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A systematic examination of preprint platforms for use in the medical and biomedical sciences setting

Jamie J Kirkham, Naomi Penfold, Fiona Murphy, Isabelle Boutron, John PA Ioannidis, Jessica K Polka, David Moher

Preprint posted on April 28, 2020 https://www.biorxiv.org/content/10.1101/2020.04.27.063578v1

Article now published in BMJ Open at http://dx.doi.org/10.1136/bmjopen-2020-041849

New to preprints and trying to figure out which preprint repository is suitable for your work? This database can help you find the right platform.

Selected by Sejal Davla

Publication norms are changing in the biological sciences with the arrival of preprint platforms that allow scientists to post manuscripts before peer-review. While physicists and mathematicians had the access to preprint repositories such as arXiv since the early 1990s, preprints were not widely accepted in life sciences until the launch of the first preprint server in 2013. Since then preprint submissions have gained popularity among all fields in biology1 and the coronavirus pandemic has skyrocketed the number of preprints in the last three months2. Therefore, preprint repositories are becoming even more crucial to disseminate scientific knowledge in a speedy manner to the community during the pandemic.

As preprints become widely accepted, there are many misconceptions about how preprint platforms function and what policies they employ. Kirkham and colleagues provide a searchable repository of 44 currently available preprint platforms in biology and medical sciences and compare and contrast their key features and policies. As a preprint and open science advocate, I find this work crucial to weigh in the pros and cons of preprint servers and use them to make evidence-based improvements in the dissemination of scientific knowledge.

There are several questions and misconceptions among researchers regarding preprint platforms. Some of the key attributes addressed by Kirkham et al are highlighted here.

  1. Who owns preprint servers? Two-thirds of platforms curated in this report are owned by scientific societies, non-profit academic groups, or funding organizations. The rest of the platforms are associated with for-profit companies or publishers. All for-profit and non-profit preprint platforms are free for authors to post a preprint. F1000 Research that provides peer-review and other publishing services requires a processing fee from the authors much like a journal.
  2. Is there a pre-screening of contents before publication? Contrary to popular belief and concerns over the quality of preprints, most platforms have an initial screening protocol that is completed within a week. The vetting process includes checks on scientific content, plagiarism, ethical and legal concerns, and compliance. bioRxiv and medRxiv, which are amongst the largest repositories also screen the content to check whether the preprint could be harmful to human health. One-third of repositories even involve researchers to screen for the relevance of content.
  3. Who can view a preprint? Most preprint platforms offer full access to preprint content to everyone, however, some new ‘First Look’ platforms such as Sneak Peek from Cell Press require user registration.
  4. What is the relationship between journal submission and preprint platforms? It remains one of the biggest concerns for the authors whether the journal of their choice will accept a preprint. The success of preprints in physics and other domains somewhat influenced journals in the biological sciences to welcome the use of preprints3 and the number of journals accepting preprints is burgeoning1. An important feature some platforms offer is to facilitate the transfer of manuscripts between preprint servers like bioRxiv and submission to journals. Preprint platforms like F1000 Research and Sneak Peek from Cell Press accept preprints only if authors submit their manuscript to their associated partner journals.
  5. Can I submit my preprint to any repository? The author has to choose a platform based on their area of research as well as where the work was conducted. Half of the platforms included in this study cover articles from multidisciplinary research. Several niche platforms exist that cater to specific subject areas or community-based objectives such as sharing work in non-English languages. There also exist regional preprint platforms that are restricted to a geographical location. For example, repositories in Africa, China, France include research work carried out in that specific geographical area.
  6. Do preprint platforms allow only manuscripts? The goal of preprints is to facilitate rapid distribution of scientific knowledge. Some platforms also allow project reports and presentations and there are designated platforms just for theses such as Thesis commons.
  7. What kind of user metrics preprint servers provide? The most common metric used by online preprint platforms is the number of downloads.
  8. Does publishing a preprint put me in trouble with funding agencies? Central funding agencies such as NIH and Wellcome Trust encourage preprint submissions prior to peer-review and allow them in grant applications. Platforms such as Open Research Central accept work funded by a specific group of funding agencies.
  9. Where can I find more information? A searchable database consisting of 44 preprint platforms is publicly available at https://asapbio.org/preprint-servers.

