An interview with principals of the Scholarly Publishing Roundtable, whose work significantly shaped the Holdren Memo on public access to federally-funded research.
An interview with principals of the Scholarly Publishing Roundtable, whose work significantly shaped the Holdren Memo on public access to federally-funded research.
Robert Harington and Melinda Baldwin discuss whether peer review has a role to play in uncovering scientific fraud.
The post Fraud and Peer Review: An Interview with Melinda Baldwin appeared first on The Scholarly Kitchen.
ASAPBio offers set of principles and guidelines for preprint feedback.
The post Guest Post: Preprint Feedback is Here – Let’s Make it Constructive and FAST appeared first on The Scholarly Kitchen.
The “version of record” is an organizing concept in scholarly publishing. It is by referent to that version that others are understood and it is the object of financial models, policies, and recognition and reward systems.
A look at developments in research integrity, and the attempt to build a universal culture of ethical and responsible practice in research as well as systems within the overall research ecosystem for such a culture to flourish.
The post Guest Post — Research Integrity: Ensuring Trust in Global Research appeared first on The Scholarly Kitchen.
After becoming a Scholarly Kitchen Chef back in July 2019, I have never stopped being amazed by the numerous dynamic issues and developments that scholarly publishing is dealing with. As a biologist by training, ‘diversity’ is the word that comes to mind.
In light of the recent anniversary of the January 6th attack on the US Capitol, we revisit Rick Anderson’s post on how journalists flag unsupported claims and blatant falsehoods, and whether preprint platforms should do the same.
The post Revisiting — Journalism, Preprint Servers, and the Truth: Allocating Accountability appeared first on The Scholarly Kitchen.
When PLOS ONE launched in 2006, few could have predicted where the journal would be fifteen years later. In a previous blog post we pondered the history of PLOS ONE: how it started, how it grew and evolved, and the ways that it has supported PLOS’ mission to transform research communication. Here, Suzanne Farley, the Editorial Director at PLOS, and Emily Chenette, the Editor-in-Chief of PLOS ONE, share their perspectives on the future of PLOS and how they would like to see PLOS ONE evolve over the next fifteen years.
Focusing on communities
Communities have always been the heart of PLOS. In their 2000 open letter that formed the nucleus of PLOS, Harold Varmus, Patrick Brown and Michael Eisen proposed the idea of an online public library that would “catalyze integration of the disparate communities of knowledge and ideas”. As PLOS evolves, our communities will remain our lodestone. We will work with researchers to co-develop solutions that address needs that they have identified. The recent integration of Dryad into the PLOS Pathogens submission system, and the inclusion in global research policy, are two recent examples of the approaches we will take.
We will also build bridges to new communities to advance Open Science. PLOS’ new journals were launched to bring openness and transparency to globally important issues in healthcare and environmental science, and future initiatives will address equally pressing societal concerns. Whether through additional journals, new policies, or other solutions, we’ll continue to engage with researchers around the world and across disciplines to develop open research practices that facilitate knowledge sharing.
We will continue supporting the community of Academic Editors, reviewers and authors that comprise PLOS. By focusing on efficiency and author service, we will ensure that PLOS ONE always offers rapid, constructive review of all manuscripts submitted to the journal. We will expand our editorial board to capture diverse perspectives in peer review, which also supports our ongoing efforts to reduce bias in publishing. We will work more closely with our Section Editors so that they are empowered to represent PLOS ONE in their communities and bring feedback, fresh perspectives and new ideas to the journal.
Over the longer term, PLOS will continue to deliver on its mission to transform research communication through cycles of innovation and interrogation, to determine what has worked and what hasn’t. Importantly, we will pursue just those initiatives that have real community support, which means really listening to our authors, readers, editors and reviewers as we experiment and push the boundaries of Open Science.
High on our list of priorities is finding new ways to make the review and publication process more efficient. This might mean working with other publishers to support broad-scale portable peer review, where authors would be free to transfer reviewers’ comments between journals and publishers. Supporting portable peer review can help address concerns about reviewer fatigue and redundancy that arise when inviting the same pool of reviewers to review the same manuscript as it is submitted to different journals. We might explore open peer review, where reviewers’ comments and Academic Editors’ decisions are posted to an existing preprint, and the manuscript is formally published once all concerns have been addressed. A system such as this supports early access to knowledge and an open discussion of a study’s strengths and limitations.
