Review Commons Experience

Some background
This post is about the publication process of our recent paper in Life Science Alliance titled “Evaluation of genetic demultiplexing of single-cell sequencing data from model species” via Review Commons (RC). I wanted to share our experience with RC as this is still quite new and I couldn’t find a lot of information about how the process actually works. For those of you unfamiliar with this service please find more info here. I really love the concept of RC because the review happens agnostic to any journal since you’ve submitted to a pre-print review service, and the reviews get publicly posted with the pre-print. In my eyes, this would mean the reviewers were not so fixated on the journal they are reviewing for and would be more focused on the science. In addition, the fact that you get to rebut the reviews on bioRxiv gives a nice way to make your dialogue with reviewers transparent and have a reviewed pre-print available online. The reason we submitted this to RC is because we believe in pre-prints and thought of this process as a new way of publishing a manuscript. Also, we are committed to publishing in non-for profit and open access journals and at the time of our submission, all of the journals affiliated with RC fit that description. That meant that wherever we decided to forward our paper to after review would be an acceptable journal for us. We submitted this to RC and were quickly assigned an editor who managed to find reviewers in good time. I like to imagine that people are more eager to review for a service like RC than for-profit publishers, but who knows. We submitted the manuscript on September 26th, directly from bioRxiv, it was sent out for review on October 11th and received the reviews on November 14th, so in total 49 days from submission to reviews. This seemed quite reasonable.

The reviews
The reviews were quite extensive from all three reviewers, which in my experience is not always the case. RC has a format that they ask for from their reviewers and I agree with these specific instructions. With this manuscript two of the three reviewers adhered quite closely to these guidelines (the reviews are publicly available with the pre-print or paper, so you can give them a read yourself. While two of the reviewers were quite focused on the science at hand, one was more interested in the novelty, or in their eyes the lack thereof. While we disagreed with the lack of novelty expressed by this reviewer (no one is using SNP-demuxing in any species except for humans!), we learned that this opinion was at least in part due to our need to better communicate the advances in our paper. Overall, we felt that these reviews were quite fair, and that we would be able to respond to them without issue. The main problem that I view with this concept of portable reviews is that if one of the three reviewers is negative, there is a good chance journals are going to be hesitant to take the paper. More specifically, if we are going to embrace portable reviews, the reviewers need to be aware that a negative review can have quite a big impact. When moving forward on what to do with this paper I was advised by some to make a new submission to a journal rather than addressing our most negative review. While we didn’t do this, it was tempting given what we felt one of the reviewers was unnecessarily negative. This unfortunately defeats one of the main advantages of using RC, as the RC model allows us to submit to up to four journals in their system without having to go back through the time consuming review process. This process of porting these reviews should, in concept, save time for both the authors and reviewers. For example, four separate submissions and review cycles should hypothetically require reviewing by twelve distinct reviewers (and likely many months of waiting), whereas with RC this would be three reviews in total. From the lab’s perspective, once we got the reviews and none were particularly critical of the science, we also felt less motivation to fight through the publication process. Anyone who wanted to see the reviews could and would be assured that it had gone through peer review and any issues that one would expect to be caught by review would be noted. Since we had the option to post a rebuttal, we also felt good that if someone took the time to read both the critiques and our response, then they wouldn’t be wary of the paper’s contents. Once the reviews were in hand we had to decide to either draft up a revision plan (i.e., a rebuttal with how we would address the reviews) or perform a full revision and submit this back to RC to be posted next to the pre-print. We opted for the former, thinking that once we submitted this to a journal it would be nice for the editor to see the revision plan and decide if they thought it was a good fit for the journal and if our rebuttal was sufficient to address the reviews. We reasoned that doing a full revision and then an editor feeling that this wasn’t sufficient or that other issues were more important would potentially lead to a waste of our time. I’m actually not sure if the reviewers are sent this revision plan or not (would be good to find out, for RC to make this more clear) as during the revision we ended up diverging a bit. In the end, we regret not going with a full revision prior to submitting to journals. We really upgraded the paper with the revisions and we believe that sending the journals just a revision plan may have led these journals to reject our manuscript out of fear that we would not follow through on our major revisions.

Publication process
This is my first paper as corresponding author and was definitely a learning process. We felt like this paper was quite important for our field and adjacent ones and we therefore hoped to prioritize journals with broad audiences. We submitted our manuscript directly through the RC portal without prior contact with editors. In hindsight, I think submitting pre-submission inquiries may be a good idea instead of these direct submissions. The editors we were suggesting were not getting the paper through the RC portal and I’m not sure if that was our fault or just how the system works (again first paper as corresponding author!). I feel that this is a bit of an issue with the RC process. When you submit directly to a journal, if the editor decides to send out a manuscript for review, they obviously have a positive enough feeling about the manuscript to take that step. With RC the editors get the paper and reviews/rebuttal after this first round of revision and likely don’t feel any attachment to the paper itself. Whether this is a good or bad thing in terms of bias, I’m not sure, but you definitely don’t have an editor “on your side”. We were pretty discouraged to have used up all four of our submissions (eLife, PLoS Biology, Development, and PLoS Computational Biology) via the portal. In total these submissions started on December 22nd and by February 2nd were complete. So ~6 weeks to submit to these four journals, not bad given that this was a big holiday period in many places.

What next?
We decided to then contact Life Science Alliance (LSA), but outside the RC portal since we weren’t allowed anymore submissions. A pre-submission inquiry linking the pre-print (which remember had the “revision plan”) was sent in and they quickly responded positively that they would like to see a revised version of the manuscript following the revision plan we had set out. We then submitted officially to the journal and continued to work on the revision. After resubmission they contacted RC to get info on who the original reviewers were, and re-sent our revised manuscript to them. The reviewers were extremely receptive of the revised manuscript and recommended it for publication! We were elated to hear the new opinions of these same reviewers, and to learn that our revisions addressed their concerns so completely. Everything was super smooth once we were in touch with editor Eric Sawey at LSA and I can only recommend the journal as super professional and efficient. We will definitely consider it in the future!

How could RC be improved, in our opinion?
We enjoyed the expedited review processes with porting reviews from journal to journal, but we believe that if we are going to embrace this concept of portal reviews that the reviews have to be done well. This doesn’t mean they can’t be critical, but comments like what we got on this manuscript: “Due to these reasons, I am not sure whether this manuscript has novelty sufficient for publication” are not helpful. It would also be nice to correspond with editors within the RC portal so that one can have more informal pre-submission inquiries within the portal instead of full submissions each time.

tldr
We would use RC again, but be more strategic about contacting editors directly via pre-submission inquiries. That said, with eLife’s new approach, our plan is to directly submit to eLife if we felt the paper had a chance there, and then try out Review Commons for direct submissions to journals that align with our values.
Get in touch if you want to hear more about our experience!

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