Pandelis Perakakis

Why think twice before submitting a preprint to bioRxiv

To explain my reasons for not supporting bioRxiv let me first restate my vision for the future of scholarly communication. As I argued back in 2010, all scientific content (papers, data, software code, etc) should be archived in a distributed network of public, open access infrastructure (e.g., institutional repositories) that will facilitate overlay services (e.g., peer review, data mining), preferably developed by volunteer academic societies and non-profit organisations using open source tools. In our 2010 NSAP paper this network was called the Global Open Archive (GOA). Today, it is the distributed network COAR promotes in its Next Generation Repositories project.

The road towards this future has several important milestones, one of them being the wide adoption of Green Open Access practices. This means that, instead of looking for OA journals to publish their work, researchers should publish their papers wherever is more suitable for them, making sure that they also post the final peer-reviewed version to a qualified (e.g., ensuring permanent archiving and interoperability) OA repository. The specific workflow many others and I propose is described in more detail here and here.

It is easy to see that this workflow is in tension with the Gold OA model, where journals and their publishers remain the central player in a competitive market, merely switching their business model from pay-to-access to pay-to-publish. For obvious reasons, the gold model is constantly being presented as the only viable solution to the accessibility problem, undermining the importance of other more transcendent issues stemming from the current journal-based system.

Having clarified this, I now come to my problem with bioRxiv. BioRxiv is the only, to my knowledge, OA article repository that does not allow authors to upload the final journal-published version of their papers (also called VOR, which stands for version of record). I was surprised to discover this when I tried to update one of my own preprints right after I received the acceptance letter from the journal. Curiously, bioRxiv already knew that the manuscript had been accepted, meaning that there had been some kind of communication with the publisher of the journal —which by the way was Elsevier. After raising this issue on twitter, bioRxiv founder Richard Sever replied that the reason for this policy is technical and related to the issuing of DOIs.

Regardless the reasons behind bioRxiv’s VOR policy, its outcome is very clear. In a green OA workflow, authors that submit their preprint to bioRxiv have to find a second repository to publish the final version of their paper once it is accepted by a journal. Apart from the unnecessary extra effort, this also means that a paper can now have three online versions with three different DOIs: bioRxiv, journal, and open access green repository. This makes bioRxiv the first green unfriendly OA repository and produces an artificial and seemingly unjustified distinction between the two fundamental functions of self-archiving: early dissemination and green OA.

An obvious reason for wanting to make this distinction is that early dissemination through a preprint archive is perfectly aligned with gold OA and therefore —contrary to green OA— poses no threat to the current journal/publisher academic validation, evaluation and communication system. In the words of Joseph Esposito (@JosephJEsposito), management consultant for the publishing industries:

Gold OA represents a business opportunity, whereas Green OA represents a business problem.

Again on twitter, responding to my concerns about bioRxiv, Stephen Curry, one of its strong supporters and listed as affiliate member on the website, explicitly revealed his preference for gold OA.

In a complex ecosystem undergoing a phase transition, even the slightest perturbation may determine the final stable state. In our case, academic publishing is about to exit a period of strong turmoil and stabilise around one of two alternative attractors, either a mutation of the current commercially-driven state, or a science-centred state built on federated public infrastructure. In this complex landscape, favouring one service over another is a crucial choice that should be made with responsibility, knowing that it may eventually make the difference between one future or the other.

Yes, bioRxiv seems like a good thing, accelerating scientific communication and all that, but at the end of the day it is part of an ecosystem we should be trying hard to disrupt and radically transform. I will not repeat here why gold OA may make things worse than they currently are. For elaborate arguments you can have look here and here. I simply wish to clarify that there is absolutely no reason for using bioRxiv instead of other repositories that support green OA (e.g., arXiv, PeerJ preprints, all OSF-powered repositories, all institutional repositories). Knowing this, it surprises me to see influential open science advocates, whose work I otherwise admire and support, to wrongly advertise bioRxiv as part of a green OA workflow where clearly it does not belong. We are all responsible for choosing more carefully which tools, services, platforms, infrastructures we use and support. In the near future these apparently innocent choices will translate into abysmal differences in how we do and communicate science.

