March highlights from the world of scientific publishing

An update on what I learnt from Twitter last month: dodgy citation metrics, mislabelled papers and journals and more.

Metrics

A wonderful Perspective piece appeared in the open access journal mBio entitled Causes for the Persistence of Impact Factor Mania. Here, Arturo Casadevall (Editor in Chief of the journal) and Ferric C. Fang treat the misuse of the journal impact factor as if it were a disease and suggest possible causes and treatments. They diagnose the main problem as: “Publication in prestigious journals has a disproportionately high payoff that translates into a greater likelihood of academic success” and that these disproportionate rewards “create compelling incentives for investigators to have their work published in such journals. ” Their solutions are not new but worth reading. (via @PeppeGanga)

A less useful post was a widely shared news feature in the Pacific Standard: Killing Pigs and Weed Maps: The Mostly Unread World of Academic Papers. This gave an interesting look at citation analysis, but it started with a rather dodgy statistic:

A study at Indiana University found that “as many as 50% of papers are never read by anyone other than their authors, referees and journal editors.” That same study concluded that “some 90% of papers that have been published in academic journals are never cited.”

This ‘study’ turns out to be a feature in Physics World from 2007 by Indiana University Librarian Lokman I Meho, in which these numbers are simply asserted, with no citation and no data to back them up. Yoni Appelbaum (@YAppelbaum) pointed out a paper by Vincent Larivière and Yves Gingras on arXiv that effectively debunks these numbers. I also found a paper from 2008 whose Discussion section cites various studies on the proportion of uncited papers – which ranges from 15% to 26% for scientific and mathematical research papers, but was much higher in the social sciences (48% uncited) and humanities (93% uncited). So the situation isn’t as bad as the Pacific Standard made out, unless you are in the humanities.

Open access

The Wellcome Trust, the UK’s largest provider of non-governmental funding for scientific research, released a dataset on Figshare of the fees paid in the 2012-13 financial year for open access publication (APCs). @ernestopriego posted an initial analysis, @CameronNeylon posted a tidied up version of the dataset and @petermurrayrust and Michelle Brook (@MLBrook) initiated a crowdsourced attempt to check whether all the articles paid for were actually made open access by their publishers. The resulting spreadsheet will continue to be used for checking whether any paid open access papers are being wrongly marked as copyright of the publisher, or being put behind a paywall, or being given a link to payment for a licence to reproduce or reuse (anyone can help with this if they wish). Peter Murray-Rust has identified some examples where these errors have been made, which seem to be mostly from Elsevier, and this prompted Elsevier to post an explanation of why this is taking so long to fix (they were alerted the problem two years ago, as Mike Taylor has explained). 

Richard Poynder (@RickyPo) pointed me to a post on Google+ by David Roberts about changes in the APCs of Elsevier maths journals. Some have been pegged to small annual increases, others have gone up 6-8%, while one has had its APC reduced by 30%. The latter just happens to be the journal for which the editorial board threatened to quit in protest at Elsevier’s continuing lack of sufficient support for open access. The APCs are generally between US$500 and US$5000. In response to this, Ross Mounce (@rmounce) pointed out that Ubiquity Press (@ubiquitypress), whose APCs are US$390, have given a full breakdown of what the APC pays for. @HansZauner asked why all publishers can’t do the same, but this seems unlikely to happen.

It was also Richard Poynder who tweeted a very useful guide to choosing an open access journal, produced by Ryerson University Library & Archives in Canada. This gives a series of tests to see whether a journal is likely to be reputable rather than a ‘predatory’ journal, including membership of OASPA, journal metrics, peer review procedure and editorial board membership. @BMJ_Open pointed out that the page implied that double blind peer review was the most widely accepted standard. The page has now been changed, perhaps in response to this comment, to say “Take into consideration that blind peer review and open peer review are both considered a credible standard for scientific publishing.”

Other open access and open data news:

  • @WoWter posted an analysis of how much it would cost the Netherlands to convert completely to gold open access.
  • The Directory of Open Access Journals (@DOAJplus) published a new application form that all journals must fill in to apply to be in the database. This includes a ‘DOAJ Seal’ that indicates the openness, indexability and discoverability of the journal. (via @MikeTaylor).
  • PLOS published an update and clarification of their open data policy, following the debates that I covered last month.
  • David Crotty wrote a good summary of the debate about PLOS’s open data policy for the @ScholarlyKitchn.
  • A new service called JournalClick was announced, which gives recommendations for open access papers to read based on what you have read (via @RickyPo).
  • A German court has ruled that the Creative Commons non-commercial (CC:NC) clause means that the material is only for personal use, so even state-owned radio stations with no advertisements, for examples, are not permitted to use CC:NC material without permission (via @petermurrayrust).
  • Duke University
    Scholarly Communications Officer, Kevin Smith

    Scholarly Communications Officer Kevin Smith (@klsmith4906) posted about two problems with Nature Publishing Group licencing: they have recently started to require Duke authors to request a formal waiver of their faculty open access policy, and their licence to publish requires the author to waive or agree not to assert their moral rights.  @grace_baynes of Nature responded in a comment.

  • @damianpattinson of PLOS posted a report of an interesting talk entitled ‘The future is open: opportunities for publishers and institutions’ that he and his colleague Catriona MacCallum (@catmacOA) gave at the UKSG conference ‘Open Access Realities’ in London in November 2013.

