2.4.2 Publication

​​​​​​​​​A. Background & Definitions

Publication, in the context of this Toolbox article, refers to the presentation of research data to the scientific community, irrespective of the format (peer-reviewed journals, poster presentation at conferences or patent applications). ​

Open access (OA) model of publication refers to free of charge, accessible online and in comparison, to traditional journals, offers less restrictive copyright and licensing barriers:

• Gold OA refers to articles published in OA journals when the publication is freely accessible on the journal's websites immediately after its publication (examples of Gold OA include PLOS and BioMed Central)
• Green OA, also referred to as self-archving, is the practice of placing a version of an author's manuscript into a repository, making it freely aaccessible to everyone. The version that can be deposited into a repository is dependent on the funder or publisher.
• Bronze OA journals offers delayed open access, i.e. after an embargo period.
• Diamond/platinum OA journals do not charge either readers or authors but require funding from external sources.

​B. Guidance & Expectations

Journals typi​​​cally have instructions for authors and requirements that should be consulted and followed (e.g. the STAR Methods section for Cell Press Journals or Reporting Checklists for Life Sciences Articles for Nature journals).

​The expectations belo​​w are meant to apply to any publication, Journal manuscript or not.​

Presentation of data and description of materials and methods used in the publication:

• ​It must be clear from the publication whether studies were run with the intention to inform a formal knowledge claim (for details see item 2.1.4 Purpose of research​)
• Publication must disclose information about all repeats, runs and replications of the experiments (if the format allows)
• For animal research, authors should be familiar with and should follow the ARRIVE 2.0 recommendations
• The publication should provide sufficient information that allow to evaluate results and to replicate the study results by other scientists (if the format allows)
• The authors should include in the manuscript unique searchable identifiers, Research Resource Identifiers (RRIDs), for biological resources (if the format allows)
• Scientists are encouraged to share data, materials and computer source codes (if applicable) that underlie performed research. ​

Study preregistration information:

• Researchers should provide information in the manuscript if, when and where the study was preregistered.
• If any post registration changes were made, the authors must describe in the manuscript what and why was changed​

Conflict of Interest description:

• All authors should disclose any potential conflict of interest, whether financial or non-financial
• All sources of funding (public and/or private) should be explicitly described​

Authorship:​

• Clearly describe contribution to the work made by each co-author,
• Justify who should be designated as "corresponding author" as well as describe her/his responsibilities

PLEASE DO NOT FORGET

• ​​To discuss and agree on authorship inclusion and exclusion criteria and the author order before the start of a new research project
• To register for ORCID​ (individual researcher identifiers) and provide ORCID identifier during the manuscript submission phase
• To consider adding this subject to a training program for new employees or refresher training (if appropriate)
• By (co-)authoring a publication, the author(s) assume the responsibility for the way in which research findings are presented and published and declare willingness to take public responsibility for all aspects of the work (Inspired by Battisti et al. 2015)​
• If raw data from published study are not included in the manuscript or are not uploaded to the open access repository, authors should be prepared to provide them upon journal, other scientists or funders request.
• Reported data must disclose all repetitions of the test regardless of the outcome (one of the Core Requirements​)

C. Resources

Reporting guidelines

• The ARRIVE guidelines 2019:
  • updated guidelines for reporting animal research [1]
  • explanation and elaboration [2]

​* The Center for Open Science's Guidelines for Transparency and Openness Promotion (TOP; [3] [4])

• PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses [5]
• ASPET journals' instructions for authors (detailed explanations with examples) [6]

Resources to support disclosure of negative (null) results:

• FIDDLE (File Drawer Data Liberation Effort) Tool [7]
• CERTAIN principles [8]​

Open access repository for science methods

• protocols.io [9]

Repositories for data

• Figshare [10]
• Open Science Framework [11]
• Dryad [12]

Repository for computer source code

• GitHub [13]

CRediT (Contributor Roles Taxonomy) to describe each author's individual contributions to the work [14]

Author identification - Open Researcher and Contributor Identifier (ORCID) iD [15]

COPE (Committee on Publication Ethics) [16]

ICMJE recommendations on Authors and Contributors [17]

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