This tutorial shows PLoS ONE reviewers how to submit their manuscript decision in Editorial Manager.

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At 10 am (PST) on Monday 26th July, PLoS ONE  moved to a new software system for our manuscript submission and peer review process —Editorial Manager® from Aries Systems (referred to as “PLoS EM”). The other PLoS titles will migrate to the new platform later this summer.

If you are a PLoS ONE author (or reviewer) who had a manuscript ‘in process’ with us before this date then your manuscript will continue to be processed in the ‘old’ system for a period of time before it is transferred to the ‘new’ system. You will receive clear notification as to where you should log in to find your manuscript, and more information about this process can be found at our explanatory website.

This new system will make it easier to track the progress of your manuscript and will provide other important user benefits such as:

•    Reliable system performance
•    Easier figure submission—one zipped file upload
•    Fast PDF preview upon submission
•    Multi-tier subject taxonomy
•    Your own home page to track the progress of your manuscript

Recently, Kent Anderson posted some misleading comments about PLoS ONE on the Scholarly Kitchen, a blog site established by the Society for Scholarly Publishing. Although several PLoS community supporters have responded swiftly and vigorously to the comments, PLoS has also decided to make a public statement because Mr Anderson’s comments were extreme and have caused bad feeling particularly among the editorial board members who work so hard to make PLoS ONE a success (on a voluntary basis).

Mr Anderson’s posting and his subsequent responses to comments misrepresent PLoS ONE in four main areas: the PLoS ONE editorial board, the editorial process; the content being published; and the overall goal of PLoS ONE.

1. The editorial board

During his post, Mr Anderson implied that the PLoS ONE Editorial Board (who are now 1,000 strong and as academic editors are responsible for the editorial decisions on PLoS ONE) are accepting sub-standard papers simply to make more money for PLoS. Several academic editors took justified exception to this in the comment thread and elsewhere. The tremendous success of PLoS ONE is in large part a result of the dedication and commitment of the PLoS ONE Editorial Board, and any implication that the PLoS ONE Board members are collectively doing a poor job of evaluating submissions is unjustified.

2. The editorial process

The PLoS ONE editorial and peer review process is very similar to the editorial process on any journal, and is clearly explained on the PLoS ONE web site. The critical difference, and the thing that makes PLoS ONE potentially revolutionary, is that the editors and peer reviewers make no judgment as to the potential impact of the work. Their goal is to focus on scientific rigour alone, although this is by no means an easy task.

Every submission goes through a very substantial quality control check before it reaches an academic editor. This check covers reporting standards, research ethics, competing interests, funding information and so on. We believe that our ‘QC check’ is one of the most extensive and rigorous processes in the industry, and it is overseen by professional editors who are frequently consulted in advance of further peer review. Submissions are then assigned to academic editors, who send the articles to external peer reviewers and take overall responsibility for the editorial decision on the submission assigned to them. Submissions are assessed specifically against the PLoS ONE editorial criteria. We also provide summary statistics on the peer review process and as repeatedly evidenced by published PLoS ONE authors, submissions typically receive excellent peer review comments and go through multiple revisions before ultimately being accepted. PLoS and the Academic Editors are committed to achieving very high standards in the editorial process.

3. The content

Mr Anderson’s post seems to be prompted by some concerns about a specific recent PLoS ONE article, which was critiqued by one of his co-editors on the Scholarly Kitchen blog. The irony here is that one of the goals of PLoS ONE is to open up this kind of dialogue post-publication, so that everyone can benefit from a more open discussion. What we are striving to do better is to capture more of this discussion and link it to the articles themselves.

Putting that one article aside, the implication of the post is that PLoS ONE content is substandard in some way, but evidence to support this claim is not provided. In fact, we do have evidence from usage, citation and media/blog coverage that the quality of content in PLoS ONE is extremely high, and would compare favourably with most journals. For example over 84% of the more than 2700 articles published in 2008 have been cited (from Scopus data), and 39% cited 4 times or more. These and other article-level metric data are publicly available (for all PLoS Journals) on our web site.

PLoS ONE has also been selected for coverage by all major indexing services, including Web of Science and Medline. A round-up of some of the most high-profile content published in PLoS ONE in 2009 was posted in January.

