Open Science

“For a growing number of scientists, though, the process looks like this:

The data that the scientist collects is stored in an open access repository like figshare or Zenodo, possibly as soon as it’s collected, and given its own Digital Object Identifier (DOI). Or the data was already published and is stored in Dryad.
The scientist creates a new repository on GitHub to hold her work.
As she does her analysis, she pushes changes to her scripts (and possibly some output files) to that repository. She also uses the repository for her paper; that repository is then the hub for collaboration with her colleagues.
When she’s happy with the state of her paper, she posts a version to arXiv or some other preprint server to invite feedback from peers.
Based on that feedback, she may post several revisions before finally submitting her paper to a journal.
The published paper includes links to her preprint and to her code and data repositories, which makes it much easier for other scientists to use her work as starting point for their own research.

This open model accelerates discovery: the more open work is, the more widely it is cited and re-used. However, people who want to work this way need to make some decisions about what exactly “open” means and how to do it. You can find more on the different aspects of Open Science in this book.

This is one of the (many) reasons we teach version control. …”

Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals | PLOS ONE

Abstract:  Introduction

Preprints have been widely cited during the COVID-19 pandemics, even in the major medical journals. However, since subsequent publication of preprint is not always mentioned in preprint repositories, some may be inappropriately cited or quoted. Our objectives were to assess the reliability of preprint citations in articles on COVID-19, to the rate of publication of preprints cited in these articles and to compare, if relevant, the content of the preprints to their published version.

Methods

Articles published on COVID in 2020 in the BMJ, The Lancet, the JAMA and the NEJM were manually screened to identify all articles citing at least one preprint from medRxiv. We searched PubMed, Google and Google Scholar to assess if the preprint had been published in a peer-reviewed journal, and when. Published articles were screened to assess if the title, data or conclusions were identical to the preprint version.

Results

Among the 205 research articles on COVID published by the four major medical journals in 2020, 60 (29.3%) cited at least one medRxiv preprint. Among the 182 preprints cited, 124 were published in a peer-reviewed journal, with 51 (41.1%) before the citing article was published online and 73 (58.9%) later. There were differences in the title, the data or the conclusion between the preprint cited and the published version for nearly half of them. MedRxiv did not mentioned the publication for 53 (42.7%) of preprints.

Conclusions

More than a quarter of preprints citations were inappropriate since preprints were in fact already published at the time of publication of the citing article, often with a different content. Authors and editors should check the accuracy of the citations and of the quotations of preprints before publishing manuscripts that cite them.

Open Research in the Humanities | Unlocking Research

“The Working Group on Open Research in the Humanities was chaired by Prof. Emma Gilby (MMLL) with Dr. Rachel Leow (History), Dr. Amelie Roper (UL), Dr. Matthias Ammon (MMLL and OSC), Dr. Sam Moore (UL), Prof. Alexander Bird (Philosophy), and Prof. Ingo Gildenhard (Classics). We met for four meetings in July, September, October and December 2021, with a view to steering and developing services in support of Open Research in the Humanities. We aimed notably to offer input on how to define Open Research in the Humanities, how to communicate effectively with colleagues in the Arts and Humanities (A&H), and how to reinforce the prestige around Open Research. We hope to add our perspective to the debate on Open Science by providing a view ‘from the ground’ and from the perspective of a select group of humanities researchers. These disciplinary considerations inevitably overlap, in some measure, with the social sciences and indeed some aspects of STEM, and we hope that they will therefore have a broad audience and applicability.

Academics in A&H are, in the main, deeply committed to sharing their research. They consider their main professional contribution to be the instigation and furthering of diverse cultural conversations. They also consider open public access to their work to be a valuable goal, alongside other equally prominent ambitions: aiming at research quality and diversity, and offering support to early career scholars in a challenging and often precarious employment landscape.  

Although A&H cover a diverse range of disciplines, it is possible to discern certain common elements which guide their profile and impact. These common elements also guide the discussion that follows….”

OPEN SCIENCE INITIATIVES: THE POSTPRINT PLEDGE

“• Is it legal to post “postprints” online? • Depends on each publisher’s policies • We compiled a list of 60 Applied Linguistics journals (from Web of Science) • Examined their copyright policies from Sherpa Romeo (https://v2.sherpa.ac.uk/romeo/) • Publishers that permit postprints: • Cambridge, Elsevier, John Benjamins, SAGE, Emerald, De Gruyter, Akadémiai Kiadó • Publisher that permit postprints on personal websites only (embargo on repositories): • Springer, Oxford University Press, Taylor & Francis • Publishers that do NOT permit on postprints before an embargo period: • Wiley (usually 24-month embargo)…

What this Pledge is NOT asking you to do: • Does not ask you to break any laws. Sharing postprints is within your rights (see table next slide). • Does not ask you to share “preprints” but to share “postprints”. • Does not limit you to publishing in these journals. • Does not require you do anything else (like boycotting certain publishers or not reviewing for them)….” 

