An extensive manual on Yoda for managing your research data.

What is Yoda?

Yoda is a research data management service supported by Wageningen University & Research (WUR). It enables researchers, students, and staff to securely store, share, archive, and publish research data throughout all stages of the research project cycle. Yoda supports data sharing across institutions, making collaboration with colleagues and external partners possible.

Yoda is built on the iRODS framework, which provides the underlying infrastructure and core data management capabilities of the system. Yoda is being developed by Utrecht University (UU), and it is designed with the FAIR principles in mind, ensuring that research data is Findable, Accessible, Interoperable, and Reusable.  
 
With Yoda, you can securely store your data in a simple and familiar ‘file-and-folder' interface, comparable to the W-drive or OneDrive.  

You can access Yoda with various clients, and it can be mapped as a network drive as well. It is not, however, optimised for seamless background syncing and doesn't fully replace traditional network drives. Instead, Yoda serves as a more secure platform for managing research data throughout its lifecycle. Yoda enables collaboration across institutions, allows the addition of metadata to the data, provides archive storage and finally, with Yoda, you can publish your research data as well. 

For more information about Yoda, please see https://www.uu.nl/en/research/yoda. 

Yoda@WUR

Many organisations, both in the Netherlands and abroad, are using Yoda. 

Yoda’s instance for WUR – Yoda@WUR - https://yoda.wur.nl/ is hosted by SURF (Dutch ITC of education and research). While University Utrecht is the main developer of Yoda, SURF oversees Yoda@WUR’s performance, stability, and maintenance. 

Yoda is listed in the WUR Approved Apps tool and is suitable for research data up to classification Serious. For more details, please see Data classification in Yoda.

Safely storing your data at Yoda@WUR

Since the Yoda@WUR instance is hosted at SURF, the data are physically stored in three geographically separated data centers in the Netherlands of SURF. SURF data centers are certified with the state-of-the-art ISO 27001 Information Security Management Standard. Data are being transferred to these data centers over an encrypted network and are not scanned or inspected in any way. Additionally, data integrity is ensured through checksum computation and comparison - an algorithm detecting the smallest errors in data transmission or storage. For more information about security measures, please see here. 

Securely sharing your data

Data in Yoda can be securely shared with WUR colleagues and external partners using 2 Factor Authentication (2FA). 2FA consists of  

1. user's email and password and 
2. login authentication through an authentication procedure.     

WUR researchers are authenticated through SRAM (SURF Research Access Management) while eduID is used for external partners. Please see SRAM and eduID for more information.  

Archiving your data

Yoda’s archive is called the Vault. Here, Yoda users can place their completed data collection, completed data analysis, completed research and data at other stages of their work that are not actively used. Please see Research Area and the Vault for more details about the Vault. 

Publishing your data 

With Yoda, you can publish your data as well. The published data package obtains its own persistent identifier (DOI – digital object identifier) and is registered in DataCite, making it findable online. For more information about the publication process in Yoda, please see Publishing in Yoda.  

How does Yoda support the FAIR principles?

Findable & Accessible – before archiving your data or publishing it, metadata MUST be filled in. Yoda enables researchers to search and retrieve data within the Yoda portal (with granted access by Yoda data manager) or online once a data package has been published. Once published, data is easily findable through a DOI and freely available, upon request, or only metadata is being published, protecting sensitive data.  

Interoperable & Reusable – Yoda enforces standardised and rich metadata that comply with domain standards, ensuring consistency and machine-readability. In addition, metadata can be reused across folders within Yoda. 

How to get started?

Creating a Yoda account

• Does your group already have a Yoda account? Please contact your group’s data manager in Yoda (this is usually your data steward), and they will help you further. If you are not sure whether your group already has a Yoda account or cannot find your data steward, please contact data@wur.nl. 

If your group does not have a Yoda account yet, please follow these steps: 

1. Determine who will perform general Yoda management tasks: To work with Yoda, someone within the group must be appointed to manage its general aspects. This person is called the data manager. Typically, the group's data steward fulfils these tasks, but anyone familiar with best practices in data management can be granted the same rights if agreed upon by the group. The data manager will receive system privileges to create new parent folders and manage users’ access rights. These responsibilities can also be shared among multiple users within the group. 

2. Send an email to data@wur.nl with the following information: 
   1. 1. For which division (research group, business unit or project) Yoda account needs to be created? Specify which science group you are a part of. 
      2. Who will perform general Yoda management for the requested account? 
      3. Who is the project leader / business unit holder / chair-group holder? Include them in cc of the email as that person will have final responsibility of data within the research group. 

