Zenodo Guide

Uploading project materials to Zenodo

How to organize and upload a set of research files before publishing it as a Zenodo record.

Terminology: In this guide, deposit refers broadly to the files and metadata you submit to Zenodo. While you are preparing them, Zenodo calls the unpublished item a draft. Once published, it becomes a record with a persistent identifier.

Before you begin

Prepare a complete, understandable set of materials before starting a new upload. Although metadata can be edited later, edits to files are only allowed shortly after publication, though a new version may be created.

• Prepare the required metadata in advance, including the title, authors/creators, resource type, and applicable license or copyright. Also gather helpful information for optional fields such as a description, keywords, related works, and funders.
• Organize and name files clearly. Zenodo lists files in alphanumeric order, so use consistent prefixes to group related material. For example, Data_ for data files. Use version numbers or dates only when they help users distinguish files. Upload open, widely supported formats when practical such as .csv, .txt, .png/tiff, and pdf.
• Check whether the record should be submitted to a Zenodo community. A project, institution, funder, or conference may have a relevant community with its own submission guidance. 

Choose how to organize the files

Zenodo accepts up to 100 files per record and a total of 50 GB under the standard limit. The file count and the importance of preserving folders should guide your choice.

NOTE: If it’s important for you to track downloads or citations for different files, the recommended approach is to upload them as separate Zenodo records and use the Related Works field to link the files.

If only part of the project is large

A hybrid arrangement can work well when only part of the project contains many related files, such as stimuli or images, or when users may want to download different parts of the project independently. Group related files in ZIP archives while leaving primary datasets, scripts, and the README as individual files. Each ZIP archive will also preserve any folder structure within that group. 

Decide whether you need a README

Include a README when the deposit contains multiple files, a ZIP archive, code, or other materials that require instructions to understand or reuse. For a small, self-explanatory deposit, completed Zenodo metadata and clear file names may be sufficient.

If you include a README, use it to explain:

• what each file or folder contains
• how the files relate to one another
• the order in which scripts or other files should be used
• required software, packages, or hardware
• any instructions needed to reproduce the analysis or reuse the materials

Tip: If you include a README, name it README.md or README.txt. During the upload process, you can choose to have Zenodo open it automatically, so users see the project instructions first. 

Avoid common problems

• Do not upload sensitive data. Remove direct identifiers and other sensitive or confidential information from the files before uploading.
• Remember that metadata is always public. Restricting file access doesn’t hide the record’s title, description, creators or other metadata. Do not include sensitive or confidential information in these fields.
• Confirm that you can share every file. Remove copyrighted, confidential, or third-party materials that you are not authorized to distribute.
• Choose the license carefully. License is a required field. Zenodo defaults to CC BY 4.0, which may not be appropriate for every type of material. Consult Zenodo’s Licenses and rights guidance to select the appropriate license or mix of licenses.
• Identify creators correctly. Creators/authors appear in the citation; contributors do not. Confirm names and order before publishing. You may also include an identifier (e.g. ORCID), affiliation and role for each person or organization.
• Use the correct DOI. Enter an existing DOI only when it identifies the exact materials being deposited, not a related publication.
• Test the materials. Open the uploaded files or ZIP archive and confirm that scripts, paths, and README instructions work as expected.
• Remove hidden system files from ZIP archives, including .DS_Store, __MACOSX, and Thumb.db.
• Review before publishing. Preview the record and check the files, metadata, visibility, and license. Metadata can be edited after publication. File corrections are permitted only within 30 days of publication. Any changes to the files after this timeframe will generally require publishing a new version, while all past versions will remain accessible.
  • To test the process without creating a permanent record, use Zenodo Sandbox.

Upload and publish the materials

1.  Start a new upload.

Sign in to Zenodo, select the plus icon in the header, and choose New upload. 

If you want the record included in a specific Zenodo community, you can open that community’s page and select New Upload to submit the draft for review before publication. Alternatively, publish the record independently and request its inclusion in the community afterward.

2.  Add the files.

Drag files into the upload area or select Upload files. Wait until all uploads are complete and remove any unintended or duplicate items.

Choose the file users see first. In the uploaded file list, select the checkbox in the Preview column for the file you want Zenodo to open automatically. If you don’t select one, Zenodo displays the first file it can preview based on alphanumeric order. If it’s a ZIP archive, the folder and file structure will be displayed.

3.  Describe the record.

Complete the required metadata, including the resource type, title, publication date, and creators/authors including yourself. For mixed materials, choose the resource type that best represents the main contribution of your upload. See Zenodo’s guidance on completing the deposit form for details about individual fields.

Connect related records and outputs. Use consistent keywords or subjects across related records to improve discoverability. When a specific relationship exists, add the other record, dataset, software, or publication under Related works using its DOI or another persistent identifier and select the relationship that best describes the connection.

4.  Choose the DOI option.

If this exact deposit already has a DOI, enter it. Do not enter the DOI of a related journal article. Otherwise, Zenodo will register a DOI when the record is published. You may reserve the Zenodo DOI first if you need to place it inside a file before publication.

5.  Set file visibility.

Choose public or restricted file visibility. Metadata remains public even when the files are restricted. Restricted files can remain restricted, be shared with selected users, allow access requests, or become public automatically after an embargo period.

6.  Save and review the draft.

Select Save draft, resolve any validation errors, and use Preview to inspect the landing page. You may also Share Access to the draft with Zenodo users or by generating a link. When the draft is complete, select Publish.

Final check

• The final file set is complete, opens correctly, and contains no unintended or sensitive material.
• The README, if included, matches the uploaded files and any folder paths used by scripts.
• The metadata and DOI choice are accurate.
• The visibility, sharing, and embargo settings match the intended access plan.
• The Preview page is clear to someone who did not work on the project.

Example:

ZIP-Code-Level Data on Rooftop Solar, Battery Storage, and EV Charging in California, 2023 - https://zenodo.org/records/23607282

Zenodo Record with README, and file structure including data, and models with multiple versions and code in Github

Zenodo guidance

Create a new upload | Prepare metadata | Manage files | Reserve a DOI | Collaborate and share  | Keywords and subjects

Manage versions | Submit a draft for community review | Submit published record to a community 

To test the process without creating a permanent record, use the Zenodo Sandbox. The Zenodo Sandbox is separate from the main Zenodo site, so you will need to create a separate Sandbox account.

Getting Started with Zenodo (transitioning from OSF Projects) [VIDEO] - Amanda Montoya