Accelerating Science with Preprints

This week ASAPbio is happening in Washington DC. This is an important meeting, being held with the support of HHMI and the NIH, devoted to exploring and encouraging the use of preprints in biology. Therefore, we thought it would be timely to explain how PeerJ Preprints works (one of very few venues for biology preprints). Also, for more context, see this guest blog post on Scientific American (from the time of the launch of PeerJ Preprints) and another explainer by us.

At PeerJ (the organization) we have two peer-reviewed journals, ‘PeerJ’ (taking its name after the organization) and ‘PeerJ Computer Science’. We also have the un-peer reviewed ‘preprint server’, ‘PeerJ Preprints’.

A preprint is effectively a piece of academic content which is still ‘in progress’ or before it has been submitted for peer review. Authors can use preprints to ‘claim priority’, to get early feedback on a manuscript, or to drive attention to a topic (for example an upcoming conference). There is evidence that work which is first published as a preprint will go on to gain more citations once it is ‘formally’ published and so many authors increasingly regard preprints as a good way to get their work ‘out there’ as early as possible.

Preprint servers have long been popular in the physics and mathematics communities (you may have heard of arXiv, the original preprint server (now 25 years old and currently posting ~100K preprints per year), however, until recently there were very few options for biologists who wanted to post a preprint. Nonetheless, ‘preprinting’ in biology is rapidly growing in popularity. Every month more and more preprints are published, and right now PeerJ Preprints (which only launched in April 2013) has already published almost more than 2,100 preprints (400 with multiple version updates). Therefore, we are pleased to be attending the ASAPbio meeting to help contribute to the wider debate and to encourage greater use of preprints in the biological sciences.

At PeerJ Preprints, it is free to publish as many preprints as you want. Authors simply upload a PDF (together with some metadata) and after basic staff checks, the preprint is typically online in fewer than 24 hours. Because of the simplicity of the process, preprints can be used for things like abstracts, posters, presentations, opinion pieces, rebuttal arguments, protocols, single observations and so on, as well as drafts of full manuscripts of course.

Authors can use PeerJ Preprints as a ‘standalone’ service (and submit their preprint to any other journal of their choosing, or not), or they can use it as part of their submission workflow to either of our journals. When submitting, authors can start the process with a peer-reviewed submission and ‘transfer it’ over to PeerJ Preprints, or they can start out as a preprint, gain feedback from the community, and then ‘transfer it’ over to be a peer-reviewed submission. When transferring from one route to the other we are able to ‘link’ the two submissions together, and thus minimize the amount of duplicate data entry that might be needed.

When a preprint is submitted, it is first checked by staff to make sure the format is correct; various of our standard requirements have been met (such as ethical or IRB approvals); that it is in scope and so on, however other than this staff check the article is not formally reviewed. Assuming it passes our checks, the preprint then goes online within ~24 hours. Preprints are prominently flagged as being “not peer reviewed” and the PDF is also marked with a bold orange header on each page explaining that this is an “un-peer reviewed preprint”.

Once online, readers can ‘ask questions’, ‘leave feedback’ or ‘post links’ to related content and each time this happens, the authors are alerted and encouraged to respond. Via this process, we have seen many preprints incrementally improved, via multiple versions, before being submitted for formal peer-review (approximately 20% of our preprints have multiple versions). In fact, right now a PeerJ preprint on our site (regarding the issue of gender effects in Github pull requests) is receiving considerable attention and extensive feedback, which the authors will presumably use to improve their article before submitting for peer-review.

Unlike some other services, all PeerJ Preprints are ‘fully’ open access using the gold standard CC BY 4.0 license, or Public Domain licensing. Published preprints receive a DOI, they are archived at industry standard locations (for example Portico), and they are indexed by Google Scholar.

Authors can update their preprint with multiple versions (perhaps in light of feedback they received), and when they do so, each version has a prominent link to the more ‘up to date’ version. If the preprint is eventually published as a peer-reviewed version at PeerJ then it will also prominently state that fact, and point to the peer-reviewed version (and vice versa).

It is in no way compulsory, or even expected, that a preprint author will go on to submit their preprint for peer-review at PeerJ, however we are finding that approximately 60% choose to do so which is very encouraging for the popularity of preprinting. Of course, many authors choose to submit their article to other journals, and there is a growing list of journals which are happy to accommodate this process.

If a preprint is also submitted for peer-review, then if it has received any feedback we make sure that we alert the Academic Editor handling that submission, and we encourage them to also take the feedback into account when managing the peer-review process for the manuscript.

Assuming a preprint ends up getting through peer-review and ends up being published as a peer-reviewed article then the preprint will note this fact (and point readers to the published article) and the peer-reviewed article will also indicate to readers that there was an earlier preprint. When this is combined with the authors making their full peer-review history public (something which ~80% of authors choose to do) then the complete history of the development of the article is made public – a very powerful thing for any interested readers!

So that is PeerJ Preprints in a nutshell – we encourage you to give it a try and post your next article as a preprint first!

Pete Binfield
Co-founder and Publisher