Reflections on Preprints (After >1 Year)

I’ve had this post brewing, as an update on my previous “Preprint Journey” post, for some time, since we hit the 1 year anniversary of our first preprint. ChemRxiv’s 2nd birthday finally got me off my schneid:

Over the past 15 months, we’ve have been some ups and downs, but we’ve learned a lot, which is the real reason for this post.
So lets start with a brief summary: since May 22, 2019, we’ve posted 5 preprints, with 4 now being published. Since we’re all about metrics, below is a look at the view and download stats for them all together, courtesy of ChemRxiv. ChemRxiv view and download stats since May 2019 Individually, just looking at downloads, they range from 53 for the latest preprint, from April 2019, to 329 for the still not published preprint from October 2018. The way I figure, this is 800+ PDFs that would otherwise not been downloaded, so win. Reflecting further, preprints provide an avenue to (legal) access to publications that end up appearing in closed access journals (without an embargo period as an author accepted version would have, see the SHERPA/RoMEO database of policies). While there are no-cost OA journals (use the Directory of Open Access Journals to find ’em, like the excellent Beilstein Journal of Nanotechnology), many—if not most—have fees, high ones at that. Preprints offer a compromise approach, of publishing in a closed-access, but no cost journal, which can be slow, while ensuring rapid dissemination and free access via the preprint.

Next, let’s start with some good developments: preprints are becoming more of a thing! You can see in the tweet above how ChemRxiv has grown and I’m seeing more and more familiar names in the ChemRxiv Twitter feed. Not to mention the stir created by the MicroED preprint (Altametric score currently >700) plus a preprinting Chemistry Nobel prize laureate, Frances Arnold. This is all fantastic and it means that Editors are more aware of preprints. Over the past year I’ve had multiple contacts with journal Editors who have said they actively monitor preprint servers and solicit submissions. We have been contacted twice regarding our preprints, but both times the preprint was already submitted. Thus, it may be worth holding off before submitting, not just to get feedback, but to get a solicitation from an Editor, eliminating the dreaded desk reject. Dr. Marshall Brennan who is in charge/behind ChemRxiv has proposed a #preprintmarketplace hashtag on Twitter to help connect authors and Editors. Unfortunately, at present it does not look like it’s really taken off.

Now to the “gotchas”: let’s talk about licenses. We ran into a snag with a journal/publisher that had a pro-preprint policy, but turned out to not accept manuscripts that had CC license. You can see the story unfold on Twitter, so here I will just summarize the important bits. Preprint licensing is not an area I had really considered; ChemRxiv by default uses CC BY-ND-NC, meaning permits reuse requires attribution (BY), but not modification (ND), or commercial use (NC)—these options are now explained, briefly, in the ChemRxiv FAQ. However—and this is important—this is not an exclusive license, meaning in the future the copyright holders (here us, the authors) can always grant additional permissions, including copyright transfer. So it’s not clear why this was an issue, but it was. Anyhow, I highly recommend taking a look at the ASAPBio license FAQ, which includes a marvelous infographic comparing the CC licensing options. Creative Commons also has a FAQ. (If anyone is curious, the issue ended up working out as follows: we agreed to select the paid OA option, they agreed to the submission, and in the end we got rejected.) Nota bene other preprint serves, e.g. bioRxiv, do offer an “All Rights Reserved” option, so that is a consideration.

As it turned out, the licensing issue was a minor snag and inconvenience, in comparison to what awaited us this April. Our submission (that was a preprint) was flagged as plagiarism and withdrawn. To make matters worse, the email provided no information regarding the source, etc.—not in-line with COPE guidelines. We tried contacting the Editor, but never got a reply. This was a major headache and source of stress and anxiety—I’m sure my lifespan was shortened. After a few days of sending emails to various addresses Journal/publisher staffinformed us that the system scored it as 93% overlap, case closed. But of course such a score meant that clearly their system was flagging it because of the preprint, which had been disclosed in the cover letter! Ultimately, the resolution came thanks to Dr. William Gunn, Director of Scholarly Communications for Elsevier whom I follow on Twitter. He got the Publishing Services Director involved who got the Publisher involved and eventually it was confirmed that the system had flagged our manuscript as plagiarism due to the preprint. In the end, it took a month to get the issue clarified and resolved. During this time, Dr. Marshall Brennan again provided support, by pointing out that ChemRxiv does iThenticate plagiarism checking of all submissions (and revisions) and revealing the similarity score of our preprint was a trivial percentage, so it was literally impossible for our manuscript to be 93% plagiarism of anything other than our preprint. I wish I had noticed this in the ChemRxiv FAQ, because it would have been reassuring to know right away. Unfortunately, in addition to the stress, this horrible month of limbo led to two manuscripts not being preprinted, as my boss had serious doubts/second thoughts about preprints. The moral of the story is that preprints are still kind of a new thing in chemistry/materials science, so be prepared to take some lumps and stick up for yourself. The good news is that with preprints and #ASAPChem becoming more of a thing, they will be more common place and soon these issues will be non-existent. In the end, about a month after the issue was resolved, we were back to preprinting…

Last topic: updating preprints. ChemRxiv is clear that preprints can be posted up until the manuscript is accepted by a journal (again, see the ChemRxiv FAQ). And preprints can—and should—be corrected, revised, etc. with all the revisions being part of the DOI. This is a really nice feature! But what about handling Reviewer comments? Can a preprint be revised based on that? Or not? Well, as the ChemRxiv FAQ points out, journal policies on this may vary—and they do! Just within ACS journals, there is a lot of variation with some journals (e.g. JACS, Langmuir) being permissive and some being clearly not (Inorganic Chemistry), and others, like ACS Sustainable Chem. Eng. making no mention in their author guidelines. So here is another thing to be aware of and be ready to contact the journal. In the case of our manuscript at ACS Sustainable Chem. Eng. the journal staff quickly responded to my email and informed us that we could only make corrections to the preprint and not upload the full revised version.

So to summarize, it’s been a bit of a rollercoaster, but totally worth it. From me, no second thoughts or doubts—I will be pushing to preprint every manuscript I’m involved in, because the benefits outweigh the snags. And the snags should be going away as awareness continues to grow. So, read up the FAQs linked above, check out the ASAPBio preprint info center, and get preprinting! And if you have any questions about our experience with preprints and ChemRxiv, do not hesitate to contact me on Twitter or via email.

Peter Sobolewski
Assistant Professor

My research interests include bioengineering and biomaterials.