Difference between revisions of "Publishing data in Zenodo"

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== '''<span style="font-size:large;"><span style="font-family:Arial,Helvetica,sans-serif;">CLEX Data&nbsp;Collection</span></span>''' ==
 
== '''<span style="font-size:large;"><span style="font-family:Arial,Helvetica,sans-serif;">CLEX Data&nbsp;Collection</span></span>''' ==
  
&nbsp;
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[[File:Zenodo Data collection.png|800px]]
  
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;"><span style="caret-color:#000000"><span style="color:#000000">You can now publish the code you use for your research with the new [https://zenodo.org/communities/arc-coe-clex/ <span style="color:blue">CLEX Code Collection</span>] on Zenodo (CCC). Journals sometimes require&nbsp;code to be published alongside data. We hope the Zenodo community will also serve as a way to share our codes in a user-friendly way. So even if you are not required to publish your code you can see this collection as an opportunity to share your work with others.</span></span></span></span>
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;"><span style="caret-color:#000000"><span style="color:#000000">You can now publish the code you use for your research with the new [https://zenodo.org/communities/arc-coe-clex-data/ <span style="color:blue">CLEX Data&nbsp;Collection</span>] on Zenodo (CDC). We are also using this collection to list all our published data in one place regardless of where it was originally published.&nbsp;If you have already published your data on another&nbsp;repository, please contact us and we can replicate your record here. We are doing this by default, if you are publishing with NCI.</span></span></span></span>
  
 
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;"><span style="caret-color:#000000"><span style="color:#000000">[https://help.zenodo.org/features/ <span style="color:blue">Zenodo</span>] is an initiative funded by CERN that allows anyone to share their research outputs and attach to them a DOI. Zenodo is funded for at least the next 20 years and so it offers a good long-term solution, as well as been widely used internationally.</span></span></span></span>
 
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;"><span style="caret-color:#000000"><span style="color:#000000">[https://help.zenodo.org/features/ <span style="color:blue">Zenodo</span>] is an initiative funded by CERN that allows anyone to share their research outputs and attach to them a DOI. Zenodo is funded for at least the next 20 years and so it offers a good long-term solution, as well as been widely used internationally.</span></span></span></span>
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== <span style="font-size:large;"><span style="font-family:Arial,Helvetica,sans-serif;">'''How to publish'''</span></span> ==
 
== <span style="font-size:large;"><span style="font-family:Arial,Helvetica,sans-serif;">'''How to publish'''</span></span> ==
  
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Publishing your code is&nbsp;easy and quick&nbsp;as long as your code&nbsp;is reasonably&nbsp;organised and has a detailed Readme file.</span></span>
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Publishing your data is&nbsp;easy and quick&nbsp;as long as your data is reasonably&nbsp;organised and has a detailed Readme file.</span></span>
  
 
#<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Create a Zenodo account, you can use your ORCID to login if you have one.</span></span>  
 
#<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Create a Zenodo account, you can use your ORCID to login if you have one.</span></span>  
#<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Create a Zenodo record for your code, uploading the relevant files. We prepared a</span>&nbsp;[[Media:Publish_your_code.pdf|step-by-step guide]]&nbsp;<span style="font-family:Arial,Helvetica,sans-serif;">on how to do this, which also cover the kind of information you should include.</span></span>  
+
#<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Create a Zenodo record for your dataset, uploading the relevant files. We prepared a</span>&nbsp;[[Media:Publish_your_data.pdf|step-by-step guide]]&nbsp;<span style="font-family:Arial,Helvetica,sans-serif;">on how to do this, which also cover the kind of information you should include.</span></span>  
#<span style="font-size:medium;"><span style="font-family: Arial, Helvetica, sans-serif;">Choose the CLEX Code Collection as community. We will get a notification of your request. Remember your code can be listed in more than one community.&nbsp;</span></span>  
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#<span style="font-size:medium;"><span style="font-family: Arial, Helvetica, sans-serif;">Choose the CLEX Data&nbsp;Collection as community. We will get a notification of your request. Remember your data&nbsp;can be listed in more than one community.&nbsp;</span></span>  
#<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">We will receive your request to join the CCC&nbsp;and check that you code is well described and in line with the [https://zenodo.org/communities/arc-coe-clex/about/ Collection policies]. If any changes are&nbsp;needed, we will contact you.</span></span>  
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#<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">We will receive your request to join the CDC&nbsp;and check that you data&nbsp;is well described and in line with the [https://zenodo.org/communities/arc-coe-clex/about/ Collection policies]. If any changes are&nbsp;needed, we will contact you.</span></span>  
  
 
=== <span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">'''Useful tips'''</span></span> ===
 
=== <span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">'''Useful tips'''</span></span> ===
  
