Difference between revisions of "Publishing options"

 
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Recently journal editors have updated their data policy and now require that data relating to the submitted paper should be made available by the authors. From the [http://publications.agu.org/author-resource-center/publication-policies/data-policy/ AGU data policy] : "..all data necessary to understand, evaluate, replicate, and build upon the reported research must be made available and accessible whenever possible ..."
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">The main reasons to publish data is to share it with others and/or following a requirement from a publisher, funder or your own institution. The specific requirements are covered in the [[Institution_data_requirements|institutional policies]] and&nbsp;</span></span><span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">[[Publisher_policies|journal&nbsp;policies]]&nbsp;pages. While these requirements might differ in some details they are all based on the [[FAIR|FAIR principles]], we can help you making a decision on how to publish your data or code in a way that satisfy these principles. This will depend&nbsp;on the kind of data and the reasons you want to publish.</span></span>
  
The aim of this change in the policy is to satisfy the principle that someone reading the paper should be able to reproduce your experiment. Again form the AGU policy&nbsp;: " For the purposes of this policy, data include, but are not limited to, the following:
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">If you are unsure about exactly which data you should be publishing, the [[CLEX_Data_policy|CLEX data policy]] and our [[Which_data_should_I_publish|guidelines]] should help you decide.</span></span>
  
*<span style="font-family: Arial,Helvetica,sans-serif;">Data used to generate, or be displayed in, figures, graphs, plots, videos, animations, or tables in a paper.</span>
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Whichever way you chose remember to report your record to CLEVER (see below).</span></span>
*<span style="font-family: Arial,Helvetica,sans-serif;">New protocols or methods used to generate the data in a paper.</span>
 
*<span style="font-family: Arial,Helvetica,sans-serif;">New code/computer software used to generate results or analyses reported in the paper.</span>  
 
*<span style="font-family: Arial,Helvetica,sans-serif;">Derived data products reported or described in a paper. "</span>  
 
  
There can be practical and even copyright limitations to do this, but these can be taken into account and it should not be an impediment to publication if properly documented. The JGR-Space Physics editor-in-chief has listed some of these challenges and clarified the scope of the policy on his [https://liemohnjgrspace.wordpress.com/2014/06/19/models-and-the-data-policy/ blog]. It is an old blog but&nbsp;includes references to model data which apply to lots of the CLEX&nbsp;data as well.
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=== <span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">'''Where should I publish my data?'''</span></span> ===
  
The [[Publisher_policies|publishing policies]] page offer a&nbsp;list of data policies and&nbsp;requirements by publisher.
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<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">There are at least three&nbsp;options and there is not a straight answer, it depends on what you are publishing and why.</span></span>
  
&nbsp;
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<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;"><u>CLEX&nbsp;Data Collection on NCI</u></span></span>
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">&nbsp; This is the best option if you have data in NetCDF format and this data could be useful for other researchers. We will help you document&nbsp;your data and make it user friendly;&nbsp;it will be part of a climate data collection and so it will be easier to discover. NCI also has more storage capacity than&nbsp;other repositories and services which are designed around the NetCDF&nbsp;format.</span></span>
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;"><u>Institutional repository</u></span></span>
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<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">&nbsp; This is adequate if you have a small dataset and it is really specific to your study or only a subset/post processing of another dataset. While institutions offer some data curation, they usually will&nbsp;not check that the&nbsp;data&nbsp;is well described, consistent and user friendly, so you might get a DOI for your record&nbsp;but no added value. If your dataset is bigger than 50-100 GB, you might not be able to publish it with one of these repositories.</span></span>
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;"><u>Zenodo, Figshare, Mendeley</u></span></span>
  
=== <span style="color:#3498db;">'''Where should I publish my data?'''</span> ===
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&nbsp;&nbsp;<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">These services are free, and you can create your own account,&nbsp;a record for your data and get a DOI fairly easily and quickly. You can also publish here different kind of materials. This can be useful if you want to publish some very specific data, for example code and data to produce a specific figure required to publish&nbsp;a paper.&nbsp;</span></span>
  