New journals

The IEEE launched its new journal, IEEE Access, which claims to be an open access megajournal and was listed as one that was ‘coming soon’ in Pete Binfield (@p_binfield)’s December 2013 post on megajournals. However, the FAQ makes clear that in fact the authors are required to sign over copyright to the publisher, and reuse is not allowed, although the papers are free to read online. A discussion with @MattJHodgkinson and @BenMudrak clarified the situation for me. Matt pointed out that the Budapest Open Access Initiative FAQ says “Open access journals will either let authors retain copyright or ask authors to transfer copyright to the publisher”. So copyright transfer is allowed within open access, but restricting all reuse means that this journal should not be called an open access journal. IEEE Access also doesn’t conform to the standard definition of a megajournal, as the FAQ states “IEEE Access will publish articles that are of high interest to readers, original, technically correct, and clearly presented.” Megajournals do not select on the basis of perceived ‘interest’, so this is not a megajournal.

Other developments

  • I haven’t kept up fully with the controversy surrounding the publication of a new method (called STAP) to produce stem cells that was published in Nature in January. Paul Knoepfler’s stem cell blog (and @pknoepfler) is the place to go for full updates, but I was concerned to read that Nature has declined to publish a ‘Brief Communication Arising’ reporting that the method does not work. It seems important to me that such follow-ups should be published in the same journal as the original paper.
  • Jocelyn Sze (@jocelynesze) pointed me to a series of 2012 articles in Frontiers in Computational Neuroscience on visions for the future of scientific publishing. This editorial by Nikolaus Kriegeskorte introduces the series.

February highlights from the world of scientific publishing

Some of what I learned about scientific publishing last month from Twitter: new open access journals, data release debates, paper writing tips, and lots more

New journals

Two important announcements this month, both of open access sister journals to well established ones.

First, at the AAAS meeting it was announced that Science is going to have an online-only open access sister journal, called Science Advances, from early 2015. This will be selective (not a megajournal), will publish original research and review articles in science, engineering, technology, mathematics and social sciences, and will be edited by academic editors. The journal will use a Creative Commons license, which generally allows for free use, but hasn’t decided whether to allow commercial reuse, according to AAAS spokeswoman Ginger Pinholster. The author publishing charge hasn’t yet been announced.

Second, the Royal Society announced that, in addition to their selective open access journal Open Biology, they will be launching a megajournal, Royal Society Open Science, late in 2014. It will cover the entire range of science and mathematics, will offer open peer review as an option, and will also be edited by academic editors. Its criteria for what it will publish include “all articles which are scientifically sound, leaving any judgement of importance or potential impact to the reader” and “all high quality science including articles which may usually be difficult to publish elsewhere, for example, those that include negative findings”; it thus fits the usual criteria for a megajournal in that it will not select for ‘significance’ or potential impact.

These two announcements show that publishers without an open access, less selective journal in its stable are now unusual. Publishers are seeing that there is a demand for these journals and that they can make money. Publishers also see that they can gain a reputation for being friendly to open access by setting up such a journal. This also means that papers rejected by their more selective journals can stay within the publisher (via cascading peer review), which, while saving time for the authors by avoiding the need to start the submission process from scratch, also turn a potential negative for the publisher (editorial time spent on papers that are not published) into a positive (author charges). The AAAS has been particularly slow to join this particular bandwagon; let’s see if the strong brand of Science is enough to persuade authors to publish in Science Advances rather than the increasingly large number of other megajournals.

PLOS data release policy

On 24 February, PLOS posted an updated version of the announcement about data release that they made in December (and which I covered last month). I didn’t pay much attention as the change had already been trailed, but then I had to sit up and take notice because I started seeing posts and tweets strongly criticising the policy. The first to appear was an angry and (in my opinion) over-the-top post by @DrugMonkeyblog entitled “PLoS is letting the inmates run the asylum and this will kill them”.  A more positive view was given by Michigan State University evolutionary geneticist @IanDworkin, and another by New Hampshire genomics researcher Matt MacManes (@PeroMHC). Some problems that the policy could cause small, underfunded labs were pointed out by Mexico-based neuroscience researcher Erin McKiernan (@emckiernan13). The debate got wider, reaching Ars Technica and Reddit – as of 3 March there have been 1045 comments on Reddit!

So what is the big problem? The main objections raised seem to me to fall into six categories:

  1. Some datasets would take too much work to get into a format that others could understand
  2. It isn’t always clear what kind of data should be published with a paper
  3. Some data files are too large to be easily hosted
  4. The concern that others might publish reanalyses that the originators of the data were intending to publish, so they would lose the credit from that further research
  5. Some datasets contain confidential information
  6. Some datasets are proprietary

I won’t discuss these issues in detail here, but if you’re interested it’s worth reading the comments on the posts linked above. But it does appear (particularly from the update on their 24 February post and the FAQ posted on 28 February) that PLOS is very happy to discuss many of these issues with authors that have concerns, but analyses of proprietary data may have to be published elsewhere from now on.

I tend to agree with the more positive views of this new policy, who argue that data publication will help increase reproducibility, help researchers to build on each other’s work and prevent fraud. In any case, researcher who disagree are free to publish in other journals with less progressive policies. PLOS is a non-profit publisher who say that access to research results, immediately and without restriction, has always been at the heart of their mission, so they are being consistent in applying this strict policy.

Writing a paper

Miscellaneous news

  • Science writer @CarlZimmer explained eloquently at the AAAS meeting why open access to research, including open peer review and preprint posting, benefit science journalists and their readers.
  • Impactstory profiles now show proportion of a researcher’s articles that are open access and gives gold, silver and bronze badges, as well as showing how highly accessed, discussed and cited their papers are.
  • A new site has appeared where authors can review their experience with journals: Journalysis. It looks promising but needs reviews before it can become a really useful resource – go add one!
  • An interesting example of post-publication peer review starting on Twitter and continuing in a journal was described by @lakens here and his coauthor @TimSmitsTim here.
  • Cuban researcher Yasset Perez-Riverol (@ypriverol) explained why researchers need Twitter and a professional blog.
  • I realised when looking at an Elsevier journal website that many Elsevier journals now have very informative journal metrics, such as impact factors, Eigenfactor, SNIP and SJR for several years and average times from submission to first decision and from acceptance to publication. An example is here.
  • PeerJ founder @P_Binfield posted a Google Docs list of standalone peer review platforms.

