# Context, credits and references

## Part of the TIER2 project

The Handbook is part of the [TIER2 project](https://tier2-project.eu/), enhancing Trust, Integrity and Efficiency in Research through next-level Reproducibility. TIER2 receives funding from the European Union's Horizon Europe research and innovation programme under grant agreement No 101094817.

The Handbook is one of the eight Pilots in TIER2, designed to develop, implement, and evaluate new reproducibility-related tools and practices, emphasising stakeholder engagement and collaboration throughout the project's duration. One of the two pilots targeted to publishers, the Handbook is known in TIER2 as **Pilot 8**, and it is [described here](https://tier2-project.eu/pilots/8). 

A TIER2 [workshop with publishers](https://doi.org/10.17605/OSF.IO/TGUXZ) in May 2023 highlighted the ongoing challenge with the sharing of datasets, code, material and other digital objects underpinning results in publications.  A **consensus priority** among the workshop attendees was the need for a **common educational and practical set of checks** to help in-house editorial staff managing the manuscripts to ensure digital objects were shared in a FAIR-compliant manner and ultimately reproducibile. However, a key requirement was to have a **small number** of checks, **feasible** and **achievable.** An **incremental alignment and consistency across journals and publishers** was the message, over an attempt to make a comprehensive but unrealistic list of checks, which ultimately will not be put in practice. 

In 2024, the academics and professionals in publishing organisations, listed below, worked to co-define and co-create the Handbook via a series of interactive workshops that focused on **two workstreams**:

1. The Checklist workstream: identifications of the checks, definition, value and implementation; where relevant, using [FAIRsharing](https://fairsharing.org/) to signpost standards and data resources, and indicate which checks can be automatised and how.
2. The Workflow workstream: definition of a consensus workflow indicating which roles should perform which checks and when during the internal manuscript process.

Although the primary target audience are in-house editors managing the manuscripts, the Handbook also provide: (i) advice to reviewers, on what compliance to the journal data policy may require, (ii) information for authors on what is expected from them by a number of journals, and (iii) requirements source for developers to drive their service provisions to publishers. 

As of February 2025, the intervention is in progress and will run for up to six months, and the results will be published in later this year, along with all underlying data.

## Leaders and participants

For more information, please, contact the pilot co-leads. 

