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Open Research Policy

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 novel statistical code pertinent to the results presented in the publication must be made available in a permanent, publicly accessible data archive or repository upon acceptance of a manuscript, with rare exceptions (see the “Details” section for more information). Archived data and novel 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” section for definitions of each bulleted 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 Paper” manuscripts in Ecology, authors must supply data as Supporting Information with the manuscript submission in ScholarOne. Authors are required to archive the same material in a public repository upon acceptance for publication in Ecology.

At the submission stage for all “Statistical Report” manuscripts in Ecology, authors must make data and novel code available in an external repository during the review process. A repository with a private-for-peer review option is recommended, but a public posting is also acceptable for review. Authors are required to archive the same material in a public repository upon acceptance for publication in Ecology.

All other ESA Journals Submissions

Raw data, metadata, and derived data products must be provided in an appropriate external archive if a manuscript is accepted. At the submission stage for most ESA manuscript types and journals (see the exceptions above), data should not be uploaded alongside your submission in the file list. Authors are not required to provide data at the submission stage, but it is strongly encouraged that authors deposit data in an external repository prior to manuscript submission to allow Subject-matter Editors and reviewers access. Many repositories now offer a private-for-peer-review option and we strongly encourage authors to use this approach.

Novel code must be supplied as private-for-peer review in an external repository during the review process. At the submission stage, code should not be uploaded with your submission in the file list.

Supporting Information Restrictions

In addition to our requirements for the presentation and archival of data and novel code, restrictions on the inclusion and formatting of specific pieces of supporting information are now in effect. The following items can only be made available as part of our Open Research Policy and cannot be included with a submission in the file list:

1) Spreadsheets (.xlsx, .csv, etc.)
2) Large tables

If the above items are included with your submission, your manuscript will be returned to you to ensure it follows our Open Research policy guidelines. The “Appendix” and “Data” designations should be considered a simple naming convention used to identify which material will be presented in PDF format (appendices) or spreadsheet format (data). For a definition of a “large table” please see “How do I know if my table is allowed as supporting information?” in our FAQ section.

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 in which 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.).

“Novel” Code: To ensure appropriate code is presented to our readers, any novel code associated with the paper must be provided with the initial manuscript submission for peer review and editorial approval. Novel code is any code that cannot be directly cited and falls under two categories:

  1. A function or package you have created yourself
  2. A function or package you have edited to the extent that you can’t simply cite an existing function or package

We require a version of record (the exact version described in the paper that allows a reader to replicate the results presented) provided in the native format of the code file.

This material must be provided in an external repository during the peer review process. We strongly encourage using a repository with a private-for-peer review option, but a public repository posting is also acceptable. If the manuscript is accepted, we require publication of the code in an external repository that permits future updates with versioning control. Novel code in 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 be properly cited and referenced.

If your code is not novel, please state this clearly in your Open Research statement. If your statement is ambiguous, the journal’s editorial staff will contact you for further details.

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. These guidelines must be followed for both final storage and any material provided as private-for-peer review.

Personal author pages on institutional websites (such as a lab or project page) do not suffice, nor do generic cloud-storage services (such as Google Drive, Box, Sharepoint, Nimbus, or Dropbox), even if these services are licensed through a university or institution.

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

  • To guarantee reviewer anonymity, repositories that are used for “private-for-peer review” sharing cannot require a reviewer to log in. Please see our FAQ section (“What are the requirements for “private-for-peer review” storage?”) for more information.
  • 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 in the ScholarOne system:

At the new submission and revision stages, please consult the numbered list below. After determining the options that apply to you, please do the following: i) Note which options apply to you and disclose the current/future availability of data and code, affirming as many as needed in the Comment Box of the “Open Research” section of the ScholarOne online submission form, AND ii) Add an Open Research statement on the manuscript’s title page that includes any extra requirements for your choice(s) for disclosing the availability of data and code. Submission requirements for each choice are shown in [bold].