December highlights from the world of scientific publishing

Some of what I learned last month from Twitter: takedowns, luxury journals, moves in peer review services and more.

‘Luxury journals’

A big talking point on my Twitter feed in December was the provocative comments about journal publishing made by Randy Sheckman as he received his Nobel Prize for Physiology and Medicine. Writing in the Guardian on 9 December, he criticised the culture of science that rewards publications in ‘luxury journals’ (which he identified as Nature, Cell and Science). He said “I have now committed my lab to avoiding luxury journals, and I encourage others to do likewise.” Although many applauded this, some pointed out that more junior researchers may not have the freedom to do likewise, and also mentioned Schekman’s potential conflict of interest as Editor-in-Chief of the new, highly selective journal eLife, which aims to compete for the best research with these journals (some responses are summarized by Stephen Curry). Schekman responded to the criticisms in a post on The Conversation, and suggested four ways in which the research community could improve the situation.

Elsevier steps up takedown notices

Subscription journals generally require the author to sign a copyright transfer agreement that, among other things, commits them not to share their paper widely before any embargo period has passed. It appears that in December Elsevier decided to increase their enforcement of this by sending takedown notices to sites where Elsevier papers were posted. Guy Leonard described what happened to him and the reaction on Twitter and elsewhere.

Various peer review developments

Jeremy Fox (@DynamicEcology), a population ecologist at the University of Calgary, explained why he likes the journal-independent peer review service Axios Review (and is joining their editorial board).

Publons, which gives researchers credit for post-publication peer review, announced that researchers can now also get credit for their pre-publication peer reviews for journals.

Wiley announced a pilot of transferable peer review for their neuroscience journals, in which reviews for papers rejected from one journal can be transferred to another journal in the scheme, thus saving time.

F1000Research announced that its peer reviewed articles are now visible in PubMed and PubMed Central, together with their peer reviews and datasets. Articles on F1000Research are published after a quick check and then peer reviewed, and indexing by PubMed and PubMed Central happens once an article has a sufficient number of positive reviews.

Jennifer Raff, an Anthropology Research Fellow at the University of Texas at Austin, published “How to become good at peer review: A guide for young scientists“, a very useful and comprehensive guide that she intends to keep updated as she receives comment on it.

Miscellaneous news

Jeffrey Beall, a librarian who has been curating a useful list of ‘predatory’ open access journals for several years, revealed his antagonism to open access as a whole in an article that surprised many with its misconceptions about the motivations of open access advocates. PLOS founder Mike Eisen has rebutted the article point by point. Although I feel that Beall’s list is still useful for checking out a new journal, it should be taken only as a starting point, together with a detailed look at the journal’s website, what it has already published, and its membership of the Open Access Scholarly Publishers Association (OASPA).

James Hayton (@JamesHaytonPhD) wrote a great post on his 3 Month Thesis blog on the seven deadly sins of thesis writing, which should also all be avoided in paper writing: lies, bullshit, plagiarism, misrepresentation, getting the basics wrong, ignorance and lack of insight.

Finally, I was alerted (by @sciencegoddess) to a new site called Lolmythesis, where students summarize their thesis in one (not always serious) sentence. Worth a look for a laugh – why not add your own?

Highlights from the scientific publishing world in October

A summary of the key things I have learned this month via Twitter: stings, harrassment and post-publication peer review.

You may have noticed that this blog is not updated very often, but that my Twitter feed is updated several (sometimes many) times a day. I have decided to to bring some highlights of this Twitter activity to my blog, so that those of you who (for some strange reason) aren’t on Twitter can get the benefit of all the interesting things I learn there every day. Of course, this summary will focus on scientific publishing and related fields. This may become a regular blog feature.

The biggest news early in October was the ‘sting’ published in Science by John Bohannon, which showed that some disreputable journals will accept even an obviously bad fake paper. There have been many, many posts and articles about this, which are listed in Zen Faulkes (@doctorzen)’s list. A few I found most insightful are:

  • A pair of two posts by @neurobonkers, the first giving a good overview and the second classifying the journals included in the sting into those that accepted or rejected the fake paper with or without peer review.
  • This post by journal editor Gunther Eysenbach, who rejected the paper. He says “It is foolish to extrapolate these findings of a few black sheep publishers and scammers… to an entire industry. This would be as logical as concluding from Nigerian wire fraud emails that all lawyers who take a fee-for-service are scammers!”
  • The suggestion by Zen Faulkes that the fake paper could be a good resource for teaching how to write a paper.

Then there was the big scandal around sexual harassment in the science writing community, which has now led to the resignation of Scientific American’s blog editor, Bora Zivovic. An overview in the Guardian science blog by Alice Bell (@alicebell) gives the low-down and this post by Jennifer Ouellette (@JenLucPiquant) is one of the more insightful on the issues.

And then PubMed launched a commenting system, PubMed Commons. This is so important that I am going to blog about it separately.

A few other interesting things:

  • The Economist published a special series of articles on science, including a long overview of the issues, including the problem of reproducing results and publishing replications, important statistical issues, fraud, retractions and peer review (including the Science sting).
  • This post by Pat Thomson (@thomsonpat) drives home the importance of the ‘take home message’ in your paper.
  • I was directed to this amazing comprehensive guide to making a conference poster, by Colin Purrington, by @deevybee and others.
  • Open Access Week ran from 21 to 27 October. The most notable related article was in the Guardian by Peter Suber: Open access: six myths to put to rest.
  • The Chemistry journal ACS Nano published an editorial suggesting that allegations of fraud in a paper should be dealt with in private by the journal concerned, not discussed openly on blogs. Blogger Paul Bracher (@ChemBark) disagrees.