We will also investigate the possibility of bringing automated tools into the editorial screening process to ensure that all published papers comply with PLOS ONE policies – not in a way that replaces experts with algorithms, but instead focuses attention on critical aspects of the manuscript. One example would be a tool that highlights potential areas of concern in research ethics or figure preparation so that the journal team can work with authors to resolve potential issues before a manuscript is sent to peer review.
We’d also like to consider how we can reduce redundancy in research. Data sharing is key to achieving this, and PLOS has long required that all relevant data supporting a study’s conclusions be shared at the time of publication. However, we can do more to enhance the visibility and usability of data published in PLOS ONE. This may mean making datasets interactive, developing closer links with data repositories, and other solutions that foster reuse. We may also move away from the idea that a published paper represents the final research output. There are all sorts of opportunities for innovation here, including live lab notebooks or other forms of preregistration, and publication of datasets as soon as they are produced.
Driving positive change
We will progress through these cycles of innovation with our communities as our partners. PLOS aims for transparency in all it does, so we will ensure that we have community support for new projects and will share insights into how we’ve decided to support or sunset new initiatives along the way. By being open about decision making, we hope to bring additional insight and feedback into how we publish high-quality content, and therefore increase accountability and trust.
As we celebrate the first 15 years of experimentation and innovation at PLOS ONE, we look forward to working with you as we continue to develop the journal to support you and your research. Thank you for being a part of this journey!
The post Peering into the future: A vision for the next 15 years of PLOS ONE appeared first on EveryONE.
2006 was a year of notable advances in human knowledge. This was the year that the gene sequence of human chromosome 1 was finalized, element 118 (ununoctium) was identified, and the first human papillomavirus vaccine was approved. Pluto was once again designated as a dwarf planet, gene sequences of Neandertal DNA were published, and Grigori Perelman’s proof of the Poincaré conjecture was independently validated (thrice!).
Against this backdrop of progress and innovation, PLOS ONE sprang to life, publishing its first papers on December 20th, 2006. Conceived to “return control over scholarly publishing to the research community”, PLOS ONE broke conventions in academic publishing by prioritizing rigor over impact, and quality over advance. Its encompassing scope welcomed research from all disciplines, including highly interdisciplinary or multidisciplinary research.
The research community immediately took notice. First a trickle, then a stream, and then a flood of submissions came in from authors around the world. Our editorial board grew and editorial policies evolved. Fifteen years later, we have published over a quarter of a million papers, while retaining our commitment to publishing all ethically and methodologically rigorous research.
Figure 1 – Cumulative publications in PLOS ONE, 2006 – 2021
To celebrate this important milestone for PLOS ONE, I reached out to several former PLOS staff members who had key roles shaping the journal and invited them to share their experiences. Their stories reflect the passion that we feel for this journal, its mission, and its community, and the important ways in which PLOS ONE has driven innovation over the years. They also point to a wild first few years, as the journal team raced to develop workflows to keep pace with the tide of submissions. Ginny Barbour, Co-Lead of Queensland University of Technology (QUT) Office for Scholarly Communication and Director of Open Access Australasia, shares her reflections on the early days of PLOS ONE:
PLOS ONE was a project that everyone at PLOS passionately believed in. It was a natural extension of the existing journals, which we hoped would make open access a viable alternative for many more authors than were able to publish in our selective journals such as PLOS Medicine, where I worked.
We had no idea how successful it would be! Right from the beginning, submissions poured in, which proved a huge challenge for our intention of publishing all objectively sound, ethical research. Editors from the other journals pitched in to help with screening and for a while we had a daily rota to share the load.
Spearheading editorial standards in reporting and research ethics
As the submission volume grew, the PLOS editorial team worked to balance PLOS ONE’s mission of publishing all rigorous research with the priority of upholding high standards of research and publication ethics. The team recognized that the high volume of submissions placed a high volunteer burden on the editorial board and reviewers. Additionally, because the journal relied on a broad, diverse, and international editorial board to manage peer review, it needed a system in place to ensure that policies and editorial standards were consistently applied. Together, these factors led to the development of a pre-review submission scan, or “subscan” step, to triage manuscripts that did not meet PLOS ONE’s editorial standards. Damian Pattinson, Executive Director of eLife, remembers the development of the subscan process:
My years at PLOS ONE were some of the happiest, and certainly the most exhilarating, of my career. When I joined in January 2010, the journal was receiving around 500 submissions per month, which Matt Hodgkinson (then a freelancer) and I would assess individually for suitability for peer review (in the process known as ’subscanning’, which I believe was originally invented by Catriona MacCallum and Emma Veitch). At that volume we were just about able to keep on top of every paper and make judgments on what was suitable, but it also quickly became clear that robust editorial policies were needed to deal with all the issues we were seeing. For example there was extraordinary variability in the ethical oversight of the research being submitted, so we worked to create policies that set high standards for animal and human research. As we grew over the following years (to almost 5000 submissions per month when I left!), these policies were adopted by other journals, including the newly-forming megajournals. As a result they became the de facto standard for a vast swathe of the literature, thereby improving ethical standards across the research community as a whole. This is perhaps one of the lesser known areas in which PLOS ONE was a pioneer, but probably the one I’m most proud of.
