Waiting to Happen: Publication lag times in Cell Biology Journals

My interest in publication lag times continues. Previous posts have looked at how long it takes my lab to publish our work, how often trainees publish and I also looked at very long lag times at Oncogene. I recently read a blog post on automated calculation of publication lag times for Bioinformatics journals. I thought it would be great to do this for Cell Biology journals too. Hopefully people will find it useful and can use this list when thinking about where to send their paper.

What is publication lag time?

If you are reading this, you probably know how science publication works. Feel free to skip. Otherwise, it goes something like this. After writing up your work for publication, you submit it to a journal. Assuming that this journal will eventually publish the paper (there is usually a period of submitting, getting rejected, resubmitting to a different journal etc.), they receive the paper on a certain date. They send it out to review, they collate the reviews and send back a decision, you (almost always) revise your paper further and then send it back. This can happen several times. At some point it gets accepted on a certain date. The journal then prepares the paper for publication in a scheduled issue on a specific date (they can also immediately post papers online without formatting). All of these steps add significant delays. It typically takes 9 months to publish a paper in the biomedical sciences. In 2015 this sounds very silly, when world-wide dissemination of information is as simple as a few clicks on a trackpad. The bigger problem is that we rely on papers as a currency to get jobs or funding and so these delays can be more than just a frustration, they can affect your ability to actually do more science.

The good news is that it is very straightforward to parse the received, accepted and published dates from PubMed. So we can easily calculate the publication lags for cell biology journals. If you don’t work in cell biology, just follow the instructions below to make your own list.

The bad news is that the deposition of the date information in PubMed depends on the journal. The extra bad news is that three of the major cell biology journals do not deposit their data: J Cell Biol, Mol Biol Cell and J Cell Sci. My original plan was to compare these three journals with Traffic, Nat Cell Biol and Dev Cell. Instead, I extended the list to include other journals which take non-cell biology papers (and deposit their data).

LagTimes1

A summary of the last ten years

Three sets of box plots here show the publication lags for eight journals that take cell biology papers. The journals are Cell, Cell Stem Cell, Current Biology, Developmental Cell, EMBO Journal, Nature Cell Biology, Nature Methods and Traffic (see note at the end about eLife). They are shown in alphabetical order. The box plots show the median and the IQR, whiskers show the 10th and 90th percentiles. The three plots show the time from Received-to-Published (Rec-Pub), and then a breakdown of this time into Received-to-Accepted (Rec-Acc) and Accepted-to-Published (Rec-Pub). The colours are just to make it easier to tell the journals apart and don’t have any significance.

You can see from these plots that the journals differ widely in the time it takes to publish a paper there. Current Biology is very fast, whereas Cell Stem Cell is relatively slow. The time it takes the journals to move them from acceptance to publication is pretty constant. Apart from Traffic where it takes an average of ~3 months to get something in to print. Remember that the paper is often online for this period so this is not necessarily a bad thing. I was not surprised that Current Biology was the fastest. At this journal, a presubmission inquiry is required and the referees are often lined up in advance. The staff are keen to publish rapidly, hence the name, Current Biology. I was amazed at Nature Cell Biology having such a short time from Received-to-Acceptance. The delay in Review-to-Acceptance comes from multiple rounds of revision and from doing extra experimental work. Anecdotally, it seems that the review at Nature Cell Biol should be just as lengthy as at Dev Cell or EMBO J. I wonder if the received date is accurate… it is possible to massage this date by first rejecting the paper, but allowing a resubmission. Then using the resubmission date as the received date [Edit: see below]. One way to legitimately limit this delay is to only allow a certain time for revisions and only allow one round of corrections. This is what happens at J Cell Biol, unfortunately we don’t have this data to see how effective this is.

lagtimes2

How has the lag time changed over the last ten years?

Have the slow journals always been slow? When did they become slow?  Again three plots are shown (side-by-side) depicting the Rec-Pub and then the Rec-Acc and Acc-Pub time. Now the intensity of red or blue shows the data for each year (2014 is the most intense colour). Again you can see that the dataset is not complete with missing date information for Traffic for many years, for example.

Interestingly, the publication lag has been pretty constant for some journals but not others. Cell Stem Cell and Dev Cell (but not the mothership – Cell) have seen increases as have Nature Cell Biology and Nature Methods. On the whole Acc-Pub times are stable, except for Nature Methods which is the only journal in the list to see an increase over the time period. This just leaves us with the task of drawing up a ranked list of the fastest to the slowest journal. Then we can see which of these journals is likely to delay dissemination of our work the most.

