Data Accessibility FAQ

Physics of Plasmas Data Accessibility Project: Frequently Asked Questions

AIP Publishing and Physics of Plasmas have launched a pilot project to link data objects underlying tables and figures in the published literature. This project supports efforts to increase access to valuable scientific data through effective citation of author-created datasets in permanent repositories. Authors who participate in this project reference one or more persistent Digital Object Identifiers (DOIs) created with AIP Publishing partner Zenodo.

Please contact us at pop-data [at] aip.org if you have comments or questions about the submission of manuscripts with links to data objects or any aspect about the Physics of Plasmas Data Accessibility Project.

About the Physics of Plasmas Data Accessibility Project

What do you mean by “datasets underlying tables and figures”

This refers to the datasets that you use to create the figures and tables in your Physics of Plasmas manuscript. Author-created data and datasets are grouped by Zenodo into an Upload. For the purposes of this project, an Upload contains one or more files comprising at least one data file that was used to create a figure or table in your manuscript. A single Upload may contain multiple files used to create multiple figures or tables, and the description of the Upload should identify these files and the corresponding figures explicitly.

Why should I make this information available?

Government and public funding agencies are encouraging scientists to make data accessible to the public and the scientific community and to promote the preservation, reuse, and improved dissemination of scientific data as intellectual units, valuable research outputs, and primary citable objects The Physics of Plasmas Data Project aims to contribute to the ongoing cultural shift toward making author-created datasets accessible and identifiable in published literature. AIP Publishing and Physics of Plasmas believe that an important step toward this goal is to make the data underlying figures and tables available through links in the published literature for verification and continued investigation, with particular attention paid to the datasets that support the argument and the main conclusions in the paper.

How can I cite datasets in my manuscript?

Authors will need to add citations to datasets in author-selected figure and table captions and in the manuscript’s references.

Although there are no global standards for how to cite data products, we follow DataCite’s recommendations. The preferred format for dataset citations in your reference list is:

XCreator(s) (Publication Year). “Title,” Publisher. Identifier

Please note:

a) Creator(s): The Author names that you have listed in the Zenodo upload
b) Publication year: The year when the data was made publicly available
c) Title: This should match the Zenodo upload.
d) Publisher: The name of the entity that holds and archives the dataset, in this case, Zenodo
e) Identifier: DOIs should be displayed as linkable, permanent URLs, including the http://dx.doi.org prefix.

Examples:
5D. Baker (2016). “Electron Spin Resonance of amorphous SiGe samples,” Zenodo. http://zenodo.org/record/45520
6Evans, Llion, et al. (2015). "Raw X-Ray CT data of CFC-Cu_GS laser flash coupon," Zenodo. http://dx.doi.org/10.5281/zenodo.18414

Information about Version and ResourceType can also be included in the reference, but is not required: Creator(s) (Publication Year). “Title,” Version, Publisher, ResourceType. Identifier

Examples:
5D. Baker (2016). “Electron Spin Resonance of amorphous SiGe samples,” Zenodo, V. 2.1, Dataset. http://dx.doi.org/10.5281/zenodo.45520
6Evans, Llion, et al. (2015). "Raw X-Ray CT data of CFC-Cu_GS laser flash coupon," Zenodo. http://dx.doi.org/10.5281/zenodo.18414

For each figure or table you wish to link to your dataset, include the following reference in your figure or table caption:

FIG. 4. This is a usual figure caption in your manuscript. [Associated dataset available at http://dx.doi.org/10.5281/zenodo.45520]5

Note the standard superscript reference to the dataset citation in your reference list.

What is a DOI?

A DOI, or Digital Object Identifier, is a unique alphanumeric string of code assigned by the publisher to a piece of digital content, such as an article, dataset, software, image, etc. The DOI, which is managed and maintained at a centralized registration agency database, becomes a persistent identifier and links to the associated content regardless of any change in its location on the Internet.

Are the datasets peer reviewed?

For manuscripts that provide linked datasets, Physics of Plasmas reviewers will be given the option to look at the datasets and address two additional questions when preparing their reviews. The answers to these two questions will be provided to the authors, but decisions on the acceptance or rejection of manuscripts will not be based on either the inclusion of linked dataset(s) or the content within the dataset(s).
For more information, please check the Review Process section in this FAQ.

What if I don’t want to cite datasets in my manuscript?

Although we encourage the Physics of Plasmas community to embrace the scope and goals of this project, participation is not mandatory for authors. Editorial decisions on the acceptance or rejection of manuscripts will not be based on either the inclusion of linked dataset(s) or the content within the dataset(s).