4. The goal of PLoS ONE

As mentioned above, the key innovation of PLoS ONE is that the peer review process involves no judgment about the potential impact of a submission. This is because our view is that the current system of sorting the almost 2 million articles that are published each year, into the existing set of 25,000 journals before publication, with all the delays and redundancy that this involves, is not the best way to organize all research findings in an online world.

Instead, PLoS ONE peer reviews submissions on the basis of scientific rigour, leaving the assessment of the value or significance of any particular article to the post-publication phase. We would fully agree that it is in the post-publication phase that PLoS has not yet achieved as much as we would like. Nevertheless, the addition of article-level metrics to all PLoS content last year is an important step in this direction and there will be further developments in this area.

PLoS ONE thus frees authors from a system of journals that is biased against publication, which means that authors can publish their work swiftly. We have been surprised and delighted that so many authors (now well over 60,000 of them) have supported PLoS ONE by sending us their submissions. As a result of this groundswell of support from the research community, the growth of PLoS ONE has been spectacular and, we believe, unparalleled in the history of scientific publishing (the journal is less than 4 years old and is on target to be the largest peer-reviewed journal in the world this year).

Given that the costs of publication are fully covered by publication fees, it is true that PLoS ONE has helped to move PLoS much closer towards independent economic sustainability. However, it is also the case that the PLoS Community Journals (PLoS Computational Biology, PLoS Pathogens  and PLoS Genetics) launched in 2005 are fully economically sustainable through publication fees and are now making a positive financial contribution to our organisation. There is no question that the financial impact of PLoS ONE is important for PLoS and for open-access publishing more broadly, but to focus purely on this aspect of PLoS ONE is to miss the real significance of PLoS ONE, which was established as an innovative publication vehicle aiming to dramatically improve the pace and efficiency of scientific communication relative to the established order of academic journals.

This significance was formally recognized last year, when PLoS ONE received a major industry award from ALPSP for publishing innovation. The judges indicated that PLoS ONE “combines the traditional values of the journal with innovative online features to create an inclusive and efficient publication channel. It is bold and successful and shaping the future of publishing.”

Finally, we must acknowledge the tremendous support of the research community who as authors, reviewers and editors have already established PLoS ONE as an efficient and effective peer-reviewed publication, which is successfully challenging the traditional notion of a journal.

Pete Binfield, Publisher (PLoS ONE and PLoS Community Journals)
Mark Patterson, Director of Publishing, PLoS

• In Track II, the most common track, authors submit a manuscript directly to the journal, which is assigned to an editor and peer reviewed (the authors are blinded to the identities of the editor and reviewers).
• Track I allows members of the National Academy of Sciences (NAS) to “Communicate” up to two papers per year on behalf of other authors; the NAS member finds at least two additional reviews and then submits the paper and reviews to the PNAS editorial board for approval (the authors are blinded to the identities of the reviewers but not the editor).
• Track III allows NAS members to “Contribute” as many of their own papers as they like, having first secured two reviews from external referees, which are also submitted to the editorial board (there is no blind peer review in this track).

This image forms Figure 1 of PLoS ONE article e8092; any reuse should cite the authors and journal

Rand and Pfeiffer looked at 2,695 papers published between June 2004 and April 2005 and compared the number of 2006 and 2009 citations for papers from each of the tracks. This week’s featured image, Figure 1 from the paper, shows that papers from Track III, the Contributed papers, had significantly fewer citations than papers submitted via the other two tracks. When they considered the citation counts of the bottom 10% of papers in each track, the researchers found that the bottom 10% of Contributed papers were cited much less often than in the other two tracks (as shown in Figure 2).

Among the top 10% of papers, however, the pattern is reversed with the top Contributed papers receiving significantly more citations than papers from Track II, the Direct submissions, as shown in Figure 3, suggesting that while on average, Contributed papers receive lower citation rates than the other two tracks, there is a much higher variance among papers in Track III.

The authors discuss in the paper potential reasons for the observed differences—NAS members can Communicate or Contribute papers on topics outside their area of expertise, for example, and can “soften” the peer review process through their choice of referees. The anonymity of referees and editors varies among the tracks and may also be a factor.