<table data-full-width="false"><thead><tr><th width="191">Name</th><th width="167">Affiliation</th><th width="170">Title</th><th width="361">Role in pilot (and TIER2)</th></tr></thead><tbody><tr><td><a href="https://orcid.org/0000-0001-5306-5690">Susanna-Assunta Sansone</a> (susanna-assunta.sansone@oerc.ox.ac.uk)</td><td>University of Oxford</td><td>University Academic Lead of Research Practice; Prof of Data Readiness; OeRC Director</td><td>Co-lead (funded partner)</td></tr><tr><td><a href="https://orcid.org/0000-0002-7702-4495">Allyson Lister</a> (allyson.lister@oerc.ox.ac.uk) </td><td>University of Oxford</td><td>FAIRsharing Content and Community Coordinator</td><td>Co-lead (funded partner)<br></td></tr><tr><td><a href="https://orcid.org/0000-0002-7614-0806">Rebecca Taylor-Grant</a> (rebecca.taylorgrant@tandf.co.uk)</td><td>Taylor &#x26; Francis</td><td>Head of Data Initiatives</td><td>Co-lead (associate partner)</td></tr><tr><td><a href="https://orcid.org/0000-0002-1496-8392">Matt Cannon </a>(matthew.cannon@tandf.co.uk) </td><td>Taylor &#x26; Francis</td><td>Head of Open Research</td><td>Co-lead (associate partner)</td></tr><tr><td><a href="https://orcid.org/0000-0003-4664-7144">Christopher Osborne</a> (christopher.osborne@anthro.ox.ac.uk)</td><td>University of Oxford</td><td>DPhil Student: improving research culture and practice</td><td>Intervention lead (funded student)</td></tr><tr><td><a href="https://orcid.org/0000-0003-4470-7027">Tony Ross-Hellauer</a></td><td>TU Graz</td><td>Group Leader</td><td>Coord group (TIER2 PI)</td></tr><tr><td><a href="https://orcid.org/0000-0002-7331-4751">Thomas Klebel</a></td><td>TU Graz</td><td>Project Manager &#x26; Researcher</td><td><br>Coord group (TIER2 Project manager)</td></tr><tr><td><a href="https://orcid.org/0000-0002-9298-3168">Liz Allen</a></td><td></td><td>independent expert</td><td>TIER2 Advisory Board</td></tr><tr><td><a href="https://orcid.org/0009-0007-6587-7814">Abigail Smith</a></td><td>Wiley</td><td>Senior Specialist, Publishing Strategy &#x26; Policy Team</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0002-9147-8397">Adam Leary</a></td><td>Oxford University Press</td><td>Senior Publisher, Open Research</td><td>Pilot member</td></tr><tr><td><a href="http://orcid.org/0000-0002-2003-9573">Andrew Hufton</a></td><td>Cell Press</td><td>Editor In-Chief (Patterns)</td><td>Pilot member</td></tr><tr><td>Annie Hill</td><td>American Psychological Association</td><td>Editorial Director, Journals</td><td>Pilot member</td></tr><tr><td><a href="http://orcid.org/0000-0003-2219-5841">Bernd Pulverer</a></td><td>EMBO Press</td><td>Head of Scientific Publications</td><td><br>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0001-9623-2225">Catriona J. MacCallum</a></td><td>Wiley</td><td>Director, Future of Scholarly Research</td><td>Pilot member (TIER2 Advisory Board)</td></tr><tr><td><a href="https://orcid.org/0000-0002-1335-0881">Chris Hunter</a></td><td>GigaScience</td><td>GigaDB Director</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0002-8889-9246">David Tovey</a></td><td>Journal of Clinical Epidemiology / Elsevier</td><td>Co-Editor</td><td>Pilot member</td></tr><tr><td>Elisa De Ranieri</td><td>Cell Press</td><td>Head of Research Integrity and Author Experience</td><td>Pilot member</td></tr><tr><td>Grace Ranola</td><td>Journal of Petrology / Oxford University Press</td><td>Publisher</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0001-8966-8688">Guy Jones</a></td><td>Springer Nature</td><td>Chief Editor</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0001-5461-3265">Hannah Sonntag</a></td><td>EMBO Press</td><td>Open Science Implementation Coordinator</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0001-5839-5787">Jess Miorini</a></td><td>Language and Cognition</td><td>Publisher</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0003-2839-4067">Kiera McNeice</a></td><td>Cambridge University Press</td><td>Research Data Manager</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0002-7571-3502">Lauren Cadwallader</a></td><td>PLOS</td><td>Open Research Manager</td><td>Pilot member</td></tr><tr><td>Libby Dunkley</td><td>Cambridge University Press</td><td>Editorial Operations Manager</td><td>Pilot member</td></tr><tr><td>Louie Sandys</td><td>Research Directions, Cambridge University Press</td><td>Publisher</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0002-6064-4313">Monica Moniz</a></td><td>Research Directions, Cambridge University Press</td><td>Publisher and Programme Manager</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0002-7134-499X">Molly Cranston</a></td><td>F1000 (Taylor &#x26; Francis)</td><td>Editorial Content Manager</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0002-5192-9835">Nicole Nogoy</a></td><td>GigaScience</td><td>Executive Editor</td><td>Pilot member</td></tr><tr><td>Pierre Nauleau</td><td>Lancet</td><td>Senior Editor</td><td>Pilot member</td></tr><tr><td><a href="https://orcid.org/0000-0001-6444-1436">Scott Edmunds</a></td><td>GigaScience</td><td>Editor-in-Chief</td><td>Pilot member</td></tr></tbody></table>

## Existing material reviewed to identify the checks

A number of documents were reviewed in order to create a consensus Checklist that would work for a variety of publishers and that incorporates the most frequently recommended elements of each source.

