
  • Info panels (blue): It contains some information about the repository and how to use it

https://github.com/QMSKI/TransparentQMSKI/blob/master/figures/zenodo_home.png

Sign up to Zenodo (only the first time)

  • Go to zenodo.org and click Sign up (top-right)
  • Sign up using GitHub, ORCID, or your email address

Upload data to Zenodo

  • Click Upload (middle of top bar)
  • Click New Upload (top-left)
  • You get a page like this:
    https://github.com/QMSKI/TransparentQMSKI/blob/master/figures/zenodo_upload.png
  • Upload your data (blu square in figure above):
    • Drag and drop files or upload file with the Choose files button
    • Click Start Upload
    • Once your data is uploaded, click Save (top-right)
    • Once the upload of all your data is completed, you can publish them by clicking Publish. Note that publishing the data is an irreversible step: You cannot un-publish your data. Data get a digital object identifier (DOI) once they get published, and thus become permanent. If you need to modify your data, you can create a new version of your dataset
  • Fill out the metadata information (purple square):
    • Communities: Type QMKSI. Zenodo will send a request to us and we will accept your data as part of our community data. Being part of the community means that your data will be listed when typing QMKSI in the Zenodo Search button
    • Upload type: Choose your data type: Publication, poster, presentation, dataset, ...
    • Basic information: These fields are self-explanatory. Note that you can reserve a DOI before publishing your data, and, for example, use it while preparing your manuscript
    • License:
      • Access right: Specify who has access to your data:
        • Open access: Anybody can access your data
        • Embargoed access: Your data will become open access after a date you specify
        • Restricted access: Your data are visible only under your conditions
        • Closed access: Your data are visible only to you
      • License: Start typing the license you want and select the autofill suggestion. If you need guidelines on how to choose a license, see here
    • Fill out the remaining fields - they are self-explanatory

Notes:

  • You can save several time by clicking Save at the top or bottom of the page
  • Once you click Publish you cannot change the published data. However you can still edit the metadata

DOI and citations

Once you have published your data, in the left banner (bottom), you can:

  • Get your DOI badge (purple rectangle): By clicking on the DOI badge, you get HTML, md, etc., code to insert the badge in your website or documents
  • See the DOI of the current version of your data, or of the whole dataset (red square)
  • See your data citation and download citation files (blue square)

Edit metadata, add new data version, and view data statistics

Once you have published your data, in the left banner (top), you can:

  • Edit your metadata (red square): Click Edit and change your metadata where needed. Save before closing
  • Create a new version of your data (red square): Click New version and upload a new version of your data following the upload instruction
  • See you data statistics (purple square): See the number of views, downloads, and more information by clicking See more details

Upload code from GitHub

Zenodo allows you to automatically upload your software from GitHub to get a DOI and make your software citable.

  • Go to https://zenodo.org/account/settings/github/ and activate the link to your GitHub repository by switching the right button to ON:

  • Go to your GitHub repository and create a release:

    • Click releases in the middle horizontal tab:

    • Click Create a new release:

    • And:

      • Fill out Tag version (see suggestions on the right) and Release title
      • Press Publish release

  • Go back to Zenodo (https://zenodo.org/account/settings/github/) and click on your repository:

    • Get your DOI badge for your website, documents, etc.
    • Click the DOI link
    • Once in your new data page, click Edit to fill out your metadata. Make sure to:

References

[1] https://en.wikipedia.org/wiki/Zenodo