Once data@wurl.nl receives the request, one of Yoda@WUR administrators will create a Yoda category for your group and grant data manager rights to your group’s data steward or other appointed colleague. Afterwards, they will in turn be able to create new subcategories and grant permissions to view and/or edit the contents of said subcategories to other users. If you would like to learn more about the tasks of data managers, please see https://www.uu.nl/en/research/yoda/guide-for-data-managers. 

When you obtain your Yoda account, you can select which client to connect to Yoda is best suited for your needs. Please see Accessing Yoda for different Yoda clients' descriptions and links to their manuals. 

Yoda@WUR has its own Teams channel, which is accessible to all Yoda@WUR users. By clicking on the link, you will be automatically added to the group - General | Yoda@WUR_Users | Microsoft Teams. In the Teams channel, you can read about maintenance interruptions and report issues to which Yoda admins respond. 

Yoda costs

Yoda Glossary

Yoda has several different environments and Yoda specific terminology. Knowing them makes working with Yoda easier.

Research Area and the Vault

Yoda is divided into two environments – the Research area and the Vault.  

The Research Area

Research area is where you store your active research. In this environment you can upload your data, edit the metadata, add or remove folders and files.  

You will know you are in your research area by the prefix “research-” that precedes your active folder name. The limit of 25TB of storage applies to the Research area alone. 

The Vault

The Vault is another name for the archive in Yoda. This is the environment where you can store your data for the long term. When archiving, a ‘snapshot’ of your data package (data and all its documentation) is placed in the vault. Once there, you cannot change it anymore (no changes to the data nor metadata are possible). If, however, you would like to modify your archived data package in the future you can easily copy it back to the Research area.

You can recognise you are in your Vault area by prefix “vault-” preceding your folder name. 

Please note that the limit of 25 TB of storage does not apply to the Vault - storage in the Vault is not included in the total cost evaulation. 

It is useful to safeguard data within the Vault at key moments during your research so that a secure version of the data is retained and available. For instance, one could imagine submitting data to the Vault when all (raw) data have been collected, when data analysis is completed, at the end of the research or at any other stage where data is not been actively used. Once the data is stored in the Vault, you are strongly recommended to delete it from the Research area, if data is no longer actively used, to free Yoda’s storage and reduce storage costs – please see Yoda storage’s systems, backups and Revisions for more information.

You can archive your entire research- folder or a subfolder within by submitting that folder to the Vault. 

Submitting your data package to the Vault is a mandatory step for publication in Yoda. 

You must first place your data package in the Vault if you want to publish it. Once your data package has been accepted to the Vault, you can submit it for publication with a simple click – see here for more information.  

The idea behind the Vault is that everything placed there is ready for publication. It is therefore important to think in advance if you would like to publish your data package. If so, then start documenting your data from the beginning of your research, which is always a good practice. To know how to document your data according to WUR standards, please see Curation checklist for Yoda@WUR and Publishing in Yoda. 

If you do not plan to publish your data package but only archive it, then the minimal requirement to submit your data package to the Vault is to fill in the obligatory fields in the Yoda Metadata form (those marked with an asterisk – please see Yoda metadata form for more information. Although we highly recommend to fill in the metadata form as complete as possible.

Once submitted, your group’s data manager may accept or reject your submission to the Vault. If the submission is rejected, your data manager will provide recommendations to improve your submission. 

Please see https://www.uu.nl/en/research/yoda/guide-to-yoda/archiving-your-data-in-yoda for more information and examples. 

Yoda Category

Whenever a new account is created in Yoda it obtains its own category. A Yoda category is the top-level ‘folder’ structure used for organizing research- groups in Yoda’s web portal. Yoda@WUR categories follow an agreed naming convention: science group – group, for instance ‘afsg-fch’ for WUR Food Chemistry group. 

Note that a category is not an iRODS object but is created for easier group management and overview and is therefore only visible in Yoda web portal and not in other Yoda clients (see Accessing Yoda for a complete list of clients to access Yoda). 

Yoda Subcategory 

Each category has governance over its subcategories which are created and managed by the organisational unit's data manager. How many subcategories are created in a category and what their function is depends on the organisational unit. Here are three examples of subcategories in a Yoda category: 

Figure 1 - example of subcategories in Yoda.

Each category has a subcategory called system where Yoda administrators specify who is the data manager of a given category. 

Please do not put any data in the system subcategory. 

In case this happens please contact data@wur.nl and we will assist you further, just note that moving data between subcategories is not a simple task. 

Within each subcategory, Yoda data managers can create research- folders where users with appropriate privileges can place their data. 

Note that a subcategory is not an iRODS object but is created for easier group management and overview and is therefore only visible in Yoda web portal and not in other clients. 