Submission to first decision time

Having written previously about journal acceptance to publication times, it is high time I looked at the other important time that affects publication speed: submission to first decision time. As I explained in the previous post, the time from submission to publication in a peer reviewed journal can be split into three phases, the two discussed previously and here and also the time needed for the authors to revise, which the journal can’t control.

A survey of submission to first decision times

I have trawled through the instructions to authors pages of the journals in the MRC frequently used journal list, which I have used in several previous posts as a handy list of relatively high-impact and well known biomedical journals. I’ve used the list as downloaded in 2012, and there may be new journals added to it now. I’ve omitted the review journals, which leaves 96.

From these pages I have tried to find any indication of the actual or intended speed to first decision for each journal. For many journals, no information was provided on the journal website about average or promised submission to first decision times. For example, no Nature Publishing Group, Lancet, Springer or Oxford University Press journals in this data set provide any information.

However, of these 96 journals 37 did provide usable information. I have put this information in a spreadsheet on my website.

20 promised a first decision within 28 or 30 days of submission. 12 others promised 20-25 days. Of the rest, two are particularly fast, Circulation Research (13 days in 2012) and Cellular Microbiology (14 days); and one is particularly slow, Molecular and Cellular Biology (4 to 6 weeks, though they may just be more cautious in their promises than other journals). JAMA and Genetics are also relatively slow, with 34 and 35 days, respectively. (Note that the links here are to the page that states the time, which is generally the information for authors.)

A few journals promise a particularly fast for selected (‘expedited’) papers but I have only considered the speed promised for all papers here.

I conclude from this analysis that, for relatively high-impact biomedical journals, a first decision within a month of submission is the norm. Anything faster than 3 weeks is fast, and anything slower than 5 weeks is slow.

Newer journals

But what about the newer journals? PeerJ has recently been boasting on its blog about authors who are happy with their fast decision times. The decision times given on this post are 17, 18 and 19 days. These are not necessarily typical of all PeerJ authors, though, and are likely to be biased towards the shorter times, as those whose decisions took longer won’t have tweeted about it and PeerJ won’t have included them in their post.

PLOS One gives no current information on its website about decision times. However, in a comment on a PLOS One blog post in 2009, the then Publisher Pete Binfield stated that “of the 1,520 papers which received a first decision in the second quarter of 2009 (April – June), the mean time from QC completion to first decision was 33.4 days, the median was 30 days and the SD was 18.” He didn’t say how long it took from submission to ‘QC completion’, which is presumably an initial check; I expect this would be only a few days.

Kent Anderson of the Scholarly Kitchen asked last year “Is PLOS ONE Slowing Down?“. This post only looked at the time between the submission and acceptance dates that are displayed on all published papers, and it included no data on decision dates, so the data tell us nothing about decision times. In a series of comments below the post David Solomon of Michigan State University gives more data, which shows that the submission to acceptance time went up only slightly between early 2010 and September 2011.

The star of journals in terms of decision time is undoubtedly Biology Open. It posts the average decision time in the previous month on its front page, and the figure currently given for February 2013 is 8 days. They say they aim to give a first decision within 10 days, and their tweets seem to bear this out: in June 2012 they tweeted that the average decision time in May 2012 had been 6 days, and similarly the time for April 2012 had been 9 days.

Other megajournals vary similarly to ordinary journals. Open Biology reports an average of 24 days, Cell Reports aims for 21 days, and G3 and Scientific Reports aim for 30 days. Springer Plus, the BMC series, the Frontiers journals, BMJ Open and FEBS Open Bio provided no information, though all boast of being fast.

What affects review speed?

If newer journals are faster, why might that be? One possible reason is that as the number of submitted papers goes up, the number of editors doesn’t always go up quickly enough, so the editors get overworked – whereas when a journal is new the number of papers to handle per editor may be lower.

It is important to remember that the speed of review is mainly down to the reviewers, as Andy Farke pointed out in a recent PLOS blog post. Editors can affect this by setting deadlines and chasing late reviewers, but they only have a limited amount of control over when reviewers send their reports.

But given this limitation, there could be reasons for variations in the average speed of review between journals. Reviewers might be excited by the prospect of reviewing for newer journals, so they are more likely to be fast. This could equally be true for the highest impact journals, of course, and also for open access journals if the reviewer is an open access fan. Enthusiastic reviewers not only mean that the reviewers who have agreed send their reports in more quickly, but also that it will be easier to get someone to agree to review in the first place. As Bob O’Hara pointed out in a comment on Andy Farke’s post, “If lots of people decline, you’re not going to have a short review time”.

A logical conclusion from this might be that the best way in which a journal could speed up its time to first decision would be to cultivate enthusiasm for their journal among the pool of potential reviewers. Building a community around the journal, using social media, conferences,  mascots or even free gifts might help. PeerJ seem to be aiming to build such a community with their membership scheme, not to mention their active Twitter presence and their monkey mascot. Biology Open‘s speed might be related to its sponsorship of meetings and its aim to “reduce reviewer fatigue in the community”.

Another less positive possible reason for shorter review times could be that reviewers are not being careful enough. This hypothesis was tested and refuted by the editors of Acta Neuropathologica in a 2008 editorial. (Incidentally, this journal had an average time from submission to first decision of around 17 days between 2005 and 2007, which is pretty fast.) The editorial says “Because in this journal all reviews are rated from 0 (worst) to 100 (best), we plotted speed versus quality. As reflected in Fig. 1, there is no indication that review time is related to the quality of a review.”