The Median times (in days) for 2013 are below. The journals are ranked in order of fastest to slowest for Received-to-Publication. I had to use 2013 because EMBO J is missing data for 2014.

Journal Rec-Pub Rec-Acc Acc-Pub
Curr Biol 159 99.5 56
Nat Methods 192 125 68
Cell 195 169 35
EMBO J 203 142 61
Nature Cell Biol 237 180 59
Traffic 244 161 86
Dev Cell 247 204 43
Cell Stem Cell 284 205 66

You’ll see that only Cell Stem Cell is over the threshold where it would be faster to conceive and give birth to a human being than to publish a paper there (on average). If the additional time wasted in submitting your manuscript to other journals is factored in, it is likely that most papers are at least on a par with the median gestation time.

If you are wondering why eLife is missing… as a new journal it didn’t have ten years worth of data to analyse. It did have a reasonably complete set for 2013 (but Rec-Acc only). The median time was 89 days, beating Current Biology by 10.5 days.

Methods

Please check out Neil Saunders’ post on how to do this. I did a PubMed search for (journal1[ta] OR journal2[ta] OR ...) AND journal article[pt] to make sure I didn’t get any reviews or letters etc. I limited the search from 2003 onwards to make sure I had 10 years of data for the journals that deposited it. I downloaded the file as xml and I used Ruby/Nokogiri to parse the file to csv. Installing Nokogiri is reasonably straightforward, but the documentation is pretty impenetrable. The ruby script I used was from Neil’s post (step 3) with a few lines added:


#!/usr/bin/ruby

require 'nokogiri'

f = File.open(ARGV.first)
doc = Nokogiri::XML(f)
f.close

doc.xpath("//PubmedArticle").each do |a|
r = ["", "", "", "", "", "", "", "", "", "", ""]
r[0] = a.xpath("MedlineCitation/Article/Journal/ISOAbbreviation").text
r[1] = a.xpath("MedlineCitation/PMID").text
r[2] = a.xpath("PubmedData/History/PubMedPubDate[@PubStatus='received']/Year").text
r[3] = a.xpath("PubmedData/History/PubMedPubDate[@PubStatus='received']/Month").text
r[4] = a.xpath("PubmedData/History/PubMedPubDate[@PubStatus='received']/Day").text
r[5] = a.xpath("PubmedData/History/PubMedPubDate[@PubStatus='accepted']/Year").text
r[6] = a.xpath("PubmedData/History/PubMedPubDate[@PubStatus='accepted']/Month").text
r[7] = a.xpath("PubmedData/History/PubMedPubDate[@PubStatus='accepted']/Day").text
r[8] = a.xpath("MedlineCitation/Article/Journal/JournalIssue/Pubdate/Year").text
r[9] = a.xpath("MedlineCitation/Article/Journal/JournalIssue/Pubdate/Month").text
r[10] = a.xpath("MedlineCitation/Article/Journal/JournalIssue/Pubdate/Day").text
puts r.join(",")
end

and then executed as described. The csv could then be imported into IgorPro and processed. Neil’s post describes a workflow for R, or you could use Excel or whatever at this point. As he notes, quite a few records are missing the date information and some of it is wrong, i.e. published before it was accepted. These need to be cleaned up. The other problem is that the month is sometimes an integer and sometimes a three-letter code. He uses lubridate in R to get around this, a loop-replace in Igor is easy to construct and even Excel can handle this with an IF statement, e.g. IF(LEN(G2)=3,MONTH(1&LEFT(G2,3)),G2) if the month is in G2. Good luck!

Edit 9/3/15 @ 17:17 several people (including Deborah Sweet and Bernd Pulverer from Cell Press/Cell Stem Cell and EMBO, respectively) have confirmed via Twitter that some journals use the date of resubmission as the submitted date. Cell Stem Cell and EMBO journals use the real dates. There is no way to tell whether a journal does this or not (from the deposited data). Stuart Cantrill from Nature Chemistry pointed out that his journal do declare that they sometimes reset the clock. I’m not sure about other journals. My own feeling is that – for full transparency – journals should 1) record the actual dates of submission, acceptance and publication, 2) deposit them in PubMed and add them to the paper. As pointed out by Jim Woodgett, scientists want the actual dates on their paper, partly because they are the real dates, but also to claim priority in certain cases. There is a conflict here, because journals might appear inefficient if they have long publication lag times. I think this should be an incentive for Editors to simplify revisions by giving clear guidance and limiting successive revision cycles. (This Edit was corrected 10/3/15 @ 11:04).