Ginny Barbour adds:
With my particular interest in publication ethics, I got asked to look especially at some of the most hair-raising submissions. The need to develop ways to handle such issues was the beginning of the rigorous PLOS ONE screening process, which in many ways led the way for the concept of ethical publishing at scale that other mega-journals adopted.
Through the years, the subscan process evolved to encompass additional checks to ensure that research was not only ethically rigorous, but met community standards to ensure reproducibility and transparency in reporting. Where existing standards existed, the journal adopted them – for example, we require PRISMA checklists and flow diagrams for systematic reviews, summary validation reports for macromolecular structures, and protocol documentation and registration for clinical trials. Where standards did not exist, but a need for standards existed in the community, PLOS developed new guidelines to fill these gaps. Matt Hodgkinson, Head of Editorial Policy and Ethics at Hindawi, explains:
Upholding rigour was always key and the development of our own guidelines for meta-analyses of genetic association studies is a good example of that. That guidance was cited in an editorial in the American Journal of Epidemiology.
Pushing the boundaries of open science
With these policies in place, publications flowed rapidly through the pipeline. PLOS ONE’s early success with its unique publication criteria soon attracted the attention of other publishers. Matt Hodgkinson remembers:
I joined in 2010 at the transition from experiment to established journal. The challenge was scale, moving from an authorship and editorial board of early-adopters and Open Access supporters to mainstream researchers as submissions rapidly climbed, helped along by the first Impact Factor being given that summer. The ONE publishing team was tiny – me, Damian, Pete [Binfield], and Lindsay King (now Howell), plus Emma Veitch and Catriona as consulting editors – and had expanded enormously by the time I left in 2016. ONE cemented the idea of publishing sound science regardless of perceived interest level or impact and the launch of competing megajournals in the wake of our success was gratifying: imitation is the sincerest form of flattery.
PLOS embraced the emergence of other new Open Access megajournals, even though the new journals introduced competition within the publishing market. After all, PLOS ONE was launched to support PLOS’ mission to transform research communication. By inspiring additional journals and ensuring that yet more research would be publicly available, PLOS ONE’s positive effects on access to knowledge extended far beyond the boundaries of its own digital pages.
In some cases, difficult editorial situations led to innovative solutions that further advanced PLOS’ mission. Iratxe Puebla, Associate Director at ASAPbio, remembers a time where PLOS ONE’s publication criteria and Open Access publishing model drove knowledge forward:
PLOS ONE was created to remove barriers: for authors to publish their work (related to scope or perceived impact) and for readers to access and reuse scientific content. Looking back at the many initiatives and papers I was involved with during my time at PLOS, there is one article that exemplifies this goal of facilitating openness.
In 2014 PLOS ONE handled a paper that reported a re-analysis of previous publications reporting the creation of “striped nanoparticles”. The authors completed a re-analysis and critique of those findings and wished to publish their work in a journal so that it would be part of the scientific record, on the same ground as the original articles. The authors had had trouble getting earlier critiques published in journals, and decided to submit the paper to PLOS ONE. This is where the first barrier went down: PLOS ONE would not reject the manuscript because it reported a re-analysis or because it relied on previously available data, the evaluation would focus on the rigor of the methodology and the validity of the conclusions.
The paper underwent a thorough peer review process and was accepted. But then we encountered a dilemma: the re-analysis required comparisons to images in the original publications where the journals owned copyright. Should we ask for permission to publish the images under a single-use license or request to republish them under the CC BY license used by PLOS ONE? While the former would have been the traditional (and easier) approach, we chose to pursue the latter. Why? Because the journal wanted to make all its content be available for reuse, for both humans and machines, without having to check individual figures in individual articles for the permitted uses. The PLOS ONE team worked with the authors and the publishers of the original articles, and we were pleased that they agreed to have the images republished under the CC BY license. As a result, the full article, including all images, is available for reuse without license-related barriers.