Your experience

I would love to find (or even do) some research into the actual submission to first decision times between different journals. Unfortunately that would mean getting the data from each publisher, and it might be difficult to persuade them to release it. (And I don’t have time to do this, alas.) Does anyone know of any research on this?

And have you experienced particularly fast or slow peer review at a particular journal? Are you a journal editor who can tell us about the actual submission to first decision times in your journal? Or do you have other theories for why some journals are quicker than others in this respect?

SpotOn London session: The journal is dead, long live the journal

I’m co-hosting a workshop at SpotOn London next week on the future of journals.

It’s time to end a long blogging hiatus to tell you about an exciting event coming up on Sunday 11 and Monday 12 November. SpotOn London (formerly called Science Online London) is a community event hosted by Nature Publishing Group for the discussion of how science is carried out and communicated online. There will be workshops on three broad topic areas – science communication and outreach, online tools and digital publishing, and science policy – and I am involved in one of the ‘online tools and digital publishing’ ones. This has the title ‘The journal is dead, long live the journal‘ and it will focus on current and future innovations in journal publishing. If you’re interested in how journals could or should change to better meet the needs of science, this is for you!

In this one-hour session we will have very short introductions from four representatives from different parts of the journal publishing world:

  • Matias Piipari (@mz2), part of the team behind Papers software for finding an organising academic papers
  • Damian Pattinson (@damianpattinson), Executive Editor of PLOS ONE
  • Davina Quarterman, Web Publishing Manager at Wiley-Blackwell
  • Ethan Perlstein (@eperlste) of Princeton University

We will then open the floor to contributions from participants, both in the room and online. We hope to cover three themes:

  1. Megajournals; their impact on the journal and on how papers are going to be organised into journals. Will megajournals lead to a two tier marketplace of high end journals and a few megajournals, with mid-tier journals disappearing from the market altogether?
  2. How do we find the papers of interest, in a world where journal brand doesn’t help? In a world where issues disappear, and researchers’ main point of contact with the literature is through aggregation points such as Google Scholar and Pubmed, what are the signifiers that we can build or support that will enable researchers to find the content that they need?
  3. Once you get down to the paper, are there any innovations that we should be using now, at the individual paper level, and what are the barriers to us doing this?

Science Online events have a tradition of being more than just conferences – they aim to involve lots of people outside the room via the SpotOn website and Twitter as well as those in the room. So although the conference itself is sold out (though there is a waiting list for tickets), you can still follow along and get involved before, during and after the event itself. This session is at 4.30pm on Sunday 11 November, so look out on the Twitter hashtag #solo12journals around then. Beforehand, you can comment on co-host Ian Mulvany’s blog post introducing the session, look at the Google Doc that shows the thought processes the organisers went through in planning the session, check for tweets on the hashtag, and follow me (@sharmanedit), Ian (@ianmulvany) and co-host Bob O’Hara (@bobohara) and/or the speakers on Twitter for updates.

One the day, comments from Twitter will be moderated and introduced into the discussion in the room by Bob, who will be doing this remotely from Germany. The whole session (and all other SpotOn London session) will be live-streamed (probably here) and the video will be available afterwards; there will also be a Storify page collecting tweets using the #solo12journals hashtag.

This interaction with those outside the room is important because with only an hour there is a limit to the depth with which we will be able to cover the range of issues around journals. With online discussion as well we hope that more points can be discussed in more detail than would otherwise be possible. It might get a little confusing! I am new to this format, so I am slightly apprehensive but also excited about the possibilities.

Thoughts on megajournals

I am particularly interested in the aspect of the session on megajournals and how they are changing journal publishing. By megajournals we mean all the journals that have been set up to publish papers after peer review that assesses whether the research is sound but doesn’t attempt to second-guess the potential impact of the work. Some, like PLOS ONE, are truly mega – they published over 13,000 papers in 2011. Others, like the BMC series from BioMed Central, probably publish a similar number of papers but divided into many journals in different subject areas. Others have been set up to be sister journals to better known selective journals – for example, Scientific Reports from Nature Publishing Group and BioOpen from The Company of Biologists. All are open access and online only.

Some of these journals are now showing themselves not to be the dumping ground for boring, incremental research that they might have been expected. When PLOS ONE’s first impact factor was revealed to be over 4, there was surprise among many commentators. The question is now whether papers that are unlikely to be accepted by the top journals (roughly speaking, those with impact factors over about 10, though I know that impact factor is a flawed measure) will gradually be submitted not to specialist journals but to megajournals. The opportunity to get your paper seen by many people, which open access publishing provides, could often outweigh the benefits of publishing in a journal specific to your specialist community where your paper will be seen by only that community. I will be very interested to hear people’s thoughts on this issue raised by this session.

Get involved

So do comment using one of the channels mentioned above. Have you recently made a decision about where to send a paper that you knew wasn’t one for the top-flight journals, and did you decide on a specialist journal, a megajournal or some other route to publication? Regarding the other two themes of the session, how do you find papers in your field, and what do you want research papers to look like?

Crowdsourcing information about journals

Crowdsourced surveys of the experience of authors with journals are useful, but I have found only a few. For now, I propose a simpler survey of information gleaned from journal websites.