Those that were used as sources for the Checklist are included in the section below, and referenced within the Guidance documents via the labels from the 'Acronym' column. Those that were not used as sources for the Checklist (e.g., they were deemed out of scope) are included in a separated section below.&#x20;

### Included Sources

<table data-full-width="false"><thead><tr><th width="133">Document</th><th width="141">Research area</th><th width="103">Acronym</th><th width="157">Sections utilised</th><th>Comments</th></tr></thead><tbody><tr><td><a href="https://doi.org/10.25504/FAIRsharing.t58zhj">ARRIVE</a></td><td>Life Sciences</td><td>ARRIVE</td><td>Section 19: Protocol registration; Section 20: Data Access</td><td><br></td></tr><tr><td>F1000 checks summary</td><td>Subject Agnostic</td><td>F1000</td><td><br></td><td><br></td></tr><tr><td><a href="https://doi.org/10.1038/s41597-022-01710-x">FAIR4RS</a></td><td>Software/code</td><td>FAIR4RS</td><td>F1, F2-F4, R1.1, R3</td><td>Excluded as too granular: F1.1 (different granularity getting additional PIDs), F1.2 (different versions get different PIDs), all A principles (dealing with longer-term preservation and resolution of identifiers), all I principles (do journals really check that software interoperates using standard formats?), R1.2 (provenance - out of scope?) and R2 (references to other software)</td></tr><tr><td><a href="https://academic.oup.com/gigascience/pages/Minimum_Standards_of_Reporting_Checklist">GigaScience Minimum Standards of Reporting Checklist</a> (was: <a href="https://doi.org/10.1186/s13742-015-0071-8)">BMC Better reporting for better research: a checklist for reproducibility</a>)</td><td>Life Sciences</td><td>GigaScience</td><td>Resource subsection; Availability of data and materials subsection</td><td>Generally out of scope for this handbook, but some recommendations are at a high-enough level to be included</td></tr><tr><td>The <a href="https://doi.org/10.1073%2Fpnas.2103238118">MDAR</a> (Materials Design Analysis Reporting) Framework for transparent reporting in the life sciences (see also <a href="https://doi.org/10.25504/FAIRsharing.d56cdd">here</a> and the MDAR <a href="https://osf.io/bj3mu/">checklist</a> and <a href="https://www.science.org/content/blog-post/improving-reproducibility">here</a>.)</td><td>Life Sciences</td><td>MDAR</td><td>Specifically, the MDAR checklist for authors. This is also explicitly intended for editors</td><td>MDAR checklist items that we are not currently including, as are trying to keep a narrow focus on reusability and reproducibility: study-level protocols, study design, statistical tests, attrition. See also MDAR here:<a href="https://www.ncbi.nlm.nih.gov/books/NBK556610/"> https://www.ncbi.nlm.nih.gov/books/NBK556610/</a>, incl comments about how 'less is more' in terms of checklist items, to increase completeness. This can be partially accomplished through domain-specific formats being used for the digital objects in the first place, and the completeness of the metadata in those formats. That lessens the burden for the editors/reviewers.</td></tr><tr><td><a href="https://www.nature.com/nature-portfolio/editorial-policies/reporting-standards">Nature Portfolio Editorial Policy Checklist</a> (another <a href="https://www.nature.com/nature-portfolio/editorial-policies/reporting-standards">link</a>)</td><td>Subject Agnostic</td><td>Nature</td><td>Code and data availability</td><td><br></td></tr><tr><td><a href="https://grants.nih.gov/policy/reproducibility/principles-guidelines-reporting-preclinical-research.htm">NIH Principles and Guidelines for Reporting Preclinical Research</a></td><td>Life Sciences</td><td>NIH</td><td><br></td><td><p>Note that the NIH states that "Journals should use a checklist during editorial processing to ensure the reporting of key methodological and analytical information to reviewers and readers." Then make this checklist visible to authors, and provide them with their own checklists to complete for you upon submission: "Require authors to fill out a checklist, ideally upon submission, to state where the required information is located in the manuscript."