The post title is taken from “Waiting to Happen” by Super Furry Animals from the “Something 4 The Weekend” single.

0 thoughts on “Waiting to Happen: Publication lag times in Cell Biology Journals

  1. Thanks for putting forward this creative method of examining the speed with which various journals publish. We are disappointed that Molecular Biology of the Cell could not be included in your analysis and are looking into why the received, accepted, and published dates for MBoC articles are not available on PubMed. It is certainly not by design. We do not intend to hide such information, and the received and accepted dates do appear for each article published on our site at HighWire and in PubMed Central.

    The MBoC editorial board is working hard to find ways to get articles out quickly. It takes a median of only 27 days for us to reach a first decision on articles that are sent to peer review. And we publish accepted papers in manuscript form within two weeks of acceptance. We feel that those statistics are a good measure of the journal’s performance. Monitoring Editors are strongly encouraged to expedite publication first by providing authors with clear guidance of what is expected of them as they revise manuscripts and second by whenever possible making decisions about revised manuscript without sending them back to reviewers.

    It can be complicated to interpret times from receipt to acceptance or receipt to publication, since those intervals include time when articles are out of the journal’s hands and are undergoing revision by the authors. As you note, journal policies about the length of time allowed for revision and the number of revisions permitted may have a significant influence on those intervals. But in some cases authors may be best served if a journal is willing to allow them time to make the major revisions that may be necessary to get an article to the point where it is a valuable contribution. Rejecting an article because it cannot be revised quickly may ultimately delay its publication even further by throwing it back into peer review at another journal. Seeing potential in a flawed article is one of the challenges an editor faces, and arbitrary revision time limits may not always be in the best interest of science.

    Mark Leader, ASCB Publications Director

    1. Mark,

      Thank you for your comment. I agree that the time to first decision is a really useful metric and probably the most informative when thinking about where to submit. This information is not readily available for most journals. A central repository of these kinds of statistics would be really useful, e.g. number of MS submitted, sent out, accepted, time to first decision, time get the paper online etc. The numbers for MBoC sound great and I’d love to see how they compare with other cell biology journals.

      I also agree that interpreting the times in my post is not straightforward. Partly because the data are undermined by clock resetting at some journals and not others. Leaving that aside, it’s clear that long delays only partly reflect on the journal. Most of the time taken is in revising the paper (doing more experiments). The blame for this delay is shared between the authors, reviewers and editors. Speeding all of this up is complicated.

      It’s great that MBoC are looking into the deposition of dates in PubMed. It might be possible to scrape them from PMC… anyway, thanks for responding.

      Steve

  2. I read your articles when they appear on the bioRxiv and become public. I think that everybody should use the bioRxiv and then the time delays for peer review, typesetting, proofing and waiting for print space become irrelevant.

    1. Absolutely. This would also settle the question of priority in cases where the journal has reset the clock on your submission. We’ve used bioRxiv, but I’m still reticent for some manuscripts that we might send to journals who do not accept preprinted papers.

  3. I’ve been told that HighWire Press, which hosts Molecular Biology of the Cell (as well as The Journal of Cell Biology), is working on a global update to its PubMed deposits, to include the received, revised, and accepted dates in the deposits. No timeline was provided, but at some point in the future the raw data for calculating lag times for these journals should be available.

  4. My last submission to JCB was well refereed, with a number of suggestions. The editor wrote back fully rejecting the paper, with a rider that if we submitted it again with the comments addressed, he would send it back to the same referees for comments. In other words, returning it for revisions.

    I’ve come to the conclusion that this was just a silly game, a way of making it look like their turnover time is shorter than it really is. I’ve consequently decided not to send anything else to JCB for the next few years. If the scientist-owned journals play games at scientists’ expense, what’s the point of them?

    1. Thanks for the comment Robert. I also think this is the purpose of the “hard reject but open door” decision. My opinion is that revisions take as long as they and the journals shouldn’t try and hide this.

      I’m curious to know where you’d prefer to send your work, if not to scientist-owned journals? In defence of JCB, it’s a good journal, well run; I’ve generally had a sane experience publishing there. I think all journals are doing this so I don’t see what good refusing to send your work there will do.

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