I was recently alerted by @melchivers (via @thesiswhisperer) to the existence of a blog by SUNY philosopher Andrew Cullison (@andycullison) that includes a set of journal surveys for the field. As Cullison explains in an overview post, the surveys consist of Google Docs spreadsheets, one for each journal, and a form interface that academics fill in with data on their experience of submitting to that journal. The information requested includes:

  • the time taken for initial review
  • the initial verdict of the journal (acceptance, rejection, revise and resubmit, conditional acceptance, withdrawn)
  • the number of reviewers whose comments were provided
  • an assessment of the quality of the reviewers’ comments
  • the final verdict if the paper was revised
  • the time from acceptance to publication
  • an overall rating of the experience with the editors
  • Some basic demographic data

This survey covers 180 journals in philosophy. The data is collated and various statistics are calculated, such as the average review time and acceptance to publication time and the average acceptance rate. Here are couple of examples: the British Journal of Philosophy of Science and Philosophy of Science.

This kind of survey could be a valuable resource for authors in a particular field who are trying to choose a journal. They are crowdsourced, so they do not rely on only one or a few people to gather data. They also provide real data on how fast journals are in practice, which might differ from the statistics or promises provided on journal websites. However, they have limitations: as pointed out in comments below one of Cullison’s posts, they suffer from reporting bias. This is important given that for many of the journals surveyed there are fewer than ten responses.

I haven’t seen any surveys like this in any other field of academia, and certainly none in biology or medicine. I would be very interested to hear if others have seen any. In biology a similar survey would probably only be useful if divided up into smaller fields, such as plant cell biology or cardiovascular medicine. Or it could focus only on the general journals that cover large areas of science, biology or medicine.

A simpler journal survey

Alternatively, or as a first step towards full surveys of journals in biomedicine, a crowdsourced survey of the information presented on journal websites could be useful. This could include information such as the promised submission to first decision time and acceptance to publication time, licensing details (copyright, Creative Commons and so on), charges, article types and length limits. This would involve only one small dataset per journal, which could fit on a single line of a spreadsheet rather than data for individual papers, so would be more manageable than Cullison’s surveys.

I have made a start on such a survey, and you can find it on Google Docs here. I have used the same set of 98 journals, derived from the UK Medical Research Council  list of journals popular with MRC authors, that I used for my open access charges spreadsheet. For every journal, the spreadsheet now contains the name of the publisher, the main journal URL, the URL for the instructions for authors, whether the entire journal is open access or not, and whether there is an open access option. There are also columns for the following information: what the website says about acceptance to publication time; whether the accepted, non-edited manuscript is published online, and what the website says about submission to first decision time. I have filled in some of these fields but haven’t yet checked all the websites for all this information.

The spreadsheet is editable by anyone. I realise that this risks someone messing up the data or adding spam text. For the columns that I don’t want you to change, I have included a partial safeguard: these columns are pulled in from a hidden, locked sheet of the spreadsheet. Please try not to delete data in any cells – just add data in empty cells. If you have any other suggestions for how to allow information to be added but not deleted, or otherwise to avoid problems, please add a comment below.

Now it’s your turn

Would you like to contribute information to this survey? If so, please go ahead and edit the spreadsheet.

If you could publicise it that would be great too.

And do you have any comments on this process, suggestions for improvement and so on?

Other questions

Have you used Cullison’s surveys and found them useful (or less useful)? Have you come across any surveys like the philosophy one for other fields? Or like my survey?

A comparison of open access publication charges

Having covered submission fees and other charges, it is about time I covered the main event, isn’t it? I’m talking about open access publication fees, also known as author publishing charges (APCs) and many other names. This is a fee for making your article free for readers to read, and usually for them to download, distribute and do whatever they like with as well.

What do you get for your money?

Before agreeing to pay a fee to make your article open access, make sure you check the licence. True open access (as defined by the Budapest Open Access Initiative) means that it should be equivalent to the Creative Commons Attribution licence (CC:BY), which allows others to copy, distribute and make derivative works, including for commercial purposes, as long as they attribute it to you. Some publishers have a similar licence but with a non-commercial clause (CC:BY-NC) – there is debate about whether the NC clause stops something being open access. Others allow reading for free but restrict other uses, which really can’t be called open access at all. If the rights of readers and re-users are restricted, you are getting less open access for your APC than if there is a CC:BY licence.

Surveys of APCs

To find journal open access charges you usually need to look on the website of the individual journal. However, several organisations have usefully put together summaries of licences and charges. The Wellcome Trust and the UK Medical Research Council (MRC) both have mandates that all research they fund must be made freely available within 6 months of publication, and they both have lists on their websites of journals that do and don’t comply with this mandate. The following lists are available:

  • The MRC has a downloadable spreadsheet listing licences and charges of the most popular couple of hundred journals in which their authors publish
  • The Wellcome Trust has a list of the top 200 journals used by their authors showing which are compliant with their mandate, but not including charges
  • BioMed Central has a page comparing their APCs and licence with those of other publishers
  • The University of California, Berkeley library collections have a similar comparison page covering many subject areas
  • The Directory of Open Access Journals (DOAJ) provides information on charges, but this doesn’t seem to be searchable
  • SHERPA/RoMEO has a list of charges by publisher

I have taken the MRC spreadsheet, converted the currencies and calculated some statistics, and the result is in a Google Docs spreadsheet here. Some journals have two different fees depending on whether the author is a member of the society that runs the journal (or has a discount for some other reason). Of the 209 journals that allowed open access publication of some kind (ie gold open access, not just allowing deposition in a repository, which is called green open access), the mean fee was US$2845.08 (£1793.60) for members or US$2881.93 (£1816.21) for non-members. The standard deviation of the fee was $729.17 (£459.71) for members or $687.09 (£438.60) for non-members. The median is $3000 (£1891.33).

Some notes on these figures. Firstly, they are from the MRC document last updated April 2011, with currencies converted using xe.com on 23 March 2012. Secondly, they cover journals in medicine and related fields, particularly biology. Thirdly, they include 8 BioMed Central journals, 10 BMJ journals, 52 Elsevier journals (including 11 Cell Press journals), 14 Nature Publishing Group journals, 17 OUP journals, 4 PLoS journals, 12 Springer journals and 48 Wiley/Wiley-Blackwell journals. The median charge is $3000 because non-Cell-Press Elsevier journals charge this amount and there are lots of Elsevier journals in the list.

