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Open Research Policy

OVERVIEW

ESA has adopted a society-wide Open Research Policy for its publications to further support scientific exploration and preservation, allow a full assessment of published research, and streamline policies across our family of journals. An open research policy provides full transparency for scientific data and code, facilitates replication and synthesis, and aligns ESA journals with current standards. As of 1-February-2021, all new manuscript submissions to ESA journals must abide by the following policy.

As a condition for publication in ESA journals, all underlying data and statistical code pertinent to the results presented in the publication must be made available in a permanent, publicly accessible data archive or repository, with rare exceptions (see “Details” for more information). Archived data and statistical code should be sufficiently complete to allow replication of tables, graphs, and statistical analyses reported in the original publication, and perform new or meta-analyses. As such, the desire of authors to control additional research with these data and/or code shall not be grounds for withholding material.

Thus, for the purpose of this policy, the following underlying material is required:

  • Raw data and metadata used to generate tables, figures, plots, videos/animations
  • Novel code or computer software utilized to generate results or analyses
  • All methods or protocols utilized to generate the data, both existing (including references) and new methods/protocols
  • Derived data products

Please see the “Details” tab for definitions of each item above.

 

For submissions made prior to 1-February-2021, and revisions and/or accepted versions of those submissions:

  • Data archiving remains optional for Ecosphere, Frontiers in Ecology and the Environment, and the ESA Bulletin.
  • For Ecology, data and code archiving remains optional with the exception of Data Papers (data required) and Statistical Reports (code required).
  • For Ecological Applications and Ecological Monographs, data archiving remains required per the previous policies for these journals (Ecological Applications policy for submissions prior to 1-Feb-2021; Ecological Monographs policy for submissions prior to 1-Feb-2021).

DETAILS

Ecology Data Paper and Statistical Report Submissions

At the submission stage for all Data Papers and Statistical Reports in Ecology, authors must supply data and code as Supporting Information to their paper on the journal platform. A second copy of the material on a public repository is required after publication.

All other ESA Journals Submissions

At the submission stage for all other manuscript types and journals, data should not be supplied as Supporting Information. Authors are not required to provide data at this stage, but it is strongly encouraged that authors deposit data prior to manuscript submission to allow subject matter editors and reviewers access. Many repositories now offer a private-for-peer-review option. Novel code must be supplied with manuscript submissions for evaluation.

After Acceptance

Following manuscript acceptance, complete data and novel code must be registered in a repository to be made available at the time of publication. ESA Publications staff will verify data and code archiving is complete before releasing files to the publisher. By depositing data and code prior to publication of a manuscript, a permanent link and formal citation can be included in the published paper.

Exceptions

Exceptions to this policy are granted only in rare cases as follows and must be fully disclosed by the author at the time of submission.

  • Sensitive and confidential information should be redacted as required, including but not limited to precise locations of sampling on private lands, indigenous territory, or sacred sites; locality data for rare, threatened, or endangered species; identity of human subjects.
  • In cases where authors are not the legal data owner and cannot release the data (for example, commercial sources for fish landings), the author should provide sufficient query information so another researcher could seek to obtain the same data, and such limitations must be disclosed at the time of manuscript submission.
  • All data on human subjects need to be anonymized to protect the identification of study participants; data from human subjects must be accompanied by an approval statement of the research project by the author(s) institutional ethics review committee.

Definitions

Raw data and metadata: Raw data are not summarized data in the form of tables of means and standard deviations. Raw data are those used to perform statistical analyses and enable reuse for new or meta-analyses. Data should be provided in non-proprietary, machine-readable formats (e.g., “.csv”). Archived data sets must be accompanied by clear and precise metadata that allow others to readily use files, describing each column of a data set (e.g., locations; elements of experimental design; experimental units; measured variables, methods to measure each variable and units; species abbreviations; etc.).

Code: To ensure appropriate code is presented to our readers, any original or modified (novel) code associated with the paper must be provided with the initial manuscript submission for peer review and editorial approval. We require a version of record (the exact version described in the paper, able to replicate the results presented). This material should be supplied as Supporting Information. However, we encourage publication of a second copy on outside platforms that permit future updates with versioning control. Novel code on an outside repository must also be properly cited and referenced in the final publication. Code that is not novel (e.g., from a standard statistical package or publicly available model) must only be properly cited and referenced.

Methods or protocols: Use of known methodology/protocols should be cited appropriately with complete references. Detailed information describing new methodology should be presented in the main text (such as within a “Methods” section) or within an Appendix to be published alongside the manuscript as Supporting Information.

Derived data products: This constitutes data which are collected from database source(s) and collated and/or processed specific to the current research. Complete data source documentation and metadata are required, along with formal citation references. Details regarding data processing steps and assumptions should be clearly defined.

