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.

How to read journal instructions for authors

Journal editors often complain that few authors seem to read their instructions for authors. But journals don’t make it easy to read these instructions. Every publisher has its own way of displaying the instructions, with differences in the wording for the same thing, in the order in which information is presented and in how the information is split over web pages.

I’m going to attempt to bring some order to the chaos by picking out the points that really matter. These are:

  • Subject areas
  • Threshold for significance
  • Article types
  • Policies
  • Length limits
  • Article format for submission

There are also some things that nearly all journals require, which I’ll summarise at the end.

Scope

The most important thing to read when you are considering whether to submit to a particular journal is what subject areas it covers. This aspect is pretty straightforward, although it is the only area covered by most commercially available tools for choosing a journal, such as Edanz’s Journal Selector and JANE.

One important aspect to consider, however, is how broad a subject area you would like the journal to cover. If your study will be of interest to readers in more than one field, you will probably want an interdisciplinary journal that covers both fields.

Threshold

There is generally some statement in the instructions for authors or elsewhere in the journal information about the impact, significance or interest threshold. This can be written in all sorts of ways. For example:

  • Nature requires that articles “are of outstanding scientific importance” and “reach a conclusion of interest to an interdisciplinary readership”
  • Blood takes into account “the originality and importance of the observations or investigations, the quality of the work and validity of the evidence”
  • Cell says “The basic criterion for considering papers is whether the results provide significant conceptual advances into, or raise provocative questions and hypotheses regarding, an interesting biological question.”

‘Megajournals’ include a statement that the journal does not select on the basis of perceived impact or significance. For example:

  • PLOS ONE says “PLOS ONE will rigorously peer-review your submissions and publish all papers that are judged to be technically sound. Judgments about the importance of any particular paper are then made after publication by the readership”
  • Frontiers says “Review editors focus on certifying the accuracy and validity of articles, not on evaluating their significance”
  • Scientific Reports says “Referees and Editorial Board Members will determine whether a paper is scientifically sound, rather than making judgements on novelty or whether the paper represents a conceptual advance.”
  • Biology Open focuses on “publication of good-quality sound research without a requirement for perceived impact”.

If you choose a selective journal rather than a megajournal, it is important to consider carefully whether your study is likely to reach their stated threshold. Get a colleague in another field to read your title and abstract and give an honest view of how groundbreaking they think it is compared with papers in various possible target journals.

You are likely to be biased towards finding your own work fascinating; never forget that editors and reviewers won’t share this view.

Article types

The instructions always include a list of the types of article that the journal publishes. Your paper must fit one of the article types and must follow the instructions for that type (especially regarding length limits).

What I call a research paper can be called by a variety of different names:

  • Original article
  • Original research
  • Research report
  • Primary research
  • Article
  • Letter

The word ‘Letter’ is used for a full (short) research paper in some journals (such as Nature journals) but for something much shorter in others, akin to the more colloquial meaning of the word letter.

Journals have a variety of criteria to distinguish between different article types. Sometimes the main difference is simply length, but often there is a difference in ‘significance’ or ‘completeness of the story’. These can be rather subjective judgements. Read a range of papers in the journal to get a feeling for the differences.

If your article isn’t a research paper, it is equally important to check whether the journal publishes articles like it. Usually journals invite review and comment articles, but some also accept unsolicited offers. Always send an email first describing your proposed review or comment, rather than just submitting it.

Policies

The policies section will vary a lot depending on the field. It will cover things like:

  • requirements for making data, software and materials available
  • ethics for animal experiments or human studies
  • adherence to subject-specific guidelines such as MIAME or CONSORT
  • adherence to authorship criteria, such as regarding ghostwriting and guest authorship (see the criteria laid out by the ICMJE)
  • whether they will accept papers that have previously been published on a preprint server or presented at a conference
  • policies on discussing the research with the media before publication.

It is crucial that your research follows all the guidelines for the journal. Violations can lead to immediate rejection.

Journals vary in how strict they are. However, if your study follows the highest possible ethical standards you are unlikely to find major differences between them. The exception to this is in journal policies on previous publication; newer journals are often less strict on this, and there is ongoing debate about the issue so instructions might change.

Format for submission

Some instructions aren’t to do with the manuscript contents itself but rather its file format and other things to do with how it is uploaded to the journal’s submission system. Publishers vary in what they require in terms of:

  • File formats allowed (commonly allowed formats for text are doc, docx, odt and rtf; TeX files may or may not be accepted)
  • Whether the text and figures should be in a single file or separate files
  • Whether the figure legends should be under each figure or at the end of the text
  • Whether a cover letter is required and what it should contain
  • Whether page or line numbers should be included
  • Whether the manuscript should be double spaced
  • Whether suggestions or exclusions of reviewers are allowed or encouraged
  • Whether submission has to be through the online system or whether post or email is allowed

Following these instructions is advisable, as online submissions systems can be inflexible. If you don’t follow the instructions there may be a delay before the manuscript is looked at by the editors or sent to review.

Length limits

All print journals and many online-only journals have length limits. It is best to keep to them at first submission, if only to avoid annoying the editors and reviewers and to avoid having to shorten your paper later if it is accepted. Some journals will reject any paper that is too long without considering it.