Rand and Pfeiffer conclude, “This analysis demonstrates that different editorial procedures are associated with different levels of impact, even within the same prominent journal, and raises interesting questions about the most appropriate metrics for judging an editorial policy’s success,” and suggest that further research on this topic is needed in order to determine whether authors choose to submit certain papers to particular tracks—to speed up the publication of stronger papers and to increase the chance of acceptance of weaker papers, for example—and the effect of press releasing a paper on its citation count.

You can find other related papers by browsing the Science Policy section of the PLoS ONE website. To receive notifications when new PLoS ONE articles are published, why not sign up for our eTOCs or one of our RSS feeds.

BZ: I’d like to start by putting a bit more detail on your scientific and medical background – what brought you into your research?

My interest in biology and medicine started during my childhood when I realized that biological systems are extremely fascinating and that there is a great need to solve our medical problems. I chose to go to medical school to gain a broad insight into medicine and biology. However, soon after I received my MD, I chose to work in the laboratory and dedicated myself only to research. It has been a wonderful journey.

BZ: What was it that attracted you to PLoS ONE in the first place?

I have always been a big proponent of open biology publishing. I strongly feel that the published scientific knowledge should be freely available to everyone who is interested. We live in an age where information can be accessed from anywhere in the world at any time. In my opinion restricting this access stifles scientific advances. When the first PLoS journal, PLoS Biology, came out I was very excited about the prospects of having freely available journals. Indeed, I sent out our best manuscript at that time to PLoS Biology, which I am proud to say was published at that early stage. Some of my colleagues were quite critical and told me not to take a risk with a PLoS journal and to try another higher impact journal. I guess when you believe in a cause you have to take a chance, which I am very happy that I did.

The premise of PLoS ONE took the concept of open biology one step further by not only freely distributing published scientific knowledge but also facilitating the review process of papers and publication speed. As scientists we have all experienced frustratingly long review processes and constant rejection of manuscripts based on the subjective criteria of some journals. While the science always has to be very solid, sometimes the significance of the work is not readily apparent. I was involved as one of the academic editors from the very inception of PLoS ONE and I am amazed to see how successful it has become, beyond my expectations!

BZ: How many hours a week would you say that you devote to PLoS ONE and when do you fit that into your busy schedule?

As section editor of Immunology I handle relatively large volume of manuscripts, some of which I choose to act on as Academic Editor (AE) myself. These days I have on average 15-20 manuscripts at any given time under my review either as AE or as assigning to other AE’s. I would say, nowadays, that I devote between 4-6 hours a week to PLoS ONE reviews, and that time allocation has been progressively increasing with the number of manuscripts. While our busy schedules only get busier, contributing to PLoS ONE is one activity I do without complaint!

BZ: How does the peer-review process on PLoS ONE work? What is the standard of peer-review on PLoS ONE?

The peer review process of PLoS ONE is not very different compared to other journals. The submitted manuscripts are assigned to either an Academic Editor (AE) or Section Editor, and they then decide to handle them himself/herself or assign them to others with different expertise if necessary. The AE typically then sends the manuscript out to review, although in rare cases if they feel comfortable they can also review it completely on their own.

Once the reviews are received, the AE then makes a decision whether to ask for minor or major modifications, accept or reject the manuscript. At this level, PLoS ONE starts to differ a bit, in that the AE needs to read the reviews carefully and decide what portion of the review does not fit the criteria set for PLoS ONE publishing. Basically, the research needs to be experimentally well performed, controlled, statistically significant and novel (although it could repeat others work if there is controversy or if it is providing additional value). The questions answered by the research also need to be significant and not trivial.

I guess the major difference in PLoS ONE criteria is the judgment we make on the impact of the work. We try to avoid asking for new experiments that would increase the impact of the manuscript once it is published. That is where we enter into the subjective realm and I think we would like that judgment to be made by the larger scientific community. In other words the true value of the published study will be determined at the post-publication level rather than being filtered during the review process.

Another perhaps more subtle difference in the PLoS ONE review process is that once the authors resubmit their papers in response to minor or major critiques, with their rebuttal, then the AE makes the final decision whether or not to accept the paper. For example, if all the questions had been satisfactorily addressed then I very rarely resend the paper for second review. I think this greatly speeds up the review process and also reduces the extra burden on the external reviewers.

BZ: How quickly does this process move?