CHOOSING A REPOSITORY

Data and code must be deposited in a permanent, trusted repository. Personal author pages on institutional websites do not suffice (such as a lab or project page), nor do personal online storage drives (such as GoogleDrive).

ESA maintains an extensive list of approved repositories; we encourage you to peruse the General Tips below and contact with any questions.

Authors will be responsible for any fees charged by external repositories to comply with the Open Research requirement.

Please note that the repository you select must present the material in English or offer a translation to English. 

General Tips:

  • A trusted repository will assign a DOI or other permanent identifier to the material and guarantees the material to be available in perpetuity.
  • When possible, choose a repository that specializes in your scientific field to promote interoperability and reuse.
  • Use of a repository run by the institution/affiliation/government agency of the author(s) is encouraged; this staff can be an excellent support system and help authors comply with institute and/or funder requirements.
  • The Dryad data repository provides a flexible platform for a wide variety of digital data.
  • A no-cost general repository option such as Figshare can be utilized.
  • Other examples of permanent repositories include GenBank for DNA sequences, ORNL-DAAC for biogeochemical data, Knowledge Network for Biocomplexity, the NSF Arctic Data Center, and the Environmental Data Initiative (EDI).
  • A Zenodo DOI must be obtained for GitHub material to ensure permanency and versioning. Instructions for obtaining a Zenodo DOI can be found here.

MECHANICS AND EXAMPLES

Online submission form:

The online manuscript submission form will include an Open Research question and authors must disclose:

(1) whether no data were collected for this study (i.e., theoretical, review, opinion, editorial papers)

(2) if data are already published, with affirmation that those publications are properly cited

(3) if data are provided as private-for-peer review as part of this submission (shared privately on a repository) and if so, where they intend to permanently archive such data if the paper is accepted for publication

(4) that data are not yet provided and if so, why, with affirmation data will be made available on a repository if the paper is accepted and with the intended repository noted

(5) that data are sensitive and cannot be provided publicly (rare; examples include sensitive species data and human subject data), with this fully disclosed and query/contact details provided so another qualified researcher could obtain the same data

(6) the availability of any novel code to be evaluated as part of the submission (provided as Supporting Information, with confirmation of where it will also be permanently archived if the paper is accepted) 

(7) For Data Papers and Statistical Reports in Ecology only, that data are provided as part of the submission as Supporting Information, and where these data will also be publicly archived if the manuscript is accepted

Manuscript file:

The manuscript file should include an Open Research statement on the manuscript’s title page that fully describes where readers can access all underlying data and/or code. Statements to the effect of “material are available from the author(s)” are not permissible. Examples of Open Research statements for accepted papers are provided below.

At the submission stage, please consult the numbered list above and include a statement that meets one of these requirements.

For final submissions of accepted manuscripts, this statement must convey complete data archiving details, including data source citations and formal Literature Citation entries. Note any access restrictions.

 

Examples of text for the “Open Research” statement

 

For data stored in a repository by authors of this research paper:

Data are available from Dryad (Smith et al. 2019): [Dryad data set DOI]

[Include complete Smith et al. 2019 entry in the Literature Citations and cite as appropriate in the main text]

 

For data previously released and published by individuals other than authors of this research paper:

Data sets utilized for this research are as follows: [citation(s) with DOI/URL data set links]

[Include complete citation entries in the Literature Citations when possible and cite as appropriate in the main text]

 

For most theoretical, review, opinion, or editorial papers, and Bulletin Photo Gallery submissions:

Empirical data were not used for this research.

 

(Rare) For data not publicly available, but available to researchers with appropriate credentials:

Data are not publicly available due to [fill in reasons, such as sensitive species data]. Data can be obtained from [provide complete query and contact details, with license and access restrictions, if any].

 

(Rare) For data that are restricted by commercial, industry, patent, government policies, regulations, and/or laws:

Data supporting this research are available from [third party source], with [restrictions, including non-disclosure agreements, licensing, other agreements], and are not accessible to the public or research community. [Provide full query and contact process for other researchers to gain access.]

 

NOTE: If your data are in either of the “Rare” statement categories, the handling editor will be asked to determine if the statement provides the detail necessary to meet ESA guidelines.

FAQ’s

This FAQ section is a living document, and we intend to expand the list. Additional questions can be submitted to gro.asenull@slanruojase

 

Q: What are the advantages of posting my data and code on a public repository?