There are usually also length limits on the title and abstract, and sometimes on other sections too. Limits on the numbers of figures, tables and references are also common.

Formatting within the manuscript

Then there are the details of how the manuscript is laid out. In general these instructions are not quite as important at the submission stage as those listed above, as any problems can be fixed once the article is accepted. However, some journals are strict about this kind of thing being done properly on first submission. And it isn’t always clear from the instructions to authors how strict they are. See my previous post about formatting for initial submission for more.

The kind of thing that journals care about in this category are:

  • Whether the abstract is subdivided into sections
  • What sections are required in the main text (usually Introduction, Methods, Results, Discussion or similar)
  • What order the sections should be in (whether the Methods come before the Results or after the Discussion)
  • Whether citations are allowed in the abstract
  • Whether the reference citations should be numbered in order or given in the form “(Author et al., 2009)”

Non-varying instructions

Finally, there are the requirements that practically all journals have, although they can be worded in a variety of ways. These include:

  • Use SI units
  • Define all abbreviations and special symbols on first use
  • Cite all figures, tables and references in the text
  • Gene symbols should be italic; protein names should be Roman.

For more on what most journals tend to have in their instructions, see the generic set of instructions provided by the International Committee of Medical Journal Editors (ICJME).

There are companies and freelance editors, including me, who can help you to comply with instructions for authors for your target journal.

Do you really have to reformat for each new submission?

There was a fascinating conversation at the blog of neuroscientist Dorothy Bishop recently. As a side point in a post on getting replication studies published, she says:

…if a journal commonly rejects papers without review, then it shouldn’t be fussy about the format in which a paper is submitted. It’s just silly for busy people to spend time getting the references correctly punctuated, or converting their figures to a specific format, if there’s a strong probability that their paper will be bounced. Let the formatting issues be addressed after the first round of review.

Palaeontologist Mike Taylor agreed in the comments:

…it seems unbelievably stupid that when preparing my research output for the world, such a huge proportion of the effort is dedicated to inserting and removing commas.

He blogged about this issue back in 2010, commenting that the value of this work by researchers is zero but its cost is enormous. In a recent article in Discover, he says:

Most journals have stringent formatting guidelines that authors must follow in submitted manuscripts. (A colleague of mine recently gave up attempts to submit his manuscript to a particular journal after it was three times rejected without review for trivial formatting and punctuation errors, such as using the wrong kind of dash. Seriously.)

I found it hard to believe that some journals are this strict. When I was an in-house editor (for Elsevier and BioMed Central), I always ignored the formatting of newly submitted papers. I was trained to focus on whether the topic of the manuscript fitted the scope of the journal and whether it would be interesting enough for the readers. I have never seen an article rejected because it was in the wrong format.

But it does seem that there are journals that reject because of formatting before they even decide whether to send a paper to referees. Mike mentions The Journal of Vertebrate Paleontology as being one, and Dorothy describes similar procedures at Journal of Neuroscience and Psychophysiology.

This seems to me to be a great waste of authors’ time. It is an insult to an author to ask them to reformat, only to then reject their paper on grounds other than the formatting – grounds that were presumably clear in the first version. If an editor is sure that they are not going to send a manuscript out to referees, why not just reject it straight away, so that the author can submit it quickly somewhere else?

I know how much time it can take to reformat from one journal style to another. In fact I quite enjoy doing this, though it helps that I am generally being paid to do it and that it is part of my job, not a distraction from important research. And I also have lots of practice in macros, wildcard searches and other tricks that make reformatting far quicker. If you’re a scientist whose main expertise is research, reformatting will be much harder and more frustrating. Scientists are good at research, and copyeditors are good at house style – why don’t journals get their (usually freelance) copyeditors to do this reformatting? The only reason I can think of is that we will charge for the work.

The best time for reformatting to journal style is after a paper is accepted. The second best is when revisions have been requested: given that there is now a good chance that the journal will publish the paper, it seems reasonable at this point to ask the author to get the formatting close to the journal style. Major things, in particular, such as whether the methods section is before or after the results, or keeping to overall length limits, are best done by the authors in revision.

I’d like to put together a list of journals that do or don’t require perfect formatting at first submission, so that authors can find out before submission what will be expected of them. This information isn’t easy to find. Of course, instructions for authors always imply that formatting should be done before submission, because (I suggest) the editors would love every author to do this, as it makes an editor’s job easier. But detailed formatting issues, like the kind of dash used (or other examples given by Mike Taylor)? I don’t believe any editor really needs this kind of thing to be sorted out by authors. If they do, they must frequently be disappointed!

If you feel that it would help your paper to get published if you reformat it precisely to the journal style before submission, I won’t stop you – after all, you will be making the job of the in-house editor easier, which might, you never know, tip the scales in your favour. And if you want to pay me to do the reformatting for you, I probably won’t say no. But at the risk of doing myself out of some work, I would recommend that authors don’t spend too much time or money on reformatting before the paper has been first submitted. And if a journal asks you to reformat when they haven’t promised to send the paper out to referees, I suggest asking why.

Your experience

Journal editors, do you expect papers to be formatted to your house style before you will consider sending them to reviewers? How strict are you about this? Why?

Researchers, which journals have asked you to reformat before they decide whether to send your paper to reviewers? Which journals don’t mind the formatting being incorrect?

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