You usually have at least three&nbsp;options and there's not a straight answer it depends on what you're publishing and why.
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">However, there are no&nbsp;standards required or anyone checking on your metadata. This means that it is up to you to make sure your data</span></span><span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">&nbsp;is as&nbsp;[[Data_terminology|FAIR]]&nbsp;as possible. This means [[FAIR_-_Findable|'''Findable''']], which is harder when your record is not part of a discipline repository or collection or you haven't used keywords in an effective manner. And [[FAIR_-_Accessible|'''Accessible''']], [[FAIR_-_Interoperable|'''Interoperable''']] and '''[[FAIR_-_Reusable|Reusable]],'''&nbsp;which means the data should have enough metadata, use discipline standards and&nbsp;be&nbsp;properly described.</span></span>
  
<u>CLEX&nbsp;Data Collection on NCI</u>: this is the best place if you have actually produced the data yourself. We'll help you document&nbsp;your data and make it user friendly, it will be part of a climate data collection and so it will be easier to discover. NCI also has more storage capacity than&nbsp;other repositories and services which are designed around the netcdf format.
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Finally, as for institutional repositories, the&nbsp;data size is limited to 50 GB and you will&nbsp;not get any additional data services apart from HTTP&nbsp;download. If you decide to go this way,&nbsp;please make sure you document your data properly,&nbsp;we are happy to provide support and review your record. If you use&nbsp;Zenodo, you can easily add your record to our Data Collection (see below)</span></span>
  
<u>Institutional repository</u>: this can be adeguate if you have a small dataset and it is really specific to your study or only a subset/post processing of another dataset. While institutions offer some data curation they usually won't check the data&nbsp;is well described, consistent and user friendly, so you will get a DOI for your record&nbsp;but no added value.
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<span style="font-size:medium;"><u><span style="font-family:Arial,Helvetica,sans-serif;"><span style="caret-color:#000000"><span style="color:#000000">CLEX Data Collection</span></span></span></u></span>
  
<u>Zenodo, Figshare, Mendeley:&nbsp;</u>these services are free and you can create your own account, create a record for your data and get a DOI fairly easily and quickly. You can also publish here different kind of materials. This can be useful if you want to publish some very specific data, for example code and data to produce a specific figure required to publish&nbsp;a paper.&nbsp;If you are publishing data that can be actually useful to others, then you want to make sure is FAIR (see above for a full description).&nbsp;Findable, which is harder when your record is not part of a discipline repository or collection or you haven't used keywords in an effective manner. Accessible, Interoperable and Reusable which means the data should have enough metadata, use standards, be&nbsp;properly described. Finally the&nbsp;data size is limited to 50 GB and you won't get any additional data services apart from HTTP&nbsp;download.&nbsp;This should be your last resort, still if you go this way please make sure you document your data properly. we are happy to provide support and review your record. We are also looking into creating &nbsp;CLEX community in Zenodo to be able to collect in one place these data records.
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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">&nbsp;We have started a [https://zenodo.org/communities/arc-coe-clex-data/?page=1&size=20 CLEX Data Collection in Zenodo] to collect in one place all our data records, regardless of how they have been published. Having one place where all our data is listed means that it is easier for anyone to discover CLEX data outputs, both for external potential users and for our own researchers and students.&nbsp;</span></span>If you have already published&nbsp;<span style="caret-color:#000000"><span style="color:#000000">your data with your own institution and/or with one of the freely available services, like Zenodo itself, let us know and we will list your record in our collection. We will use your original metadata record, data&nbsp;access url and existing&nbsp;DOI (if available) as official source.</span></span></span></span>
  
If you're confused feel free to ask us we are always happy to provide advice and support.
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">If you are confused feel free to ask us, we are always happy to provide advice and support.</span></span>
  
=== <span style="color:#3498db;">'''Where should I publish my code?'''</span> ===
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<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">'''Where should I publish my code?'''</span></span>
  