The 'research-' group

A research- group, also known as a parent folder is the main folder where you store your data and it always starts with the word “research-“. In a parent folder, users with appropriate privileges can handle their data, create new subfolders, add metadata,... and share their work with colleagues.  

The organizational unit’s data manager oversees the creation of new research- groups and adding new members who can have different privileges: 

• Viewer: can only view and download (read only access) the data within a research- group.

• Member: can handle data (view, upload, download, modify or delete) within a research- group (read/write access).

• Manager: has read/write access and can add or remove members to the research- group. 

Please note that whoever has access to a research- folder automatically obtains access to all its subfolders.  

Simultaneously, when creating a new research- group, a vault- group (vault- folder) is created, automatically linked to the newly created research- group. Because the Vault is set up in a way that does not allow any changes to the data package within, including the name of the vault- group, this means that once a research- group is created, it cannot be renamed. It is therefore crucial to think about your folder structure beforehand.

If you want to rename your research group, you must create a new research group and copy all your data to it.

The research- group and the vault- group are iRODS objects and are therefore visible and accessible in allYoda clients, contrary to the (sub)category. 

Yoda's storage systems, backups and revisions

Yoda’s two environments, the Research area and the Vault, are stored on different storage systems. When you place your data in the Research area, it is stored on a Ceph disk in the SURF data centers. Data placed in the Vault is stored in Object store. For more information about Ceph disk and Object store, please see: https://servicedesk.surf.nl/wiki/spaces/WIKI/pages/62227609/How+the+service+is+provisioned.  

The limit of 25 TB of storage only applies to the Research area. Used storage in the Vault is not included in this limit. It is therefore recommended to archive your data frequently and then delete it from the research area regularly to reduce storage costs. 

Backup of your data in Yoda 

The research area is backed up through a Point In Time (PIT) backup. It is stored on the Object store and retained for 2 months. Please see https://servicedesk.surf.nl/wiki/spaces/WIKI/pages/62227612/Backups+and+user+data+Point-in-Time+PIT+recovery for more information. 

The data in the Vault (placed on Object store), is replicated (not backed up) 3 times to geographically separated data centers in Amsterdam (Science Park, Sloterdijk and Amsterdam Zuid). 

If you would like to access a previous version of your data (in the research area or the vault) that cannot be accessed through Yoda revisions (see below), please contact data@wur.nl and we will help you further. 

Yoda revisions

Whenever you save a file in Yoda (the Research area) using the same name, Yoda creates a new version of your file, a revision. A revision is a snapshot of the file at the time of saving. In case you need to restore a previous version of a file, you can simply search through revisions and select which one you want. 

Yoda keeps multiple revisions on a decreasing time granularity scale - more revisions in recent history and fewer revision further back in time. The revisions are stored for a maximum of 16 weeks, after which they are deleted. To restore file versions, please see https://www.uu.nl/en/research/yoda/guide-for-data-managers/finding-and-restoring-data.  

Accessing Yoda

You can access Yoda through various methods: 

• Yoda web portal - https://yoda.wur.nl/
• Map Yoda as a Network Disk through Cyberduck
• Use Command Line Interface (CLI) tools to access Yoda:
• iCommands
• GoCommands
• iBridges (Graphical user interface (GUI) or CLI) 

The method you choose to access Yoda depends on your needs and preferences. All methods are safe to use, but some offer better upload speed (CLI tools, Cyber Duck), have better stability (CLI tools), and more configuration options (CLI tools). Please see https://www.uu.nl/en/research/yoda/guide-to-yoda/accessing-yoda for detailed descriptions of all Yoda clients.

Since WUR supports only Windows OS, the manuals of Yoda clients for Mac OS and Linux systems are not supported. However, some instructions can be found here https://www.uu.nl/en/research/yoda/guide-to-yoda/accessing-yoda. 

Please note: for older Yoda versions several other methods were available, like mapping Yoda as a network drive using Windows native WebDAV client of WinSCP. Both methods have compatibility issues with newer versions of Yoda and are therefore not supported any longer.

Figure 2 - comparison of functionalities for different access methods to connect to Yoda. Figure was taken from https://www.uu.nl/en/research/yoda/guide-to-yoda/accessing-yoda.

The manuals on how to install all the mentioned Yoda clients on your WUR computers can be found in the top right corner of this document, as a separate attachment.

Yoda metadata form

One of the core functionalities in Yoda is the ability to add metadata to the research- group level and its subfolders and is a key step to making your data FAIR.