The MRC list also includes journals in the Lancet stable (The Lancet, The Lancet Neurology and The Lancet Oncology, published by Elsevier ), which charge £400 ($634.47) per page. I’m not sure how many pages the average research paper is, but at 6 pages this would be £2400 ($3808.46) and at 10 pages it would be £4000 ($6344.70).

Waivers

These fees may seem very high to some. Don’t forget that many publishers have waivers for those who cannot afford to pay the APC. PLoS offers a waiver for anyone who does not have funds to cover the fee (and I’ve heard informally that they ask no questions). BioMed Central gives an automatic waiver to authors from a WHO list of developing countries, and also considers waivers and discounts on a case by case basis. I haven’t researched all publishers to find out their policy on waivers – perhaps that’s for a future post! If you can’t afford the APC for a journal to which you would like to submit your paper, I suggest explaining this when you submit and asking for a waiver or discount.

Your experience

Do you know of other sources of information on APCs for different journals or on average APCs? Have you spotted any errors in my spreadsheet?

Journal submission fees: why are they so rare?

In a previous post I discussed fees that journals charge for colour printing, per page or for supplementary material. All those fees are charged only to authors whose papers are accepted. Here I’ll look at fees that are charged to the authors of all submissions, included those that are rejected.

In 2010 a report on submission fees by Mark Ware was published by the Knowledge Exchange, a collaboration of the UK Joint Information Systems Committee (JISC) with similar organisations in Denmark, Germany and the Netherlands. This followed a study investigating whether submission fees could play a role in a business model for open access journals. They concluded that for journals with a high rejection rate in particular, submission fees can help to make the open access publication fee more reasonable and could thus make the transition to open access easier.

Although the report focuses on submission fees in the transition to open access, they also noted:

In certain disciplines, notably economic and finance journals and in some areas of the experimental life sciences, submission fees are already common.

Which journals charge a submission fee?

The Knowledge Exchange report includes a table of journals that already charge a submission fee. For biology journals, these fees are listed as mostly being around US$50-75.

I’ve checked on the journal websites for a selection of those listed in this report, and some seem to no longer charge for submission – in particular, the US$400 submission fee that Ideas in Ecology & Evolution charged when it launched in 2008 seems to have now been dropped, and I can’t find any mention of submission fees on the websites of Journal of Biological Chemistry or FASEB Journal.

The journals that I could verify as charging submission fees are:

  • Journal of Neuroscience (Society for Neuroscience) has a submission fee of US$125 (as well as the page charges and colour printing charges mentioned in the previous post)
  • Hereditas (an open access Wiley-Blackwell journal) charges 100 euros (US$133)
  • Stem Cells (Wiley-Blackwell, with an open access option) charges $90
  • Journal of Clinical Investigation (American Society for Clinical Investigation) and Cancer Research (American Association for Cancer Research) charge US$75
  • several other journals mentioned in the Knowledge Exchange report charge around US$50.

Elsevier say in their FAQ that you need to look in each journal’s guide to authors to find out if they charge submission fees (as with other charges).

All the above except Hereditas are subscription journals.

Why submission fees, or why not?

The Knowledge Exchange report interviewed publishers about the pros and cons of submission fees. Unfortunately, they don’t give any details of who was interviewed, except that they were ‘stakeholders including publishers, libraries, research funders, research institutions and individual researchers’, or the text of the interviews, so it is difficult to interpret the results. However, from these interviews the report identified the following advantages:

  • The costs of publication are spread over more authors
  • The fee may put off authors from submitting ‘on spec’ to a journal where they know their paper has only a tiny chance of getting accepted, thus saving work for the journal.

The disadvantages mentioned included:

  • The fee might put off authors and thus make the journal less competitive
  • It was unclear whether funders would cover the charge (though interviews with funders for the study suggested that they would)
  • It would require administration.

Given the findings of this report, I’m surprised that more journals don’t charge a submission fee. I would be surprised if it put off speculative submissions (the time it takes for a paper to be reviewed is surely a bigger cost to the authors than a charge at the level of US$50-100). But for  open access journals with high rejection rates, as the report says, it seems particularly appropriate. Is the risk of seeming uncompetitive with other journals the only reason why these fees aren’t being widely tried?

This is interesting in the context of the statements by Nature Publishing Group that Nature couldn’t go open access because they would have to charge a very high publication fee. I’ve heard this most recently from Alison Mitchell at the debate ‘Evolution of Science’ in Oxford in February: she said that the publication fee would need to be about £10,000 (US$15,850) for Nature research journals and £30,000 (US$47,550) for Nature (see the video of the debate – this statement is at 17 minutes 30 seconds).

A conversation on Twitter with Heather Piwowar (@researchremix, a postdoc with Dryad studying data use among researchers) and Ethan Perlstein (@eperlste, an evolutionary pharmacologist at Princeton University) about this NPG statement led me to Jan Velterop (@Villavelius, a director of Aqcknowledge.com and a former colleague of mine at BioMed Central), who has written on submission fees several times on his blog. He kindly emailed me with further thoughts.

Jan’s most recent blog post summarises his reasons for liking submission fees:

The basic reason I am in favour of submission fees is that it makes scientific publishing really the service industry that it is, its main task nowadays having nothing to do with publishing per se, but mainly with arranging peer review and quality assurance of one sort or another.