The first review process takes on average about a month, since the main limitation is to find the right reviewers and receive their reviews.  However, once the authors respond with their rebuttals that typically takes less than a week to issue final decision. This is particularly true in my case as I like to reach a quick decision at this stage to avoid any delays in publishing the work. After that, the PLoS ONE production staff ensure the paper rapidly appears online, a process that is also relatively fast compared to most other journals.

BZ: What’s the general quality of submissions like?

The general quality of submissions, in my experience of 200+ manuscripts, have been solid. There is a some sort of bell curve though. Occasionally we see some fantastic papers and also some rather mediocre studies, which are sound and should be published but nothing to be excited about. Most manuscripts fall somewhere in the middle. I should mention and thank all the reviewers who have, in the overwhelming majority, been incredible in improving the quality of the submitted manuscripts. I think that most authors also appreciate this as the comments are generally very constructive.

BZ: What would you say is the ‘best’ paper you have handled and why?

I will refrain from answering this question, because as I mentioned above “best” is quite subjective. I think that should be determined by the test of time and how that published work leads to unexpected new discoveries by others.

BZ: What do you feel makes PLoS ONE relevant to scientists?

I think an unbiased and relatively fast review process should be very appealing to all scientists. Also, as the success of PLoS ONE shows, scientists want to get their work out as soon as possible so they can focus on new experiments rather than wasting time back and forth on arduous review processes that ask for more and more experiments to increase the impact of their work.

Ultimately, it is the authors of the paper who are responsible for their work. I think every paper should be able to stand on its own and its impact should be determined individually rather than through theoverall impact factor of the journal. I think in the age where technology advances and information flows at ever faster speeds, PLoS ONE helps clear one of those bottle necks in science and I I think that is relevant.

BZ: And finally, what would you say is the thing about Open Access that most excites you?

The ability of anyone, anywhere to access scientific knowledge through the Internet is really a dream come true. I think this will usher a new era where both clinicians and researchers will be able to immediately fact-check or read the details of the published work, rather than worrying about having subscription to the journals.

BZ: Thank you very much for your time. It was great talking to you.

Q: I have just submitted a manuscript to PLoS ONE. How long will the review process take?

A: Our authors often ask us how long it will take before they receive an initial decision on their submission to PLoS ONE and we appreciate that having worked on the research for months or years, authors are often anxious to receive news of the suitability of their manuscript for the journal as soon as possible—we endeavour to ensure that the review process is efficient, as well as rigorous. The following information should help to clarify what happens to your manuscript after submission.

1)     In-House Quality Control (Tech Check). All new submissions are quality checked by our editorial staff, who look both for technical criteria (for instance, do all the manuscript files open correctly?) and content-related criteria (for example, have the authors appropriately declared any potential competing interests?). See our earlier blog post for more detail on this process and for some tips to help your manuscript clear this stage as swiftly as possible. Be aware that we may well need to send the manuscript back to you with requests for more information, which must be provided before we can proceed, however we try to get this check completed within a few days of submission (depending on your response times to our questions). It is only once a manuscript passes QC that we consider it to be formally submitted into our system (as until that point there may be problems with the submission that would prevent us starting the peer review process).

2)     Section Editor Assignment. Most manuscripts are assigned to one of our Section Editors. The main role of the Section Editor is to assign the paper to an Academic Editor (AE) who will handle the review process. At present we do not have a Section Editor to cover every subject area in which we publish but the editorial staff will assign an AE if there is no Section Editor in the field. Authors can recommend appropriate Section Editors via their cover letter. The  process of Section Editor assignment normally takes 1-2 days, although sometimes one of the PLoS staff editors may wish to discuss the paper internally at this stage before proceeding with the review.

3)     Academic Editor Assignment. The peer review of each manuscript is handled by one of our editorial board members, who acts as the AE. We ask authors to suggest suitable AEs when submitting their manuscript to help us to assign it to an AE as quickly as possible. As a general rule we would encourage you to suggest as many suitable Academic Editors as possible – you are asked to suggest some at the time of submission, but please feel to add as many suggestions as you like to your cover letter (we do read the cover letter!). The length of this part of the process can vary depending on the number of AEs we have within a particular discipline and also depending on the time of year (our AEs are often busiest during the summer period, the winter holiday season and in the run-ups to NIH grant deadlines).