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

2. Data are already published and publicly available, with those publications properly cited in this submission. [If choosing this option, include complete citations for the publicly available data sets you used for your manuscript. You must also include complete citation entries in the References section when possible and cite as appropriate in the main text. If the material was retrieved from an external database that does not use permanent identifiers for datasets, you must provide the necessary query details another qualified researcher would need to obtain the same data you accessed from the external database. Please note: This option is used only for material that is currently publicly available. Do not use this option to refer to the link where your data will eventually be made available if the manuscript is accepted.]

3. Data are provided as private-for-peer review (shared privately or publicly on a repository). [If choosing this option, in the Open Research statement you must provide an active link to where the material is currently stored and state the intended repository where data will be permanently archived if the paper is accepted for publication. Data files can NOT be uploaded with your manuscript in the system.]

4. Data are not yet provided. [If choosing this option, you must disclose why in the Open Research statement, affirm data will be permanently archived if the paper is accepted for publication, and note the intended repository. Stating data will only be provided upon acceptance of the manuscript is permissible but be advised the Subject-matter Editor or reviewers may request to see this data during review if deemed necessary.]

5. Data are sensitive and cannot be provided publicly (rare; examples include sensitive species data and human subject data). [If choosing this option, in the Open Research statement you must fully disclose what data are private and provide complete query and contact details so another qualified researcher can obtain the data. You must provide what data sets you can, with the sensitive data points redacted as necessary. This anonymized data must be provided following the standard archiving guidelines of our Open Research policy. ]

6. This submission uses novel code, which is provided, per our requirements, in an external repository to be evaluated during the peer review process. [Novel code files MUST be provided as private-for-peer review in an external archive. A repository with a private-for-peer review option is recommended (such as Dryad or Figshare), but a public repository such as GitHub is acceptable. If choosing this option, your Open Research statement must include the link to the private-for-peer review storage location and state the intended repository where the code will also be permanently archived if the paper is accepted for publication. If your code is not novel, please state this clearly in your Open Research statement.]

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 and/or code that are currently available in a repository as private-for-peer review:

Data and/or code are provided as private-for-peer review via the following link: [Link to external storage location]

[Include an active link to the current location where data and/or code can be retrieved] 

For data that are not yet provided, but will be archived upon acceptance:

Data are not yet provided [Include the reason that data are not yet provided]. Upon acceptance data will be archived in [Include the name of the external repository you will be using].

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

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

[Include complete Smith et al. 2019 data set entry in the Literature Cited and cite as appropriate in the main text. Please note: This option is used only for material that is currently publicly available. Do not use this option to refer to the link where your data will eventually be made available if the manuscript is accepted.]

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 Cited when possible and cite as appropriate in the main text]

For data retrieved from a public database:

[Description of specific dataset retrieved] was retrieved from [name of database, including hyperlink]. Query details for retrieving the relevant data are as follows: [provide the necessary query details another qualified researcher would need to obtain the same data].

[Query details should give specific information to direct a reader to download the same data sets you used for your manuscript and should be tailored to the database. Examples of query details include, directions to search pages, search terms used in web forms, the specific names of data sets you used from an available collection, etc. You should not simply state what data in your manuscript came from the database; you should describe how to retrieve it from the database.

If the query details are especially lengthy or complex, you can instead include the specific query details in an appendix and use the following format for the final sentence “Query details are described in [the appendix location where query details are provided]”. This should point to a specific point of your appendix (such as a table or labeled section) where a reader can find the query details.]

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]. Upon acceptance, anonymized data will be archived in [Include the name of the external repository you will be using].

(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. [Provide full query and contact process details for other researchers to gain access.]

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

Frequently Asked Questions

This section is a living document, and we intend to expand the list. Additional questions can be submitted to esajournals@nullesa.org

 

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. Just like the main manuscript and other files, this material is provided to reviewers as part of the reviewing package. Novel code must be made accessible via an external archive during all stages of the review process. A repository with a private-for-peer review option is recommended (such as Dryad or Figshare), but a public repository such as GitHub is acceptable.

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 requires formal archiving of the original script that generated it. In cases in which 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 are the requirements for sharing novel code (required) and data (not required) during the review process?

A: Authors are not required to provide data as during the review process at initial submission but it is strongly encouraged. Novel code, however, must be provided during the review process.