References:

  1. Abdill RJ, Blekhman R. Tracking the popularity and outcomes of all bioRxiv preprints. Elife. 2019;8:e45133. Published 2019 Apr 24. doi:10.7554/eLife.45133
  2. Nicholas Fraser, Liam Brierley, Gautam Dey, Jessica K Polka, Máté Pálfy, Jonathon Alexis Coates. Preprinting a pandemic: the role of preprints in the COVID-19 pandemic. bioRxiv 2020.05.22.111294; doi:10.1101/2020.05.22.111294
  3. Cobb M. The prehistory of biology preprints: A forgotten experiment from the 1960s. PLoS Biol. 2017;15(11):e2003995. Published 2017 Nov 16. doi:10.1371/journal.pbio.2003995

Questions for the authors:

  1. During the ongoing pandemic, some preprint platforms are changing their policies and not accepting certain kinds of work. Does this defy the purpose of preprints in your opinion?
  2. Are there additional screening measures that need to be employed by preprint repositories to limit the publishing of bad science?
  3. One of the biggest benefits of preprints is that authors receive feedback from everyone. Are there any repositories that do not allow/limit user engagement?
  4. Who initiates removal/retractation of preprints from the platform? Is it solely the responsibility of the platform? Do preprint platforms permanently remove objectionable content?
  5. Do First Look platforms that have partner journals offer preprints free-of-charge/without journal subscription?
  6. Are there any disadvantages to using platforms that do not provide DOI vs the ones that do?
  7. Do all preprint platforms archive manuscripts that are retracted?

Tags: open science, preprint, preprint platforms

Posted on: 18th July 2020

doi: https://doi.org/10.1242/prelights.23194

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Author's response

Naomi Penfold (NP) and Jessica Polka (JP) worked together on these answers. Initials are used to attribute perspectives, and both have reviewed each other’s work. shared

1. During the ongoing pandemic, some preprint platforms are changing their policies and not accepting certain kinds of work. Does this defy the purpose of preprints in your opinion?

NP: As we see from many researchers’ hesitation to read or post preprints, some element of quality control is important. Readers don’t want to have to filter through a lot of content that they don’t think is ready for them to read yet. And the current pandemic has really brought into focus the responsibility that any content hosts and disseminators have: we see that news spreads fast online, and it’s hard to revise any early impressions once the information is evaluated – many people will hear “X causes Y” and never spend time checking back in on whether that’s true in the end. As long as it’s easy for people to spread content before (and sometimes despite) any reviews come in and the community establishes what is agreed and disputed, I think it’s sensible for preprint platforms to adapt to the situation at hand, and prioritize protecting human health.

What I think is important in this case is that any quality control measures are decided by and the process involves a diverse set of researchers, and maybe even other stakeholders who have an interest in trusting the quality control process.

JP: Even preprint servers with very lightweight screening processes do exclude content they deem to be non-scientific or otherwise out of scope, so there is always some degree of subjective judgement there.

2. Are there additional screening measures that need to be employed by preprint repositories to limit the publishing of bad science?

NP: I think preprint platforms are useful for supporting more people to be included in scientific discourse, whether sharing their findings with a manuscript or assessing other people’s manuscripts and providing feedback and review.

Following on from your first question – I think we’re talking here about content that is not deemed harmful to human health. Readers should be prepared to critically evaluate preprints themselves, and I think it is useful to remind readers of that responsibility. Of course, platforms can help readers out by filtering out obviously inappropriate, potentially harmful or pseudoscience content so the reader needs only to read and evaluate scientific content. However, I think the concept of “bad science” is one that can easily lead to bias – if this form of gatekeeping is used, I think it needs to be done in a way that allows the research community to be able to understand and trust the process by which science is being judged as “bad” or “good’. Further, whether or not “bad science” is shared, I think it is useful for the community to share what they mean when they judge something as “bad science” – so anyone contributing to a field of research can be aware of the standards that the others in the field expect from them: as well as sharing feedback directly to the authors, I would support greater transparency in the overall decisions made by any preprint platforms as to whether or not a preprint submission should be posted online.