4)     Peer Review. PLoS ONE allows AEs to make a decision on a paper in three ways: 1)  by soliciting formal reviews from external referees; 2) by reviewing the manuscript themselves, based on their own knowledge and expertise; and 3) through consultation with other members of the editorial board. Inevitably, the length of the review process will vary depending on the route the AE uses to make a decision (although about 90% of papers are sent to review by  external experts—see our website for more information). We ask authors to suggest potential referees when submitting. We may or may not use those suggestions, at the discretion of the Academic Editor. We ask external reviewers to submit their reports within ten days (although, of course, referees do sometimes ask for more time) and as soon as the AE has received all of the expected reviews, they are prompted to log on to our manuscript submission and send a decision to the authors.

On average, these four stages take about a month, in total, although, of course, because this is an average, the peer review of some manuscripts will inevitably take longer than this and it can be difficult for us to make any guarantees as to how long the process will take for a specific manuscript. If you would like to check on the status of your manuscript during the review process, you can do so by logging on to the manuscript submission system or by contacting plosone [at] plos.org (quoting your manuscript tracking number).

Q: I have just submitted a manuscript to PLoS ONE. How long will the review process take?

A: Our authors often ask us how long it will take before they receive an initial decision on their submission to PLoS ONE and we appreciate that having worked on the research for months or years, authors are often anxious to receive news of the suitability of their manuscript for the journal as soon as possible—we endeavour to ensure that the review process is efficient, as well as rigorous. The following information should help to clarify what happens to your manuscript after submission.

1)     In-House Quality Control (QC) Check. All new submissions are quality checked by our editorial staff, who look both for technical criteria (for instance, do all the manuscript files open correctly?) and content-related criteria (for example, have the authors appropriately declared any potential competing interests?). See our earlier blog post for more detail on this process and for some tips to help your manuscript clear this stage as swiftly as possible. Be aware that we may well need to send the manuscript back to you with requests for more information, which must be provided before we can proceed, however we try to get this check completed within a few days of submission (depending on your response times to our questions). It is only once a manuscript passes QC that we consider it to be formally submitted into our system (as until that point there may be problems with the submission that would prevent us starting the peer review process).

2)     Section Editor Assignment. Most manuscripts are assigned to one of our Section Editors. The main role of the Section Editor is to assign the paper to an Academic Editor (AE) who will handle the review process. At present we do not have a Section Editor to cover every subject area in which we publish but the editorial staff will assign an AE if there is no Section Editor in the field. Authors can recommend appropriate Section Editors via their cover letter. The  process of Section Editor assignment normally takes 1-2 days, although sometimes one of the PLoS staff editors may wish to discuss the paper internally at this stage before proceeding with the review.

3)     Academic Editor Assignment. The peer review of each manuscript is handled by one of our editorial board members, who acts as the AE. We ask authors to suggest suitable AEs when submitting their manuscript to help us to assign it to an AE as quickly as possible. As a general rule we would encourage you to suggest as many suitable Academic Editors as possible – you are asked to suggest some at the time of submission, but please feel to add as many suggestions as you like to your cover letter (we do read the cover letter!). The length of this part of the process can vary depending on the number of AEs we have within a particular discipline and also depending on the time of year (our AEs are often busiest during the summer period, the winter holiday season and in the run-ups to NIH grant deadlines).

4)     Peer Review. PLoS ONE allows AEs to make a decision on a paper in three ways: 1)  by soliciting formal reviews from external referees; 2) by reviewing the manuscript themselves, based on their own knowledge and expertise; and 3) through consultation with other members of the editorial board. Inevitably, the length of the review process will vary depending on the route the AE uses to make a decision (although about 90% of papers are sent to review by  external experts—see our website for more information). We ask authors to suggest potential referees when submitting. We may or may not use those suggestions, at the discretion of the Academic Editor. We ask external reviewers to submit their reports within ten days (although, of course, referees do sometimes ask for more time) and as soon as the AE has received all of the expected reviews, they are prompted to log on to our manuscript submission and send a decision to the authors.

