Preprints, publications and publishing ethics

Posted on July 20, 2021   by Alex Mulhern

The Microbiology Society’s sound science and open access journal, Access Microbiology, will be converting into an open research platform early next year. This platform will include posting all article versions as preprints, with a transparent peer review process and acceptance required for full publication.

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In previous blogs we have frequently spoken of the difference between posting a preprint and publishing an article – but what do these terms really mean? How are they actually different?

Today we look at preprints, publishing and publication ethics!

Preprints and published articles

A preprint is a version of a scientific manuscript that has been posted online, that has not completed the formal peer review process, i.e., it has not been editorially accepted for publication. They are primarily intended for research use, rather than reporting to lay audiences, but are also useful in demonstrating the precedence of discoveries, and as a means to protect intellectual property. They are usually assigned a digital object identifier, or DOI (more on them later!) and become a permanent part of the scientific record. Therefore, researchers should have a relatively high level of confidence in their research output, if they are to post the preprint online. It is worth stressing that the content of a posted preprint is wholly the responsibility of the author, not the Microbiology Society as a publisher; it has not completed peer review and has not been accepted for publication on the platform.

The published article, also known as the Version of Record, is the peer reviewed, fully formatted, final version of the article. Suitable for reporting to a lay audience with a high level of confidence that the results have been thoroughly scrutinized, and the conclusions stated in the manuscript are true to the underlying data.

The significant difference between the two has become far more important in the last 18 months as many initial results of experiments around SARS-CoV-2 were shared through preprints, and many mainstream media outlets began reporting on preprints directly. To ensure readers are aware when an article is a preprint on our platform, and should be treated as such, we will be taking numerous steps to highlight this clearly on the article, such as posting them as watermarked PDFs to indicate they are as such, and providing none of the branding of a typical Microbiology Society published article.

We will also screen all articles to ensure a base level of quality – with the relevant declarations over competing interests, funding sources and any ethical approval statements included in the first posted preprint, to offer some greater measure of security.

During the submission process, we will be allowing authors a swift route to post their research as a preprint – with the benefit of manuscript review tools to allow them to make critical changes at that very first step – and then running them through a more traditional peer review process, eventually – hopefully leading to the article being accepted and published as the Version of Record. This is also the point at where much of the value added by publishers comes in, through technical, promotional and reputational stewardship.

As the preprint and the eventual published article are on the same platform, and connected by their DOIs, citations accrued to the preprint count toward the article as well.

Digital Object Identifiers (DOIs)

DOIs are unique identifiers for discrete objects – whether physical or digital and are standardised by the International Organization for Standardization. They are designed to be 'resolvable' and ‘persistent’, so that it is always possible to find the object (via, even if a platform changes its name or ceases publishing.

Handily, they allow for iterations – which means that the open research platform can assign a new DOI to each specific version of the preprint and eventual published article.

What’s more – this iteration allows us to assign a DOI to each of the reviews posted alongside the preprint, through which we can ensure the reviews are permanently linked to the publication. And if you search for an earlier version of the manuscript using the DOI you will be taken to that specific version, with a pop-up to let you know that there is a more recent version available.

Image manipulation, ethical misconduct and dangerous papers

The Editorial Office will perform a series of checks to ensure the ethical materials (such as patient consent forms) and statements are present, and will flag any alarming content to our Editors-in-Chief for a scientific screen. In this instance, these articles will not be posted online at all. But there could come a time when potentially damaging material is posted as a preprint. What would occur in this very rare circumstance?

While a preprint server would classically leave the preprint posted – in exceptional cases, they may add a note of concern. Our responsibility as a Society publisher is not just to the scientific record, but to the microbiological community and our membership. If a damaging paper is posted on the platform – for example, sharing medical information that is fundamentally incorrect and could cause harm – we need to consider the wider ramifications of leaving this preprint online.

Editors handling papers will be asked to handle the posted preprint like any article under submission at a traditional journal, and will highlight these areas of major concern to the office and the Society – wherein an investigation will take place over the fidelity of the paper, and the potential damage to the wider community. This may include an Editor spotting discrepancies in figures and images, concerns over the providence of the underlying data and any other suspicions of misconduct.

Therefore, there may be very rare, exceptional circumstances for us to remove posted preprints from the platform. The DOI will remain resolvable, allowing readers to see the title and authors, but no PDF of the article will be publicly available, and a note will explain the reasons why it has been removed.

Where preprints have ethical concerns but are not deemed damaging to the wider Society, these will still go through full peer review and may have an additional note added to highlight the concerns.

The Microbiology Society is a member of the Committee on Publication Ethics (COPE), and will consult with the rest of the membership on cases that have not yet received formalised guidance to develop future policies that will safeguard the scientific record.

If you have comments on anything you have read here, we would love to hear from you. Please contact Alex Howat at [email protected].