More and more frequently you are reuqired to publish also your code by journal editors. This is important to make your research reproducible, in particular for the paper reviewers. It&nbsp;can&nbsp;also be an opportunity to share a successful code with other researchers. If your code is properly published and someone else uses it, then it is easier for them to cite you as the author. Like data, code represents part of your work and funders are starting looking at all research products not only papers when reviewing applications. Putting your code on GitHub or another version control service helps to keep track of the code, expose it to others and manage pontetial issue sans enhancements. But GitHub is not ideal if you want to pinpoint the code you used for a paper or to create some data. Zenodo is a platform that integrates well with GitHub to allow you&nbsp;[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwiL1tLP8snvAhVL7XMBHUolAmIQFjAAegQIAhAD&url=https://guides.github.com/activities/citable-code/&usg=AOvVaw1VVBoyAZecm_pcXGudJRHP to publish automatically every release]. Zenodo will keep a snapshot in time of your code and assign a DOI to it. if you're not using GitHub you can simply upload your files directly in Zenodo. These are the reasons we started a Zenodo community for a&nbsp;[https://zenodo.org/communities/arc-coe-clex/?page=1&size=20 CLEX Code Collection (CCC)]in 2020. We published there some of our code and&nbsp;code used to produce papers as&nbsp;required by journal editors. We are now looking into broadening this and actively seek contributions of code, notebooks etc that might be useful to others. Zenodo has given our codes much more visibility than GitHub and some of the code has receveid lots of views and downloads.&nbsp;
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Like data, code represents part of your work and funders are starting to&nbsp;look&nbsp;at all research products not only papers when reviewing grant applications, also some journals require you to publish your code alongside the data. Putting your code on GitHub or another version control service helps to keep track of the code, expose it to others and manage potential issues and&nbsp;enhancements. However,&nbsp;GitHub is not ideal if you want to pinpoint the code you used for a paper or to create some data.</span></span>
  
=== <span style="color:#3498db;">'''How to publish'''</span> ===
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">We started a Zenodo community for a&nbsp;[https://zenodo.org/communities/arc-coe-clex/?page=1&size=20 CLEX Code Collection (CCC)]&nbsp;in 2020. Zenodo is a platform that will mint a DOI for your code and integrates well with GitHub. Initially we published some of our own codes and&nbsp;code used to produce papers as&nbsp;required by journal editors. We are now looking into broadening this and actively seek contributions of code, notebooks etc that might be useful to others. Zenodo has given our codes much more visibility than GitHub and some of the codes have&nbsp;lots of views and downloads.</span></span>
  
*[[Publishing_with_NCI|Publishing with NCI]]
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'''<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Publishing options diagram</span></span>'''
*Publishing with your instituion
 
*Publishing code in Zenodo CLEX Code Collection
 
*Publishing data in Zenodo CLEX Data Collection (.. to come)
 
  
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[[File:Where to publish.jpeg|800px|Publishing options]]
  
 
&nbsp;
 
&nbsp;
  
  
=== <span style="color:#3498db;">'''Reporting to CLEVER'''</span> ===
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=== <span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">'''How to publish'''</span></span> ===
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">We are not providing here specific advice if you are publishing with an institutional repository or other non-specific repositories. However, the steps involved in both preparing the files and filling in the metadata form will be very similar to what we cover in "Publishing data in Zenodo". So, you can refer to that wiki page and the step by step guide linked into it for useful advice.</span></span>
  
Whichever way you decide to publish your data, as part of the NCI collection or with a repository provided by your institution, remember to add your published record to [https://climateextremes.org.au/clever-dashboard/ CLEVER]&nbsp;the CLEX reporting hub, in the "Publications and Datasets" section.
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*<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">[[Publishing_with_NCI|Publishing with NCI]]</span></span>
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*[[Institution_data_requirements|<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">Publishing with your institution</span></span>]]
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*<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">[[Publishing_software|Publishing code in Zenodo CLEX Code Collection]]</span></span>
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*[[Publishing_data_in_Zenodo|<span style="font-family:Arial,Helvetica,sans-serif;"><span style="font-size:medium;">Publishing data in Zenodo CLEX Data Collection</span></span>]]
  
You will need to record there only the main information: author, title, doi and citation.&nbsp;It will only take a couple of minutes.&nbsp;Published datasets are part of the Centre&nbsp;KPIs and something we have to report to our funders.
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<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">'''Reporting to CLEVER'''</span></span>
 +
 
 +
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">Whichever way you decide to publish your data, as part of the NCI collection or with a repository provided by your institution, remember to add your published record to [https://climateextremes.org.au/clever-dashboard/ CLEVER]&nbsp;the CLEX reporting hub, in the "Publications and Datasets" section.</span></span>
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 +
<span style="font-size:medium;"><span style="font-family:Arial,Helvetica,sans-serif;">You will need to record only the main information: author, title, DOI&nbsp;and citation.&nbsp;It will only take a couple of minutes.&nbsp;Published datasets are part of the Centre&nbsp;KPIs and something we have to report to our funders.</span></span>
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&nbsp;
  
[[Category:Data]]
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[[Category:Data induction]]

Latest revision as of 00:39, 14 July 2021

The main reasons to publish data is to share it with others and/or following a requirement from a publisher, funder or your own institution. The specific requirements are covered in the institutional policies and journal policies pages. While these requirements might differ in some details they are all based on the FAIR principles, we can help you making a decision on how to publish your data or code in a way that satisfy these principles. This will depend on the kind of data and the reasons you want to publish.

