Barcamp Open Science 2022

Save the date! – Online 7th March 2022 #oscibar Barcamp Open Science is a friendly and open scpace for those interested in making open science happen and to connect with open science communities. In true Barcamp style the day long event is made up of session suggested by the wider community. If you want to test out an idea, share a project, or have a question you think the open science community…

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Building a Tool to Find Translated Scientific Articles

You know an article exists, but cannot read its language. So you go to our tool, paste the Digital Object Identifier of the article and get a list with translated versions. You manage your articles in a reference manager and notice that an article on your reading list is now also available in your mother tongue. You are really enthusiastic about a new article that was just published…

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Fifteen Years of PLOS ONE

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. 

The post Fifteen Years of PLOS ONE appeared first on EveryONE.

GenR and Co-Producing Guides for Open Science Communities

Image: GenR’s [guide needed] – in style of Wikipedia’s popularized slogan [citation needed], sources here PNG and SVGCC BY SA 4.0. #guideneeded GenR invites you to join it on a new editorial direction for 2022. The plan is to co-produced short actionable guides to support and promote—Open Science communities, and Open Science values and culture. Many Open Science communities have projects and…

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Announcing the Single Source Publishing Community Launch!

The Single Source Publishing Community (SSPC) is focused on scholarly publishing and is a meeting place for researchers, educators, publishers, and software developers. The community looks to help Single Source Publishing (SSP) technology to work better for Open Access, Open Science, in learning, and for Bibliodiversity. Drop in on our discussion board, join the monthly ‘SSPC Show & Tell’ sessions…

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Community Open Principles in the Time of the Pandemic

Online webinar will address these questions via the experiences of invited open science communities including the following speakers: Dr. Ana Persic, UNESCO; Dr. Arianna Becerril García, AmeliCA; Dr. Johanna Havemann, Open Science MOOC; and Osman Aldirdiri, AfricArXiv. June 30, 2021, at 01:00 PM in Universal Time UTC: Webinar: Community Open Principles: Before, During and After the Global Pandemic…

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University of Ottawa signs agreement with PeerJ for innovative new Institutional Author Membership model to fund Open Access

“We are delighted to announce that University of Ottawa have signed up to an innovative new approach to fund Open Access publishing. Funded by the University of Ottawa Library, authors affiliated with the University of Ottawa may publish in PeerJ journals using a new Three-Year Membership; the Membership allows authors to publish up to three articles at any time within a three-year period….”

University of Ottawa signs agreement with PeerJ for innovative new Institutional Author Membership model to fund Open Access

“We are delighted to announce that University of Ottawa have signed up to an innovative new approach to fund Open Access publishing. Funded by the University of Ottawa Library, authors affiliated with the University of Ottawa may publish in PeerJ journals using a new Three-Year Membership; the Membership allows authors to publish up to three articles at any time within a three-year period….”

Open Metrics Require Open Infrastructure

By: John Chodacki, Martin Fenner, Daniella Lowenberg

Today, Zenodo announced their intentions to remove the altmetrics.com badges from their landing pages–and we couldn’t be more energized by their commitment to open infrastructure, supporting their mission to make scientific information open and free.

“We strongly believe that metadata about records including citation data & other data used for computing metrics should be freely available without barriers” – Zenodo Leadership

In the scholarly communications space, many organizations rally around the idea that we want the world’s knowledge to be discoverable, accessible, and auditable. However, we are not all playing by the same rules. While some groups work to build shared infrastructure, others work to build walls. This can be seen by the use of building barriers to entry around freely open information, or, information that should be open and free but isn’t. 

In light of emerging needs for metrics and our work at Make Data Count (MDC) to build open infrastructure for data metrics, we believe that it is necessary for corporations or entities that provide analytics and researcher tools to share the raw data sources behind their work. In short, if we trust these metrics enough to display on our websites or add to our CVs, then we should also demand that they be available for us to audit. 

This isn’t a new idea. The original movement to build Article Level Metrics (ALMs) and alternative metrics were founded on this principle. The challenge is that while infrastructure groups have continued to work to capture these raw metrics, the lopsided ecosystem has allowed corporations to productize and sell them, regardless of there being a true value-add on top of open information or not. 

We believe that the open metrics space should be supported, through contributions and usage, by everyone: non-profits, corporations, and community initiatives alike. In supporting open metrics, though, it is particularly important to acknowledge the projects and membership organizations that have moved the needle by networking research outputs through PIDs and rich metadata. We can acknowledge these organizations by advocating for open science graphs and bibliometrics research to be based on their data, so that others can reproduce and audit the assumptions made. Other ideals that we believe should guide the development of the open metrics space include:

  • Publishers and/or products that deal in building connections between research outputs should supply these assertions to community projects with full permissive CC0 license. 
  • Companies, projects, and products that collect and clean metrics data are doing hard work.  We should applaud them. But we should also recognize when metrics are factual assertions (e.g., counts, citations), they should be openly accessible. 
  • Innovation must continue and, similarly, productization can and should help drive innovation. However, only as a value add. Aggregating, reporting, making data consumption easier, building analysis tools and creating impact indicators from open data can all be valuable. But, we should not reward any project that provides these services at the expense of the underlying data being closed to auditing and reuse.
  • Show our work. We ask researchers to explain their methods and protocols and publish the data that underlies their research. We can and must do the same for the metrics we use to judge them by–and we must hold all actors in this space accountable in this regard as we work toward full transparency.   

These principles are core to our mission to build the infrastructure for open data metrics. As emphasis shifts in scholarly communication toward “other research outputs” beyond the journal article, we believe it is important to build intentionally open infrastructure, not repeating mistakes made in the metrics systems developed for articles. We know that it is possible for the community to come together and develop the future of open metrics, in a non-prescriptive manner, and importantly built on completely open and reproducible infrastructure.

Partnership at the heart of PLOS ONE: The Role of Academic Editors

From its inception, PLOS ONE’s mission has been clear: to create an inclusive venue for all rigorous scientific research irrespective of its perceived impact. Moreover, PLOS wanted to create a journal for, and run by,