On average, these four stages take about a month, in total, although, of course, because this is an average, the peer review of some manuscripts will inevitably take longer than this and it can be difficult for us to make any guarantees as to how long the process will take for a specific manuscript. If you would like to check on the status of your manuscript during the review process, you can do so by logging on to the manuscript submission system or by contacting plosone [at] plos.org (quoting your manuscript tracking number).

This procedure has originated from our belief that there are certain actions which are most appropriately conducted post-publication (as opposed to pre-publication) and determining the ‘degree of advance’ of a submission is one of those things which can only be done by the wider community, once the publication has joined the literature. Therefore, it was very gratifying to spot an article (published back in 2007) which appears to vindicate this approach from the point of view of highly cited authors. The article Rejecting highly cited papers: The views of scientists who encounter resistance to their discoveries from other scientists” by Campanario and Acedo found the following (from the abstract):

We studied the views of scientists who experience resistance to their new ideas by surveying a sample of 815 scientists who are authors of highly cited articles. The 132 responses (16.2%) received indicated that only 47 scientists (35.6%) had no problems with referees, editors, or other scientists. The most common causes of difficulty were rejection of the manuscript, and scepticism, ignorance, and incomprehension. The most common arguments given by referees against papers were that the findings were an insufficient advance to warrant publication, lacked practical impact, were based on a wrong hypothesis, or were based on a wrong concept. The strategies authors used to overcome resistance included obtaining help from someone to publish problematic papers, making changes in the text, and simple persistence. Despite difficulties, however, some respondents acknowledged the positive effect of peer review.

In our opinion, it is unacceptable that good scientific work is rejected simply because it lacks ‘insufficient advance’ or ‘practical impact’. We believe that all good science should be presented to the world as quickly as possible, and the wider scientific community should then be the ones who decide whether an article was important or not. This has been one of the major motivations behind our development of ‘article-level metrics’ (which provides transparent data on each article, for readers to make use of when forming their own opinion on the paper) and we hope to have some exciting announcements on this front in the next few weeks.

If you are a highly cited author (or aspire to become one) then we welcome your submissions!

This procedure has originated from our belief that there are certain actions which are most appropriately conducted post-publication (as opposed to pre-publication) and determining the ‘degree of advance’ of a submission is one of those things which can only be done by the wider community, once the publication has joined the literature. Therefore, it was very gratifying to spot an article (published back in 2007) which appears to vindicate this approach from the point of view of highly cited authors. The article Rejecting highly cited papers: The views of scientists who encounter resistance to their discoveries from other scientists” by Campanario and Acedo found the following (from the abstract):

We studied the views of scientists who experience resistance to their new ideas by surveying a sample of 815 scientists who are authors of highly cited articles. The 132 responses (16.2%) received indicated that only 47 scientists (35.6%) had no problems with referees, editors, or other scientists. The most common causes of difficulty were rejection of the manuscript, and scepticism, ignorance, and incomprehension. The most common arguments given by referees against papers were that the findings were an insufficient advance to warrant publication, lacked practical impact, were based on a wrong hypothesis, or were based on a wrong concept. The strategies authors used to overcome resistance included obtaining help from someone to publish problematic papers, making changes in the text, and simple persistence. Despite difficulties, however, some respondents acknowledged the positive effect of peer review.

In our opinion, it is unacceptable that good scientific work is rejected simply because it lacks ‘insufficient advance’ or ‘practical impact’. We believe that all good science should be presented to the world as quickly as possible, and the wider scientific community should then be the ones who decide whether an article was important or not. This has been one of the major motivations behind our development of ‘article-level metrics’ (which provides transparent data on each article, for readers to make use of when forming their own opinion on the paper) and we hope to have some exciting announcements on this front in the next few weeks.

If you are a highly cited author (or aspire to become one) then we welcome your submissions!

These individuals often work in an anonymous capacity, in their spare time, and for no remuneration. They are the unsung heroes of the academic journal publication process and both ourselves (the publishers), and the recipients of their advice (the authors and our academic editors) greatly appreciate and value their efforts.

Therefore, in common with many other journals, we are publicly acknowledging and thanking these individuals via our web site. We had already made a page with our most frequent reviewers, but we have now gone back through our  database to make sure that all 9,000 people who submitted a review (through end-2008) are appropriately credited and thanked.  We will be updating these pages annually going forwards, and I would like to add my personal voice to thanking them for their contributions.