If you are unsure about exactly which data you should be publishing, the CLEX data policy and our guidelines should help you decide.

Whichever way you chose remember to report your record to CLEVER (see below).

Where should I publish my data?

There are at least three options and there is not a straight answer, it depends on what you are publishing and why.

CLEX Data Collection on NCI

  This is the best option if you have data in NetCDF format and this data could be useful for other researchers. We will help you document your data and make it user friendly; it will be part of a climate data collection and so it will be easier to discover. NCI also has more storage capacity than other repositories and services which are designed around the NetCDF format.

Institutional repository

  This is adequate if you have a small dataset and it is really specific to your study or only a subset/post processing of another dataset. While institutions offer some data curation, they usually will not check that the data is well described, consistent and user friendly, so you might get a DOI for your record but no added value. If your dataset is bigger than 50-100 GB, you might not be able to publish it with one of these repositories.

Zenodo, Figshare, Mendeley

  These services are free, and you can create your own account, a record for your data and get a DOI fairly easily and quickly. You can also publish here different kind of materials. This can be useful if you want to publish some very specific data, for example code and data to produce a specific figure required to publish a paper. 

However, there are no standards required or anyone checking on your metadata. This means that it is up to you to make sure your data is as FAIR as possible. This means Findable, which is harder when your record is not part of a discipline repository or collection or you haven't used keywords in an effective manner. And Accessible, Interoperable and Reusable, which means the data should have enough metadata, use discipline standards and be properly described.

Finally, as for institutional repositories, the data size is limited to 50 GB and you will not get any additional data services apart from HTTP download. If you decide to go this way, please make sure you document your data properly, we are happy to provide support and review your record. If you use Zenodo, you can easily add your record to our Data Collection (see below)

CLEX Data Collection

 We have started a CLEX Data Collection in Zenodo to collect in one place all our data records, regardless of how they have been published. Having one place where all our data is listed means that it is easier for anyone to discover CLEX data outputs, both for external potential users and for our own researchers and students. If you have already published your data with your own institution and/or with one of the freely available services, like Zenodo itself, let us know and we will list your record in our collection. We will use your original metadata record, data access url and existing DOI (if available) as official source.

If you are confused feel free to ask us, we are always happy to provide advice and support.

Where should I publish my code?

Like data, code represents part of your work and funders are starting to look at all research products not only papers when reviewing grant applications, also some journals require you to publish your code alongside the data. Putting your code on GitHub or another version control service helps to keep track of the code, expose it to others and manage potential issues and enhancements. However, GitHub is not ideal if you want to pinpoint the code you used for a paper or to create some data.

We started a Zenodo community for a CLEX Code Collection (CCC) in 2020. Zenodo is a platform that will mint a DOI for your code and integrates well with GitHub. Initially we published some of our own codes and code used to produce papers as required by journal editors. We are now looking into broadening this and actively seek contributions of code, notebooks etc that might be useful to others. Zenodo has given our codes much more visibility than GitHub and some of the codes have lots of views and downloads.

Publishing options diagram

Publishing options

 


How to publish

We are not providing here specific advice if you are publishing with an institutional repository or other non-specific repositories. However, the steps involved in both preparing the files and filling in the metadata form will be very similar to what we cover in "Publishing data in Zenodo". So, you can refer to that wiki page and the step by step guide linked into it for useful advice.

Reporting to CLEVER

Whichever way you decide to publish your data, as part of the NCI collection or with a repository provided by your institution, remember to add your published record to CLEVER the CLEX reporting hub, in the "Publications and Datasets" section.

You will need to record only the main information: author, title, DOI and citation. It will only take a couple of minutes. Published datasets are part of the Centre KPIs and something we have to report to our funders.