*<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">A code can have several authors, they all should agree to the code publication and to list the record in the CLEX Code Collection. All authors should have made a significant contribution to the code, you can refer to the CCC [https://zenodo.org/communities/arc-coe-clex/about/#authorship_policy authorship policy] if in doubt.&nbsp;</span></span>  
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*<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">A dataset can have several authors, they all should agree to the dataset&nbsp;publication and to list the record in the CLEX Data&nbsp;Collection. All authors should have made a significant contribution to the data, you can refer to the CDC [https://zenodo.org/communities/arc-coe-clex-data/about/#authorship_policy authorship policy] if in doubt.&nbsp;</span></span>  
*<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">Having your code on a version control repository (and possibly GitHub) is highly recommended but it&nbsp;is not a requirement to publish on Zenodo, you&nbsp;can still publish your code without one.</span></span>  
+
*<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">Make sure your files are following any relevant standards,&nbsp;if they are netcdf files they should follow both [[Conventions|CF and ACDD conventions]]. We are happy to help you preparing them.</span></span>  
**<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">If you have your code in a GitHub repository you can give Zenodo access to your repository and every time you create a new release you Zenodo record will be updated automatically. <link></span></span>
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*Make sure the files have descriptive names and are [[Best_practices_for_directories_and_files|organised in files and directories]] in a way that facilitate their access and use.
**<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">Every time you change files you&nbsp;have to create a new version of the record and a new DOI&nbsp;will be minted. Any other field can be updated at any time without need for the record to be republished.</span></span> 
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*If your data has already been published elsewhere and the Zenodo record is a copy,&nbsp;we will upload here only the [[Dataset_readme_file_template|Readme file]] and add links to the original records for data download.  
*<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">If you do not want to create your own Zenodo account, we can create a record for you. In that case, let us know that you want to publish via the helpdesk.&nbsp;If your code is well documented, it might take as little as 20 minutes for us to add&nbsp;&nbsp;your repository to the Zenodo community. &nbsp;</span></span><span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">Please note that having your own Zenodo account will give you more control on your code. It is especially recommended if you are likely to release new versions in the future, as we might not be able to set up automatic&nbsp;updates as&nbsp;the owner of the record might be&nbsp;different from the GitHub repository owner.</span></span>  
+
*Remember you can only publish datasets which are less than 50GB
 +
*We will soon release a code to help you uploading the files programmatically, so they can be directly transferred from a server via the Zenodo API. In the meantime, if you want to use the API just send us an email and we will facilitate the process.&nbsp;  
 +
*<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">If you do not want to create your own Zenodo account, we can create a record for you. In that case, let us know that you want to publish via the helpdesk.&nbsp;If your data is well documented and organised, it might take as little as 20 minutes for us to add a record&nbsp;to the Zenodo community. &nbsp;</span></span><span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">Please note that having your own Zenodo account will give you more control on the record. It is especially recommended if you are likely to release new versions in the future.</span></span>  
  
 
=== <span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">'''Requirements'''</span></span> ===
 
=== <span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">'''Requirements'''</span></span> ===
  
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">We set up policies covering the use and contribution to the Collection. These are shown if full on the&nbsp;[https://zenodo.org/communities/arc-coe-clex/about Zenodo community page], but can also be downloaded here.</span></span>
+
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">We set up policies covering the use and contribution to the Collection. These are shown if full on the&nbsp;[https://zenodo.org/communities/arc-coe-clex-data/about Zenodo community page], but can also be downloaded here.</span></span>
  
 
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">They include:</span></span>
 
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">They include:</span></span>
  
*<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">The CCC scope: outlining the scope of the collection and the main requirements for a code to be accepted.</span></span>  
+
*<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">The CDC scope: outlining the scope of the collection and the main requirements for a code to be accepted.</span></span>  
 
*<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">The Authorship policy: this is based on the &nbsp;[[Australian_Code_for_the_Responsible_Conduct_of_Research|Australian Code for the Responsible Conduct of Research (2018]]) and covers who can be&nbsp;considered and author or a collaborator.&nbsp;</span></span>  
 
*<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">The Authorship policy: this is based on the &nbsp;[[Australian_Code_for_the_Responsible_Conduct_of_Research|Australian Code for the Responsible Conduct of Research (2018]]) and covers who can be&nbsp;considered and author or a collaborator.&nbsp;</span></span>  
*<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Contributors guidelines: more in depth guidelines on how to contribute code to the Collection.</span></span>  
+
*<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Contributors guidelines: more in depth guidelines on how to contribute data&nbsp;to the Collection.</span></span>  
 
*<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Retention and Retraction policy: defining the few cases in which we might retract a record and the procedure we will follow.</span></span>  
 