If an author provides material during the review process, the repository must guarantee reviewer anonymity. A repository cannot require a reviewer to log in to access the material. Personal author pages on institutional websites (such as a lab or project page) also do not suffice, nor do generic cloud-storage services (such as Google Drive, Box, Sharepoint, Nimbus, or Dropbox), even if these services are licensed through a university or institution.

The best practice is to use a repository that provides a direct link to the “private-for-peer review” material with no log-in required, such as Figshare or Dryad. A public-facing repository such as GitHub will also be acceptable.

Q: What do you mean by “private-for-peer review”?

A: “Private-for-peer review” refers to the process of storing material temporarily as private during the review process, with access provided by a direct anonymous link to the material. For material that is provided during the review, private-for-peer review options are recommended (such as Dryad or Figshare), but a public repository where material can be viewed anonymously, but it is not stored privately (such as GitHub) is acceptable. We do not allow generic cloud-storage services for private-for-peer review or for final archival of material, even if these services are licensed through a university or institution.

Q: What are the requirements for “private-for-peer review” storage?

A: Authors are not required to provide data as “private-for-peer review” at initial submission but it is strongly encouraged. Novel code, however, must be provided as private-for-peer review. 

If an author provides material as “private-for-peer review”, the repository must guarantee reviewer anonymity. A repository cannot require a reviewer to log in to access the material as “private-for-peer review”. Personal author pages on institutional websites (such as a lab or project page) also do not suffice, nor do generic cloud-storage services (such as Google Drive, Box, Sharepoint, Nimbus, or Dropbox), even if these services are licensed through a university or institution. 

The best practice is to use a repository that provides a direct link to the “private-for-peer review” material with no log-in required, such as Figshare or Dryad. A public-facing repository such as GitHub  be acceptable. 

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 my accepted manuscript is 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. Manuscript files will not be sent to the publisher for typesetting until this requirement is met.

Q: Can I embargo the data or code associated with my accepted manuscript in order to release the data or code at a later time?

A: No, we do not permit any kind of data or code embargo following manuscript acceptance. Related data and code must be publicly available before the final manuscript is sent to the publisher for typesetting. The desire of authors to control additional research with these data and/or code shall not be grounds for withholding material.

Q: What should I name my data or code package in the external repository?

A: To avoid confusion and possible errors, data and code packages should not be named the exact same name as your manuscript title. Use a descriptive name for data and code packages which meets the guidelines of the repository. A suggested format is “Data from: [manuscript title]” or “Code for: [manuscript title]”. Do include a reference to your related ESA journal publication in data and code deposits.

Individual files in your data or code deposit should be given unique and descriptive file names that can be referred to when necessary (for example: “Ungulate_geospatial_data.xlsx”). Please do not use the format “Data S#”, “Appendix S#”, “Table S#”, or any similar “Item S#” name for the material being placed on a data or code repository, as this naming convention is used by the publisher for supporting information hosted on the journal platform and can result in confusion during file processing and for readers at all stages.

Q: What repository should I use if I have a very large dataset?

A: In previous cases, authors with very large datasets in the 100s of GB range have successfully used Figshare or Knowledge Network for Biocomplexity to meet the requirements of our Open Research policy.

Q: How do I know if my table is allowed in an appendix as supporting information?

A: Appendix tables cannot be provided as spreadsheet files. If your table requires a spreadsheet format, it must be provided under the Open Research policy. Appendix tables will be published in PDF format and should be presented in the clearest and most readable format possible, with font sizing at 8-pt or larger. Appendix tables can be no longer than two pages. If an appendix table is too large, staff may require you remove it and provide it as data under the Open Research policy for ease of re-use. Exception: “Data Papers” in Ecology should provide data in spreadsheet format.

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. After you have submitted your manuscript, your statement will be checked by the journal’s editorial staff and they will request clarifications if necessary. Specific questions can be directed to the journal’s editorial staff .

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 the journal’s editorial staff 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 assessed 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 need 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 the journal’s editorial staff with any questions for manuscript preparation or regarding previously published materials.