A: Advantages of using a permanent repository include:

  • Visibility: Making your data/code available online (and linking it to the journal publication) provides a new pathway for others to learn about your work.
  • Citability: All data/code you deposit will receive a persistent, resolvable identifier that can be used in a citation.
  • Workload reduction: If you receive individual requests for data/code, you can simply direct them to files in the archive.
  • Quality control: storage of data in a permanent public repository encourages complete transparency and discourages the falsification of data and other fraudulent publication practices in ESA journals.
  • Preservation: Your data/code files will be permanently and safely archived in perpetuity.
  • Impact: You will garner citations for both the research paper and data/code product through the reuse of your data/code.
  • Potential for greater collaboration: Other scientists searching for data to perform meta-analyses or develop new hypotheses may involve you as a collaborator and author.
 
Q: Do I need to archive my data prior to manuscript submission?

A: Only for Data Papers and Statistical Reports in Ecology. For other manuscript types and journals, it is not required at submission but is strongly encouraged. If you are depositing data in a repository at the manuscript submission stage, we suggest keeping it “private for peer review” and this data deposit should not specify the journal since the paper is not formally accepted. Except for Data Papers and Statistical Reports in Ecology, at the submission stage we only require confirmation of understanding of the policy and mention of the intended repository for verification purposes.

 

Q: Do I need to provide my novel code at the time of manuscript submission?

A: Yes, novel code is required in order to be evaluated and approved. Just like the main manuscript and other files, this material is strictly confidential during the review process, and is provided to reviewers as part of the reviewing package. Novel code files should be provided as supporting information with your initial submission. Files should be placed in a compressed folder named “Code” and labeled as “Supporting Information for review and publication”.

 

Q: How should I prepare my code?

A: Best practices guidelines advise authors to use a scriptable statistical environment, generating statistical code that is sufficiently complete to allow replication of tables, graphs, and statistical analyses reported in the original publication, and perform new or meta-analyses. Every number, every p-value, and every graph require formal archiving of the original script that generated it. In cases where published results are challenged or questioned, these scripts will be used to reconstruct the published analyses, which is the critical first step towards resolving the dispute.

 

Q: What happens if I have archived my data and my paper is not accepted by the journal?

A: Your data on the repository remains there and can be linked to a new submission at a different journal. Your data deposited on a repository should not specify a related journal publication until the paper is formally accepted.

 

Q: Can I provide my data or code after the manuscript is accepted and released online?

A: No, data and code links must be verified and included in the final file sent to the publisher. Authors will need to archive data/code as part of the final submission process.

 

Q: What should I name the data package on the data repository?

A: We do not suggest giving the data package the exact same name as your manuscript title. Use a descriptive name for the data package that meets the guidelines of the repository. Do include a reference to your related ESA journal publication. 

 

Q: Will ESA help me craft my Open Research statement?

A: Please make every effort to review and follow the statement examples provided in the “Mechanics and Examples” section. Your statement will be checked by ESA staff and they will request clarifications if necessary. Specific questions can be directed to gro.asenull@slanruojase

 

Q: The repository requires the journal publication DOI before releasing the data. How can I obtain the DOI for my ESA journal paper to link to it?

A: The publisher will assign the DOI shortly after their receipt of the files, and most data repositories can amend the data release to include this detail when requested to do so. Contact us if your paper is accepted and your repository is not able to accommodate this.

 

Q: ESA will link the paper to the data set, but how can I link the data set to the paper?

A: Please work with your repository to link the data set back to the journal release. This requires some finesse because the journal article will not yet be released.

 

Q: I would like to deposit data in Dryad. Does your journal provide manuscript information to them?

A: Yes! Please let us know you will be using Dryad when uploading your manuscript submission, and we can simplify your data submission process with Dryad. Detailed Dryad submission instructions will be provided at manuscript acceptance.

 

Q: Are there fees associated with depositing data?

A: Authors are responsible for fees associated with data deposits. Authors of Ecological Monographs contributions that choose to deposit data in Dryad will be accessed a reduced fee. Repository fees typically range from $0 to $120 for most data sets, with structured, incremental fee increases for very large deposits (these are generally structured by ranges of gigabytes). Sites like Figshare are a no-cost option, as are many university library repositories.

 

Q: When referring to the published paper and/or data set, should I cite the paper, the data set, or both?

A: Both items are considered research output, and both should be cited as appropriate.

 

Q: What precautions should be taken with sensitive human subject data?

A: If you work with human subjects, be sure to follow all relevant guidelines for the protection of personally identifying information (PII) as specified in your Institutional Review Board (IRB) application and approval. Data needs to be sufficiently anonymous so that identity cannot be surmised from the data set.

 

Q: What additional resources are available?

A: We encourage authors to explore the FAIR principles and Powers and Hampton (2019) in Ecological Applications (Open Access: https://doi.org/10.1002/eap.1822). Authors, editors, reviewers, and readers are encouraged to reach out to us with any questions for manuscript preparation or regarding previously published materials.