In time, we expect to see more peer review happening on preprints, and I hope preprint platforms will continue to support readers to assess any preprints for themselves, and benefit from any peer reviews of the content that are already available – whether a traditional review or other kinds of indicators. It would be useful to be able to evaluate how much review a preprint has received too, so the reader knows to what degree content has been critically evaluated by the time they are reading it.

JP: These standards for science can change rapidly, or the need to communicate them may change rapidly, and we have seen this recently with COVID-19 research. For example, not without some controversy, medRxiv and bioRxiv decided against considering papers that rely on in-silico predictions of drug efficacy, reasoning that the potential damage to public health outweighs the benefit of early dissemination.

Even informal comments on a preprint can be very valuable in correcting the record. For example, a notorious preprint claiming similarity between SARS-CoV-2 and HIV was withdrawn by authors within 2 days of posting after the paper received many critical comments.

3. One of the biggest benefits of preprints is that authors receive feedback from everyone. Are there any repositories that do not allow/limit user engagement?

NP: For providing feedback to authors, I don’t know of any platform for which the author names, affiliations and contact information are not clear, even if that is within the PDF of the preprint itself – so feedback provision is not limited.

Nonetheless, it’s interesting you use the word ‘engagement’ there. Allowing comments, annotations, likes, or other forms of interaction to provide public feedback on a preprint is one thing. But when feedback interactions like this happen, I think it’s important to notify the preprint author(s) and anyone who has shown an interest in the preprint (like you might bookmark something to follow or read later). This is what will bring them back to the preprint to check in on the new feedback and see if that affects their own understanding. I think one of the reasons Twitter is used for talking about new preprints is that people can easily get involved in the conversation and follow it. So, in answer to your question, I think that until there is a good experience with how authors and readers follow the conversation around a preprint, all true ‘engagement’ is limited.

4. Who initiates removal/retractation of preprints from the platform? Is it solely the responsibility of the platform?

NP: Most platforms will respond if any author or reader flags an issue that could mean withdrawing a preprint, and most platforms will be the ones who actually withdraw or remove the preprint, following their process. To maintain the scholarly record, it is preferable to withdraw (leave the content on the web, but clearly mark it as withdrawn and provide a reason where possible). Sometimes content is removed completely – if that’s in the first few days of its release then it may not affect the citation trail much. There are cases where content is removed after many months, and that makes it more likely that someone may have cited work that is now no longer available.

JP: We are working with attendees of a recent workshop, #bioPreprints2020, to propose standard definitions for withdrawal and removal (which is necessary under certain legal or ethical circumstances) and conditions under which those terms and procedures might be used.

5. Do First Look platforms that have partner journals offer preprints free-of-charge/without journal subscription?

NP: The content shared on some journal-associated platforms on SSRN, such as Preprints with the Lancet and Cell Sneak Peek, require readers to register and log-in in order to view the full content. These accounts are free-of-charge and are not the same as a paid subscription, as far as we are aware.

6. Are there any disadvantages to using platforms that do not provide DOI vs the ones that do?

NP: DOIs provide a persistent identifier and web address for content, even if the host’s URL for the content changes. This makes them useful for citation practices. However there are many citable forms of communication that do not have DOIs, including webpages and blog posts, so not having a DOI does not necessarily mean your preprint could not be cited. In academia, DOIs are also viewed as important for showing the legitimacy of a piece of content: whether in a reference list for your own manuscript or when presenting your own works in grant and job/promotion/tenure applications.

7. Do all preprint platforms archive manuscripts that are retracted?

NP: The majority of preprint platforms use a service to archive their content, and what this will mean in practice depends on the service agreement. However, it is common for journals and preprint platforms to use a mechanism called ‘dark archiving’, which means that the content is preserved but not accessible unless a condition is ‘triggered’, such as the preprint platform ceasing operations (and therefore not being able to host the content itself anymore). The service agreements are not publicly available, and we do not know whether retracted content is included in the archiving agreement for preprint platforms.

If you’d like to find out more, the service commonly used by preprint platforms is Portico, and their website describes their service in greater detail. You can look up what they preserve by searching by the publisher (for example, bioRxiv and medRxiv are preserved, listed under Cold Spring Harbor Laboratory as the publisher).

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