Can I use supplemental material for the datasets underlying tables and figures in my manuscript?

No. Submission of supplemental materials differs from the citation of datasets in the following ways. Supplemental materials are files intended either to aid the reviewer or for publication alongside the manuscript. Supplemental materials are usually too lengthy or of too limited interest for inclusion in the articles. AIP Publishing makes supplemental files available online and linked to the published article. Authors are still welcome to submit supplemental materials, and authors should follow the existing instructions for supplemental materials. In contrast, author-created citable datasets are created and stored within a sustainable and long- lived data repository. Each dataset has a unique digital object identifier (DOI), and these datasets are meant to promote the preservation, reuse, and improved understanding of your data as published, in contrast to supplementing your published data. The Physics of Plasmas Data Project aims to contribute to the ongoing cultural shift toward making author-created datasets accessible and identifiable in published literature. AIP Publishing and Physics of Plasmas make the datasets easily accessible to readers through direct links to the dataset landing pages on the repository from the figure and table captions and appropriate citations in the reference list.

What about data accessibility mandates by my funding agency?

The Physics of Plasmas Data Project is complementary to, but not a substitute for, data accessibility mandates by many funding agencies. By linking to the datasets underlying the tables and figures from the body of the published article and the reference list, the project supports the requirement that underlying digital research data be made accessible, reusable, and citable for and by the scientific community. There may be additional requirements from your funding agency that our project does not address.

 

Submitting Datasets and Linking Them to My Manuscript

How do I link datasets to my Physics of Plasmas manuscript?

Preparing and submitting a manuscript with linked datasets underlying figures and tables is straightforward. Here are the detailed steps to follow:
Step 1: Register with Zenodo and familiarize yourself with the policies and operation of the site. Refer to Zeondo’s FAQ for more information.
Step 2: Upload the datasets into Zenodo.

  • We recommend that you share datasets underlying the tables and figures that support the main conclusions in your paper. Please group related datasets into a single upload in Zenodo whenever possible (e.g., they all share the same group of authors).
  • When configuring your datasets, authors should use open-source file formats wherever possible.
  • Make sure to provide sufficient information in Zenodo’s metadata fields to make the datasets useful to others. Authors should enter clearly written information into the required dataset “Description” field. This description should explain the contents, format, and structure of the files within your dataset and also identify specific files used to create individual figures and tables in your manuscript.
  • Once your dataset has been completely uploaded, you are ready to save and publish your dataset. Select “Open Access” in Zenodo’s Access tab. Most authors will select “Creative Commons CCZero” as the open-access license. Finally, click on the “Submit” button to permanently publish your dataset.
    • IMPORTANT: Once your dataset has been submitted, you will only be able to edit the metadata fields. The datasets can no longer be edited or changed once you have clicked the “submit” button.

Step 3: Take note of the DOI provided for each upload.
Step 4: List each upload as a separate citation in the reference list of your manuscript.
Step 5: Prepare citations to the dataset(s) in the figure and table captions of your manuscript as in the example above. (Note that the http://dx.doi.org prefix and the usual numerical reference to the citation in your reference list should be included.)
[Associated dataset available at http://dx.doi.org/10.5281/zenodo.45520]5
Step 6: Log into the Physics of Plasmas Manuscript Submission System (PXP).
Step 7: Under the “Dataset Deposition” tab, specify the table and/or figure numbers associated with the datasets and include the related DOIs.
Step 8: Complete your manuscript submission.

What if one (or more) of my datasets has already been published in a data journal?

If datasets underlying figures or tables in your Physics of Plasmas manuscript have already been described in an article published in a data journal, you must cite that article within the body of your Physics of Plasmas manuscript and include the reference as you would with any citable resource.

I need to place an embargo on my dataset to restrict access until after the article has published. Is this possible?

Unfortunately, this feature is not available at this time. If authors participate in this Data Accessibility Project, datasets linked to figures and tables in Physics of Plasmas must be made open-access on Zenodo. This allows reviewers to review the dataset without restriction. The AIP Publishing team plans to investigate mechanisms that will allow authors to link embargoed datasets as this pilot project evolves.

What if I want to submit more than the datasets underlying the figures and tables (e.g., raw data)?

The scope of this project is currently limited to datasets underlying figures and tables in Physics of Plasmas manuscripts. Raw (or primary) data, considered as a direct output of a measurement, can be included as part of your Zenodo upload, but the upload must include and identify the data files used to create your figures and tables in the manuscript.