Of course, this might not be what publishers want their main task to be…

Another argument for them that he lists is:

It removes the suspicion that OA journals might be tempted to accept more than they should just because of the money that accepted articles bring

And what about the disadvantages? Jan tells me that journal publishers are wary of introducing new fees that other journals don’t charge (see the ‘competitiveness’ point above). They are particularly wary because of a bit of history I didn’t know about:

One of the reasons why commercial journals dominate STM these days is the fact that society journals, still mostly independent in the 1960′s, charged page charges. Commercial journals made much of the fact that (then) they didn’t, and so attracted a growing percentage of authors, who could publish with them for free…

Among the reasons publishers are not too keen are:

1) The risk that authors ‘defect’ to journals without charges. After all, that happened before.

I can see that given this history, journals might be more cautious than otherwise.

Jan goes on to mention a reason I hadn’t heard before:

2) The risk that authors might expect transparency with regard to the speed, peer-review, and acceptance/rejection procedure. If you only have to pay when accepted (as is the case for the current author-side payment OA journals), you may not care too much about the speed, quality of the peer review, and acceptance processes, but if you have to pay even if you are rejected, then that becomes a very different story. Publishers know that they cannot guarantee any quality in that regard – with a few exceptions, perhaps – and fear the pressure of quality requirements on them if they were to move in that direction.

This is a very good point. It is certainly difficult to give guarantees about the speed or quality of peer review, which relies on voluntary work by researchers. It is related to a disadvantage listed in Jan’s recent blog post:

The need to be able to justify rejections properly, particularly if challenged (after all, submitters have paid for an assessment)

Jan also gives a third reason that intrigues me: that the level of submission fees might reveal information about a journal’s rejection rate that they would rather be kept quiet:

if they reject only about a tenth of the submissions, then obviously the submission charge cannot be very much lower than 9/10th of the publication charge for the same revenue to be achieved

So a journal might want to be seen as very selective, rejecting a high proportion of submitted articles, but they might actually have a lot lower rejection rate than this. For example say a journal with a rejection rate of 90% was considering a submission fee of $50 and a publication fee of $1000 (and all authors pay the submission fee, whether accepted or not). Then for every 9 articles accepted, the journal would receive $9000 in publication fees, plus $4500 for the 90 articles submitted, making $13500. But if the same fees were applied to a journal that rejects only about 10%, then for every 9 articles accepted, they would get only $9000 plus $500 for the 10 submitted articles ($9500). The number of articles accepted is public, whereas the number rejected isn’t. To get the level of fees they would receive if they had a 90% rejection rate they would need to charge a submission fee of ($13500 – $9000)/10 = $450. This level of submission fee is unlikely to be acceptable to authors.

(My calculation comes out with a submission fee half what Jan estimates, which I think is because I am assuming both a submission fee and a publication fee are charged, whereas he is assuming only a submission fee.)

In conclusion, the main advantage of submission fees is also their main advantage in other circumstances: that they would reduce the number of submissions. So if a journal has a high rejection rate, it makes sense to charge a submission fee, but otherwise it doesn’t. This actually applies to subscription and open access journals equally – in both cases a submission fee provides extra revenue, which could be used to reduce other charges, included subscriptions, page charges or publication fees (or to increase profits of course). The main reason why high-rejection-rate journals aren’t currently charging submission fees seems to be because it would make them less competitive, but given that these journals are by definition the place that people want to be published, this doesn’t seem a very strong argument. I wouldn’t be surprised if one journal tries submission fees and other then followed suit in the next few years.

Your experience

Have you paid a submission fee to a journal? Would you consider it if it meant a lower level of other charges, such as page charges or fees for open access publication?

Journal editors: has your journal considered a submission fee? If you don’t have one, why not? If you do, why?

Journal news for February

News related to scientific journal publishing since 4 February.

Elsevier withdraws support for the Research Works Act

Since I covered this infamous draft US law and the associated boycott of Elsevier by academics (here and in news here) the flood of blog posts on the topic has continued, and I won’t attempt to summarise them here. But the pressure seems to have had an effect: on 27 February Elsevier announced that it is no longer supporting the act, although they ‘continue to oppose government mandates in this area’.

Meanwhile, a new act has been proposed, the Federal Research Public Access Act (FRPAA), which would mandate that all research funded by every federal funder with a budget over $100 million should be made open access 6 months after publication.

Industry group ‘threatens’ journals to delay publications

The Lancet has reported (pdf) that the Mining Awareness Resource Group (MARG) has written to several scientific journals advises journals not to  publish papers from a US government study of diesel exhaust and lung cancer until a court case and congressional directives are ‘resolved’. The editor of Occupational and Environmental Medicine, Dana Loomis, is quoted as saying ‘It is vague and threatening. This has a chilling effect on scientific communications—a matter of grave concern.’

New open access journal

The open access journal Biology Open has been launched by the Company of Biologists. The journal aims to provide the research community with ‘an opportunity to publish valid and well-conducted experimental work that is otherwise robbed of timeliness and impact by the delays inherent in submission to established journals with more restrictive selection criteria. ‘

Twitter and paper citations

An arXiv preprint has found a correlation between mentions of a paper on Twitter and its later citations.

Criteria for the UK Research Excellence Framework 2014 announced

The Higher Education Funding Council for England (HEFCE) has announced the criteria and working methods that the panels for the assessment of research using the Research Excellence Framework (REF 2014) will use. REF will use citations as part of assessment but not impact factors or other bibliometrics (see page 25 of the full report for the statement regarding citations in the biology and medicine panel). Researchers at English universities will no doubt be scrutinizing the guidelines carefully.

* * * *

I’m sorry there hasn’t been a weekly Journal News recently, as I had hoped, and that this update is rather brief. I hope that the usefulness of these news updates depends more on their content than their regularity. If you want (much) more frequent updates from the world of journals and scientific publication, do follow me on Twitter!

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