*<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Retention and Retraction policy: defining the few cases in which we might retract a record and the procedure we will follow.</span></span>  
  
 
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Because we are using the Zenodo platform also any [https://about.zenodo.org/policies/ policy set by Zenodo] has to be honoured.</span></span>
 
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Because we are using the Zenodo platform also any [https://about.zenodo.org/policies/ policy set by Zenodo] has to be honoured.</span></span>
  
<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;"><span style="caret-color:#000000"><span style="color:#000000">We are not checking the quality of your code, as long as the Collection policies are satisfied and your code is in line with the Collection scope, it will be accepted. The only requirement currently is for your description of the code to be reasonably comprehensive. However, if you would like some advice and feedback on a code, we are happy to help you. As usual you can contact us via the CWS helpdesk.</span></span></span></span>
+
<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;"><span style="caret-color:#000000"><span style="color:#000000">We are not checking the quality of your data, as long as the Collection policies are satisfied and your data is in line with the Collection scope, it will be accepted. The only requirement currently is for your description of the data&nbsp;to be reasonably comprehensive, and for the files to be [[FAIR_-_Accessible|accessible]]. However, if you would like some advice and feedback on your data, we are happy to help you. As usual you can contact us via the CWS helpdesk: cws_help<at>nci.org.au.</span></span></span></span>
  
 
&nbsp;
 
&nbsp;
  
 
[[Category:Data induction]]
 
[[Category:Data induction]]

Revision as of 23:07, 13 July 2021

CLEX Data Collection

Zenodo Data collection.png

You can now publish the code you use for your research with the new CLEX Data Collection on Zenodo (CDC). We are also using this collection to list all our published data in one place regardless of where it was originally published. If you have already published your data on another repository, please contact us and we can replicate your record here. We are doing this by default, if you are publishing with NCI.

Zenodo is an initiative funded by CERN that allows anyone to share their research outputs and attach to them a DOI. Zenodo is funded for at least the next 20 years and so it offers a good long-term solution, as well as been widely used internationally.

We will curate the Collection for the duration of CLEX, but the records will be still available and visible well past CLEX termination.

How to publish

Publishing your data is easy and quick as long as your data is reasonably organised and has a detailed Readme file.

  1. Create a Zenodo account, you can use your ORCID to login if you have one.
  2. Create a Zenodo record for your dataset, uploading the relevant files. We prepared a step-by-step guide on how to do this, which also cover the kind of information you should include.
  3. Choose the CLEX Data Collection as community. We will get a notification of your request. Remember your data can be listed in more than one community. 
  4. We will receive your request to join the CDC and check that you data is well described and in line with the Collection policies. If any changes are needed, we will contact you.

Useful tips

  • A dataset can have several authors, they all should agree to the dataset publication and to list the record in the CLEX Data Collection. All authors should have made a significant contribution to the data, you can refer to the CDC authorship policy if in doubt. 
  • Make sure your files are following any relevant standards, if they are netcdf files they should follow both CF and ACDD conventions. We are happy to help you preparing them.
  • Make sure the files have descriptive names and are organised in files and directories in a way that facilitate their access and use.
  • If your data has already been published elsewhere and the Zenodo record is a copy, we will upload here only the Readme file and add links to the original records for data download.
  • Remember you can only publish datasets which are less than 50GB
  • We will soon release a code to help you uploading the files programmatically, so they can be directly transferred from a server via the Zenodo API. In the meantime, if you want to use the API just send us an email and we will facilitate the process. 
  • If you do not want to create your own Zenodo account, we can create a record for you. In that case, let us know that you want to publish via the helpdesk. If your data is well documented and organised, it might take as little as 20 minutes for us to add a record to the Zenodo community.  Please note that having your own Zenodo account will give you more control on the record. It is especially recommended if you are likely to release new versions in the future.

Requirements

We set up policies covering the use and contribution to the Collection. These are shown if full on the Zenodo community page, but can also be downloaded here.

They include:

  • The CDC scope: outlining the scope of the collection and the main requirements for a code to be accepted.
  • The Authorship policy: this is based on the  Australian Code for the Responsible Conduct of Research (2018) and covers who can be considered and author or a collaborator. 
  • Contributors guidelines: more in depth guidelines on how to contribute data to the Collection.
  • Retention and Retraction policy: defining the few cases in which we might retract a record and the procedure we will follow.

Because we are using the Zenodo platform also any policy set by Zenodo has to be honoured.

We are not checking the quality of your data, as long as the Collection policies are satisfied and your data is in line with the Collection scope, it will be accepted. The only requirement currently is for your description of the data to be reasonably comprehensive, and for the files to be accessible. However, if you would like some advice and feedback on your data, we are happy to help you. As usual you can contact us via the CWS helpdesk: cws_help<at>nci.org.au.