I want to provide background information about the dataset. How can I do it?

This is the right attitude! In order for the underlying datasets to be intelligible, citable, and reusable, they need to be provided with the appropriate background information. As you upload your files into Zenodo, you are requested to fill in metadata fields, i.e., information about your uploads, such as creators, title, creation date, technical details, and so on.
It is said that datasets are only as good as their metadata; therefore, we recommend that you also include information on the method, how the data was analyzed and treated, and any other information that may be relevant to understanding, citing, and eventually reproducing your results. You should provide this information in the “Description” box when you create your dataset. Please carefully and completely describe your data and how it relates to the figures and tables in the manuscript in the “Description” box of the dataset.
Other Metadata fields in Zenodo are divided into:
Required: Information that must be provided
Recommended: Information that is optional, but strongly recommended
Optional: Information that is not required but provides an enhanced description

We strongly encourage you to use all the applicable fields to provide the most complete information about your upload(s).

I have non-proprietary software that can be shared to open, view, or use the dataset(s). How can I make it available?

You can add information about the software to Zenodo’s metadata fields related to your dataset uploads. In addition, you can upload the non-proprietary software in Zenodo, obtain a DOI for it, and insert it as a supplement to your upload by using the “Related/Alternate Identifier” field.

Can I link datasets after my manuscript has been accepted?

No. Linking underlying datasets to figures and tables in a Physics of Plasmas manuscript is part of the initial submission process.

Is there a cost to the authors for participating in this project?

There is no cost for the authors to take part in the Physics of Plasmas Data Project. Furthermore, Zenodo is free within certain upper limits: It currently accepts files up to 2GB. Note that you can have several 2GB files per upload. Check here for more information on Zenodo’s policies and file size limits.

 

Review Process

I am a Physics of Plasmas reviewer. What will I be expected to do if I receive a manuscript with underlying linked datasets?

Reviewers are asked to answer two optional questions to assist in the evaluation of this pilot project and to help AIP Publishing and Physics of Plasmas develop a valued means to link published manuscripts to sustainable and long-lived data repositories. The answers to these two questions will be provided to the authors, but decisions on the acceptance or rejection of manuscripts will not be based on either the inclusion of linked dataset(s) or the content within the dataset(s).

I have submitted a manuscript with linked datasets underlying figures and tables. What happens to my datasets during revision?

If the reviewer comments make clear that additional information is needed in the metadata associated with the dataset in Zenodo, you can update the metadata fields without uploading a new dataset or obtaining a new DOI. You can then proceed with the submission of your revised manuscript. If the reviewer comments make clear that changes to the dataset are required, you will need to upload a new dataset in Zenodo and obtain a new DOI. When revising your manuscript, be sure to update the DOI links in the figures, tables, and references. You can then proceed with the submission of your revised manuscript.

 

Data Repositories

What data repository can I use?

We have partnered with the Zenodo data repository for the Physics of Plasmas Data Project. Created through the European Commission’s OpenAIREplus project in 2013 and hosted at CERN near Geneva, Switzerland, Zenodo is a digital repository open to all research outputs from all fields of science, regardless of funding source, and specifically addressing everybody and everything not served by a dedicated service: the so called “long tail” of research results. Authors who must use different data repositories in order to satisfy institutional, funding agency, or other requirements may still cite data; however, these manuscripts may not benefit from future enhancements of data accessibility resulting from AIP Publishing’s partnership with Zenodo.

Why did Physics of Plasmas choose to partner with Zenodo?

For the launch of the data accessibility project, we focused on generic repositories in order to offer a useful option to all Physics of Plasmas authors. We opted for Zenodo because it:

  • Addresses the “long tail” of science; this means that the repository is open to all research outputs from all fields of science, regardless of funding source and affiliation.
  • Is committed to long-term preservation of the research outputs it hosts.
  • Uses CERN’s technical infrastructure in building and operating large-scale digital repositories.
  • Is not-for-profit.

Click here for more information on Zenodo.

My institution/laboratory/funding agency uses a different data repository. Can I use that repository instead of Zenodo?

We are launching the Physics of Plasmas Data Project through our partnership with Zenodo in order to maintain consistency of integration with our submission system. If you already have your datasets uploaded in a data repository more closely related to your specific field or your institution, you are welcome to include the appropriate citation in the manuscript’s reference list. Please refer here for the citation format that we recommend.