Using Yoda, researchers can add structured metadata to their research group and its subfolders. When creating a new group (research- folder) the Yoda system automatically preselects the metadata schema named default-3.  This default option is supported by WUR. Please note, with future upgrades, the name of the default metadata form may change to default-[number>3]. Regardless, the default choice by the system will always be supported by WUR. 

(Note:  more metadata forms are available here.) 

When you click on the Metadata button within your research- group, an online metadata form appears. After filling it in and saving your changes, your metadata will be stored in a  yoda-metadata.json. This file is editable in other (source code) editors as well.  

Adding metadata is mandatory before archiving or publishing your data. For archiving, it is sufficient to fill in only the obligatory fields (marked with an asterisk symbol), though it is recommended to fill in as much as possible. If you decide to publish your data package, we recommend completing the metadata form – please see the Curation checklist for data packages in Yoda@WUR for more guidance. 

default-3 metadata schema

The default-3 metadata form conforms to the DataCite metadata standards, making the data package easily findable in data catalogues once published. It broadly describes the data package, how it can be reused and cited.  

The fields in the metadata form have clear short descriptions. Please see the default-3 metadata description, the default-3 metadata description from SURF and the Curation checklist for data packages in Yoda@WUR for more detailed information about each of the fields. If you have any questions about the default-3 metadata form, please reach out to data@wur.nl. 

Customised metadata schema 

It is possible to customise your own metadata scheme, which can be incorporated into Yoda@WUR. Such schemes, however, require regular maintenance and updating. Maintenance of customized schemas must go along Yoda maintenance and updates schedule and is not such a simple feature. Therefore, data@wur.nl will not take responsibility for maintaining customised data schemes. They are the responsibility of the research group that developed them. Before starting a customised metadata schema in Yoda, please carefully read Metadata schemas in Yoda. 

Only data packages using default-n metadata schemas will be findable online after publication. Customised metadata schema will not be visible once published. 

In Yoda, a metadata schema contains more information than just the metadata itself. A metadata schema validates the metadata of a data package and contains information about how this metadata is displayed in the Yoda web portal. Therefore, a Yoda metadata scheme actually consists of two parts: 

• A JSON schema file that is used to validate metadata of a data package.

• A UI schema file that contains information about the display of the schema in the web portal.  

Please note, when creating a new custom metadata schema, you must include all the fields from the core-2 metadata schema.  

If you would like to create a customised metadata scheme in Yoda: 

1. Carefully read the instruction Metadata schemas in Yoda to get a general overview of what is required for a new metadata schema. Note, experience with programming and command line interfaces is required.
2. Think about the structure of your schema and design it. We would recommend you start with the default-3 schema, study it and adjust it to your needs.  
3. Give your metadata schema a name.
4. After doing the preparation detailed above, contact data@wur.nl. We will arrange a meeting to discuss your wishes about your schema and give access to our Yoda@WUR test instance where you can test your new schema.
5. Document your work well so that others from your group have sufficient information to maintain the new schema in the future. 

Publishing in Yoda

Publishing your data is one step closer to making your data FAIR (Findable, Accessible, Interoperable, Reusable). 

Data classification in Yoda

To secure your data properly, they first need to be correctly classified. Yoda uses different terminology in classifying data than the terms used at Wageningen University and Research (WUR)- data classification. However, these terms are equivalent. 

In the table below, you can see the relation between data classification terms used in Yoda and at WUR. 

If you have data with the critical/disruptive classification, please contact data@wur.nl or your groups’ Information Security Officer (ISO). 

Yoda treats all the data under the classification of ‘serious’, even if they are classified as public.  
 
If your data is classified as sensitive but you would still like to publish it in Yoda, please contact data@wur.nlfor support and follow the steps described here. 

Data access rights

With Yoda, you can publish your data with various access rights: 

• Open: both metadata and the content of your data package are published and therefore visible and available online.

• Restricted: only metadata is published and therefore visible and available online. The content of your data package is available only upon request.

• Closed: only metadata is published and therefore visible and available online. The content of the data is not available for sharing. 

If you have classified your data as sensitive/serious or critical/disruptive then you can choose for Restricted or Closed access.  

In addition, it is possible to publish your data package under an embargo date, which you can specify in the metadata form. If you publish your data Open access and under an embargo, your data becomes available only after the specified embargo date.

How to publish your data in Yoda

Please follow these step-by-step instructions on how to publish your data. 

Before you can submit your data package for publication in Yoda, your data package must be placed in the Vault. To make this process more efficient, we recommend that you consider the purpose of your data package at the beginning of your research project. Is it your goal to publish your data package? In this case, start thoroughly documenting your work from the start, also, think about the folder structure, completely fill in the Metadata form, provide README files and all the other necessary documentation described in WUR’s curation checklist. 