</p><p>Replicates (mentioned here) have not yet been added to this spreadsheet, as unsure if that was too domain specific.</p></td></tr><tr><td><a href="https://doi.org/10.31219/osf.io/x85gh">Promoting Reusable and Open Methods and Protocols (PRO-MaP)</a>: Draft recommendations to improve methodological clarity in life sciences publications, Leite et al.</td><td>Life Sciences</td><td>PRO-MaP</td><td>Specifically, Section and Table 3 (Publishers and editors) was used in this review.</td><td>PRO-MaP does not include study-level protocols or study design. I am not including them here for the reasons stated in PRO-MaP ("Study design protocols include many details that are essential to understand and critically evaluate the study, but are less likely to be reused (e.g. because the study population, inclusion and exclusion criteria are unique to the study)." However, we can include them if required (e.g. with a GUPID).</td></tr><tr><td><a href="https://doi.org/10.1038/d41586-019-03959-6">REAPPRAISED</a> checklist for evaluation of publication integrity</td><td>Subject Agnostic, started in Life Sciences</td><td>REAPPRAISED</td><td><p>E - Ethics; A - Analysis and Methods;</p><p>D - Data duplication and reporting</p></td><td>Much of this does NOT fall under reproducibility checks so hasn't been included. Integrity checks are interesting but out of scope for the reproducibility handbook.</td></tr><tr><td><a href="https://static-content.springer.com/esm/art%3A10.1038%2Fs41591-021-01552-x/MediaObjects/41591_2021_1552_MOESM2_ESM.docx">STORMS</a> (another <a href="https://www.stormsmicrobiome.org/">link</a>)</td><td>Life Sciences</td><td>STORMS</td><td>Section 8 (Reproducibility); 16 and 17 (Supplements and supplementary data)</td><td>The majority of this checklist is too fine-grained for use within the Handbook.</td></tr><tr><td><a href="https://osf.io/kgnva/wiki/home/">TOP/COS checklist for editors/reviewers</a>. See also <a href="https://osf.io/55eu7">https://osf.io/55eu7</a> (Checklist for Authors implementing Level 1);<a href="https://osf.io/87v93"> https://osf.io/87v93</a> (Checklist for Editors Levels 1 and 2).</td><td>Subject Agnostic</td><td>TOP1; TOP2</td><td><br></td><td>There are additional fields in these TOP checklists that haven't been included here around replication, pre-registration of analysis plans, and preregistration of studies. All seem out of scope for the more general approach we've been taking. There are also additional requirements around digital object transparency that seem to go into too much detail at this stage.</td></tr><tr><td><a href="https://doi.org/10.25504/FAIRsharing.4a9e19">RDA / CURE-FAIR</a></td><td>Subject Agnostic</td><td>CURE-FAIR</td><td>Things 1, 2, 5, 6, 8</td><td>All included sections ("Things") are high-level without particular implementation details as relevant for manuscript submissions. However conceptually many "Things" align with the Handbook, and are represented accordingly in the guidance.</td></tr><tr><td><a href="https://doi.org/10.5334/dsj-2020-005">Developing a Research Data Policy Framework for All Journals and Publishers - Data policy standardisation and implementation IG</a></td><td>Subject Agnostic</td><td>RDA RDPF</td><td>Definition of exceptions, Data repositories, Data citation, Data licensing, Data availability statements (DASs), Data formats and standards</td><td>While this work is focused on journal data policies as a whole, some segments of this framework do align with the Handbook.</td></tr></tbody></table>