13 thoughts on “Why think twice before submitting a preprint to bioRxiv”

  1. I wasn’t aware biorXiv are the only ones doing this. You are right, this is a problem. Could one circumvent it by simply uploading all versions before one submits them to the journal? In that way, the VOR would also be on biorXiv, even before anyone knows it will be the VOR?

    1. This article confuses the publisher-formatted VoR (which very few publishers allow to be uploaded, and which isn’t required for Green OA compliance) with the author-formatted AAM (incorporating all revisions to the manuscript)

      Thus AAMs by definition cannot be uploaded before submission. Depending on how automatic and how fast the communication between biorXiv and the publishers is, maybe there is a brief window of time to upload immediately after the acceptance is sent, but that hardly seems like a solution.

      I cannot see any author-friendly reason for this policy, it is purely in the publishers’ benefit.

      1. Thank you for this clarification. Although it hardly changes the main message of the article, I agree that we can better define the problem as biorxiv’s policy not to accept the AAM.

      2. Sorry, I meant that authors could just upload each (not all, sorry for the confusion) version to biorXiv before they upload them anywhere else. Thanks for pointing out my mistake.

          1. If the author has not yet signed a copyright transfer agreement (which typically happens only upon acceptance) there is no copyright issue.

  2. Thank you for this important post. I also didn’t know that bioRxiv does not allow VOR uploads (thus is a problem for Green OA). I would like to be sure that it authorizes AAM upload (although it probably has no mean to distinguish an AAM from a normal intermediate preprint version before a new DOI is issued).
    As Jessica says, authors should be able to do what they want with their AAM as soon it’s before they transfer their copyright

  3. I re-read my preprint about preprint servers the other day It looks like the conclusions still hold: “It appears that open science is just one focus of preprint servers and further improvements will be dependent on preprint server policies and priorities rather than overcoming any technical difficulties”, just replace ‘open science’ with ‘green OA’ or whatever else you think preprint servers should achieve.

    For we take the view that we don’t want to be a repository and won’t post anything that’s already published. However, when it comes to updating we take the view that we’ll post an author accepted version or whatever else the publisher allows to make the link to the latest version as clear as possible.

    I don’t personally agree with the bioRxiv policy, but I can see where they’re coming from. Their aim isn’t green OA and posting AAMs creates work for them. At the end of the day, as with journals, authors have a choice of preprint servers: if you want more options than just CC BY then don’t post with, if you are really behind green OA, then avoid bioRxiv.

  4. I don’t think this really changes much for me with respect to my views on BioRXiv. The condition that the article must be unpublished at the time of submission is in the submission guide: “An article may be deposited in bioRxiv in draft or final form, provided that it concerns a relevant scientific field, the content is unpublished at the time of submission, and all its authors have consented to its deposition.”

    So if you want to deposit your accepted manuscript in BioRxiv I think you can, provided you are posting or updating your manuscript prior to acceptance. In other words, if you post/update to BioRxiv as you submit/resubmit, you will be making your AAM available via bioRxiv. You should still post your AAM to your institutional repository (or if the journal is OA, your final copyedited/typeset VOR). But bioRxiv is probably just using this mechanism to ensure they are in the clear with respect to copyright.

    1. That doesn’t sound right, though – some publisher policies specifically forbid the uploading of the AAM, and whether the authors do it before or after the final acceptance doesn’t really matter, as far as I know (at least not when it comes to the obligations of the authors, copyright law might possibly be different).

      1. Well if you’re submitting to a publisher that doesn’t allow you to update your preprint as your manuscript moves through peer review then that’s not really bioRxiv’s fault. It sounds more like Wiley are the bad guys for forbidding anything other than the submitted (not peer reviewed) version being posted to a preprint ( Even Elsevier allows updating preprints ( although they only say it’s OK on airxiv and repec and so it’s a bit ambiguous. Again that’s not bioRxiv’s fault. As long as you update your preprint while it’s a pre-print (i.e. not yet published) they should take your updates.

  5. Pingback: Where to deposit your preprint – Peer Community In

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