See the Vault as a necessary stepping stone to publication. Not everything that is in the Vault will get published (for instance, raw data, or intermediate steps in the research worth archiving), but everything that is published in Yoda is placed in the Vault.  

Once your data package has been accepted to the Vault by your group’s data manager, you can submit it for publication. You will have to agree to the Terms and Conditions (see below) and provide all documentation described in the WUR’s curation checklist.  

Yoda data managers and/or WUR data librarians will evaluate your submission for publication. If you have provided everything specified in the WUR curation list, your publication will be approved. Otherwise, WUR data librarians will guide you and help you with improving your documentation. To do that, you will have to first copy the data package back to the Research area, add missing documentation, submit it to the Vault and only then for publication. To minimise this back-and-forth, we strongly recommend documenting your data package well before placing it into the Vault.  

Once your data package is ready for publication, a data manager and/or data librarian will approve it, and within a few minutes, your work can be available online. 

Once published, your data package will obtain a permanent digital object identifier – a DOI (more about DOI) and a public landing page. With the DOI, you can cite the data package, register it in Pure (for data packages published in Yoda, this is done automatically) or promote it through social media. The public landing page, starting with https://publication.yoda.wur.nl will contain all metadata about your data package and information about data access.   

Here is an example of a Yoda@WUR publication with open access: 
https://publication.yoda.wur.nl/full/WUR01/WHMZ2L.html 

Here is an example of a Yoda@WUR publication with restricted access:  https://publication.yoda.wur.nl/full/WUR01/8PT7T6.html 

Here is an example of a Yoda@WUR publication with closed access: https://publication.yoda.wur.nl/full/WUR01/OAETKJ.html 

In addition, the metadata data will be registered in DataCite so that your data package is easily findable online.  

Terms and Conditions for publishing in Yoda

One of the last steps before publishing your data is to read Yoda@WUR’s Terms and Conditions and agree to them if you wish to publish your data package through Yoda.  

This is the text you will need to carefully read and agree to if you want to publish your data through Yoda@WUR: 

Important - You are about to agree to a publication in Yoda@WUR 

As a WUR researcher, I declare that:  

• I am qualified to publish the data package; I am the creator of the data package or act with express consent and on behalf of the creator(s), and am allowed to publish the data according to my chair-group holder or business unit manager.

• The metadata properly describes the data package, in particular, the license and data package access levels have been chosen in accordance with institution/consortium policies and have been reviewed by the creator. 

• The data package adheres to research data management principles concerning, amongst others, folder structure, file naming, and data/information representation.  

• The data package includes elaborate documentation that adheres at minimum to the terms presented in the WUR guidelines (www.wur.eu/datadocumentation)

• The data package has been evaluated by a Yoda@WUR data manager when submitting to the vault and will be evaluated again for submittal for publication.

• I understand that once published, the metadata can be found and read publicly.  

• I understand that if the data access level is set to "open", then the data can be found and accessed publicly. Sensitive information should usually not have an "open" access level.  

• I understand that if the access level is set to another value, then the data package cannot be accessed publicly (although the metadata can be read) and a separate license.txt file needs to be present in the data package.  

If you comply and agree with the above, then you can check the box and press Confirm agreement; otherwise please press Cancel. Should you require further support, please contact your Yoda@WUR data manager or contact the Yoda@WUR team at data@wur.nl. 

Publishing a newer version of an existing data package 

If you made some new progress with your research and would like to add these new results to the already published data package, that is possible in Yoda, too. During the publication steps (see step-by-step instructions you can choose to link the publication to an existing one. Yoda will assign the new data package to the same base DOI and register it as a new version of the earlier data package.

De-publishing your data

Once the data package is published and once it obtains a DOI, it can be findable and accessible (if this option has been chosen) by everyone on the internet. That is why it is very important that you are sure that what you are publishing is correct, well-structured and well-described. Assume that once your data package is published it will remain published and part of the academic record.

If however, you have a good reason why your data package should be de-published (e.g. due to privacy issues), this is also possible in Yoda. You will have to provide a good reason for it and explain on the publication landing page why your data package is not available anymore. Your data package and its DOI will still be registered and part of academic record, but it will not be findable online once de-published. 

If you have a good reason to unpublish your data package, please contact data@wur.nl. 

SRAM and eduID

Yoda@WUR uses  SURF Research Access Management -  SRAM method to ensure a secure log-in to Yoda through 2 Factor Authentication - 2FA. 

Internal Yoda@WUR users

External Yoda@WUR users

What is eduID?

Questions & Support

Do you have any questions? Feel free to contact us at data@wur.nl.