### Excluded

| Document name                                                                                                                      | Research area      | Comments                                                                                                                                         |
| ---------------------------------------------------------------------------------------------------------------------------------- | ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------ |
| [AAAI Reproducibility Checklist](https://aaai.org/conference/aaai/aaai-23/reproducibility-checklist/)                              | Computer Science   | There is some overlap with this work, but broadly speaking this resource is focused on details that are not in scope for us.                     |
| [Checklist for an Open Research Action Plan](https://www.ukrn.org/2021/11/03/open-research-action-plan/)                           | Subject Agnostic   | Not related to this work at all; discounted                                                                                                      |
| [CONSORT](https://doi.org/10.25504/FAIRsharing.gr06tm)                                                                             | Life Sciences      | n/a (too specific)                                                                                                                               |
| [FAIR software checklist and tool](https://ardc.edu.au/article/new-self-assessment-tool-to-promote-fair-research-software/)        | Software/code      | No additional information - just an implementation of FAIR4RS                                                                                    |
| GCCP                                                                                                                               | Life Sciences      | n/a (too specific)                                                                                                                               |
| GCCP, GIVIMP, SciRAP GD211                                                                                                         | -                  | n/a (too specific)                                                                                                                               |
| [MICCAI Reproducibility Checklist](https://miccai2021.org/files/downloads/MICCAI2021-Reproducibility-Checklist.pdf)                | Medical Imaging    | reproducibility checklist for authors, to then be used by reviewers etc. However, it too was too narrow in scope and discounted for this review. |
| [PRISMA](https://doi.org/10.25504/FAIRsharing.gp3r4n)                                                                              | Life Sciences      | n/a (too specific)                                                                                                                               |
| [Reliability and reproducibility checklist for molecular dynamics simulations](https://www.nature.com/articles/s42003-023-04653-0) | Molecular Dynamics | Too narrow in scope; discounted for this review                                                                                                  |

### Possible relevance in the future

| Document name                                                                                                                                                                                       | Comments                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Publishers comments at[ https://docs.google.com/document/d/1B9glUjJRvLvV-QrOdW96WNM8bOglyyPzjZHTVYreFik/edit](https://docs.google.com/document/d/1B9glUjJRvLvV-QrOdW96WNM8bOglyyPzjZHTVYreFik/edit) | I have already reviewed those items but may be worth revisiting in future                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
| Review the questions ARGOS has for RMPs (Elli P)                                                                                                                                                    | <p><br></p>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| [Reproducible Research Publication Workflow: A Canonical Workflow Framework and FAIR Digital Object Approach to Quality Research Output](https://doi.org/10.1162/dint_a_00133)                      | This paper was read and assessed, but is not directly relevant to this review. It describes an example canonical workflow for publishers to follow when assessing the digital objects associated with manuscript submission. While useful in the context of a workflow, it is not directly relevant to this checklist. Note that one thing publishers mentioned in our meetings is how publisher workflows both vary widely and are often private due to concerns about too much information about checks being released and possibly getting into the hands of paper mills. Integration of our checklist into an example workflow might be one method to use in future as we build the intervention. |
| [Enhancing Peer Review Standards for Quality Research Publications](https://doi.org/10.21428/51e64700.fcd86e15)                                                                                     | Still in development                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |

### Other material

Inspiration for the organisational structure of the checklist has come, in part, from: Woodford, C. J., Treloar, A., Leggott, M., Payne, K.., Jones, S., Lopez Albacete, J., Madalli, D., Genova, F., Dharmawardena, K., Chibhira, N., Åkerström, W. N., Macneil, R., Nurnberger, A., Pfeiffenberger, H., Tanifuji, M., Zhang, Q., Jones, N., Sesink, L., & Wood-Charlson, E. (2023). The Global Open Research Commons International Model, Version 1 (Version 1). Research Data Alliance. <https://doi.org/10.15497/RDA00097>

The 'example' section within each [checklist element](/understanding-the-checklist/checklist-elements.md) contains a practical example of how that element is assessed using one of the following manuscripts:&#x20;

\[1] Buljan I, Pina DG and Marušić A. Ethics issues identified by applicants and ethics experts in Horizon 2020 grant proposals \[version 2; peer review: 2 approved]. F1000Research 2021, 10:471 (<https://doi.org/10.12688/f1000research.52965.2>)

\[2] Marchant G, Chevance G, Ladino A *et al.* Behavioural patterns of university students during the COVID-19 pandemic: A cross-sectional study of the effects of active transportation, uninterrupted sitting time, and screen use on physical activity and sitting time \[version 3; peer review: 1 approved, 2 approved with reservations]. *F1000Research* 2025, 11:568 (<https://doi.org/10.12688/f1000research.117843.3>)

## Version updates

Here is a short summary of updates to the site:

* 9 September 2025: variety of small changes for grammatical clarity. Addition of RDA resources that had not yet been listed within Included sources.
* 3 March 2025: added 13th check and this versioning section.
* 12 February 2025: updated participants table
* 16 July 2024: initial release


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