Figure 2 – Do striped nanoparticles exist? Figure 3 from Stirling J, Lekkas I, Sweetman A, Djuranovic P, Guo Q, Pauw B, et al. (2014) Critical Assessment of the Evidence for Striped Nanoparticles. PLOS ONE 9(11): e108482. https://doi.org/10.1371/journal.pone.0108482
Centering our community
In the first decade after launch, much work at PLOS ONE focused on developing internal policies to guide robust review of the hundreds of submissions we received each week and building up the editorial board to handle these submissions. As PLOS ONE passed a decade of publishing, the journal team considered the future of PLOS ONE and academic publishing. Joerg Heber, Research Integrity Officer at Lawrence Berkeley National Laboratory, discusses how he brought changes to the journal to ensure that it would continue to deliver on its mission and meet the needs of its community:
I became PLOS ONE’s Editor-in-Chief in November 2016, just prior to its 10-year anniversary. In many ways, the journal was at a turning point with falling submissions owing to competition by other journals. In response, we went back to the basics: a focus on author service. We refreshed our editorial board with 3,000 new Academic Editors, which helped to improve manuscript turnaround times. And we improved the editorial screening of submissions to ensure their scientific validity. These successes provided us with a solid basis from which we could continue editorial innovations in publishing, such as published peer review history or support of registered reports. PLOS ONE was (and I reckon still is) a fast-paced, wild and intensely stimulating environment, and all these successes would not have been possible without the tremendous dedication and supreme talents of all those that contribute to the journal from all departments within PLOS!
The improvements that Joerg helped to put in place ensured that author service – and a focus on our community – remained at the heart of the journal. While expanding our editorial board, we put in place a team dedicated to supporting our Academic Editors. We established a publication ethics team, who rigorously investigate pre- and post-publication concerns raised on PLOS ONE papers. We also developed four specialized editorial teams within the journal – devoted to Life Sciences, Behavioral and Social Sciences, Physical Sciences and Engineering, and Public Health and Medicine – composed of staff editors with the expertise needed to offer constructive support to authors, reviewers and Academic Editors throughout the review and publication process.
This foundation provided the necessary support for subsequent innovations at the journal. We’re now in a strong position where we can look out, look around, and ask our communities how we can help them open their research. In recent years we’ve facilitated posting of preprints to allow authors to share their findings with the community earlier and establish priority for their research. We’ve enabled authors to publish the peer review history of their manuscripts, supporting transparency in peer review and bringing recognition to reviewers. We have also launched Registered Reports, Study Protocols and Lab Protocols to support credit, transparency and reproducibility in research and combat publication bias.
We’ve also committed to better serving our communities by working to improve diversity, equity and inclusion in publishing. Indeed, in partnership with researchers from South Africa, New Zealand, the USA, and Kenya, we have co-developed a new policy to increase inclusion in global research. We have also recently published collections of papers on Health and Health Care in Gender-Diverse Communities, Diagnostic Tests in Low-Resource Settings, and Health Inequities and Disparities Research, and launched a Call for Papers on Cancer and Social Inequity. To spur broader change, we’ve also joined forces with other publishers in calling to make scholarly publishing more diverse and inclusive.
Where do we go from here? Suzanne Farley, the Editorial Director at PLOS, and I will discuss our vision for PLOS ONE and PLOS more generally in a future blog post. Importantly, nothing that we hope to accomplish, and nothing that we’ve accomplished in years past, would have been possible without the support of our community – the 9500+ Academic Editors, hundreds of thousands of reviewers, and millions of authors and readers who have made PLOS ONE into the journal it is today. This milestone is possible because of you. Thank you all for supporting Open Science and joining us in our efforts to transform research communication.
Manuscript Exchange Common Approach (MECA) committee members champion the benefits of standardizing the transfer of papers between journals.
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Part 2 of this series looking at open access developments in Canada examines the changing processes and infrastructure needs for open science.
Roger Schonfeld argues that openness and politicization together have enabled public trust in science to erode. And science is insufficiently trustworthy. The scholarly communication sector must not ignore this situation.
Today’s post looks back on the Journal of Emerging Investigators as it approaches it’s 10th anniversary of providing a forum from middle school and high school students.