A Synthesis of the Formats for Correcting Erroneous and Fraudulent Academic Literature, and Associated Challenges | SpringerLink

Abstract:  Academic publishing is undergoing a highly transformative process, and many established rules and value systems that are in place, such as traditional peer review (TPR) and preprints, are facing unprecedented challenges, including as a result of post-publication peer review. The integrity and validity of the academic literature continue to rely naively on blind trust, while TPR and preprints continue to fail to effectively screen out errors, fraud, and misconduct. Imperfect TPR invariably results in imperfect papers that have passed through varying levels of rigor of screening and validation. If errors or misconduct were not detected during TPR’s editorial screening, but are detected at the post-publication stage, an opportunity is created to correct the academic record. Currently, the most common forms of correcting the academic literature are errata, corrigenda, expressions of concern, and retractions or withdrawals. Some additional measures to correct the literature have emerged, including manuscript versioning, amendments, partial retractions and retract and replace. Preprints can also be corrected if their version is updated. This paper discusses the risks, benefits and limitations of these forms of correcting the academic literature.

 

A Light in the Dark: Open Access to Medical Literature and the COVID-19 Pandemic

Introduction. This study was designed to evaluate the accessibility of peer-reviewed literature regarding COVID-19 and the ten diseases with the highest death toll worldwide.
Method. We conducted extensive searches of studies concerning COVID-19 and other diseases using the Web of Science, and the Google and Google Scholar search engines.
Analysis. Open access rates were obtained from the Web of Science database, taking into account different types of publications and research areas. Quantitative analyses based on random samplings were used to estimate the potential increase of open access rates achievable with open archiving of post-prints.
Results. The open access rate of COVID-19 papers (89.5%) largely outnumbered that of the ten most deadly human diseases (48.8%, on average). We estimated that most of the gap (70%) could be bridged by making available online, post-print manuscripts.
Conclusions. The pandemic represents a real breakthrough, in scientific publishing, towards the goal of health information for all, demonstrating that much greater access to medical literature is possible. The green road may be the best way to bring open access rates of peer review of other major diseases closer to that of COVID-19. However, it needs to be implemented more effectively, combining bottom-up and top-down actions and making the open science culture more widespread.

 

eLife and PREreview extend partnership to boost community engagement in open peer review | For the press | eLife

eLife and PREreview are pleased to announce their continued partnership to engage more diverse communities of researchers in peer review.

eLife and PREreview formally teamed up last year following their collaborations on a number of initiatives. Now, as eLife moves towards a new ‘publish, review, curate’ model that puts preprints first, the organisations will increase their efforts to involve more early-career researchers, and researchers from communities that are traditionally marginalised within the peer-review process, in the public review of preprints. Their work will involve further integrating PREreview into Sciety – an application developed by a team within eLife to bring open evaluation and curation together in one place – and opening up new opportunities for more researchers to participate in public review.

The rise of preprints — University Affairs

“Peer review, despite its flaws, is one of the most important pillars of the scientific process. So preprint servers, which make scientific papers that have yet to be reviewed or published available online, have been slow to catch on in many fields.

But then came the pandemic.

“COVID changed everything,” says Jim Handman, executive director of the Science Media Centre of Canada. Scientists, science communicators, and journalists who had been wary of using preprints in the past suddenly felt the urgency to get important new information out as fast as possible to help deal with the unprecedented public health threat. The use of preprint servers skyrocketed. Now, everyone is adapting to this new way of working, developing best practices to harness the benefits of increased speed and wider reach while mitigating the risks of sharing unreviewed science.

Most of the time, the world of scholarly publishing moves at an almost glacial pace. New publications can take months or even years to wind their way through the process of peer review and publication. Even then, they can be hard to access for most people. So 30 years ago, some scientists started posting their work in online repositories before it had been formally reviewed and published. ArXiv, which shares research on math, physics, and astronomy, was the first to launch in 1991. It was followed by repositories for other subject areas over the next few decades….”

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Guest Post – Open Access in Japan: Tapping the Stone Bridge – The Scholarly Kitchen

“April Fool’s Day is not really a thing in Japan, so whereas many companies in the West tend to avoid the first of the month when making important announcements, it is in no way unusual that the Japan Science and Technology Agency (JST), the nation’s second-largest public-sector research funder chose April 1st, 2022 to unveil its revised open access policy and implementation guidelines with a typical lack of fanfare outside of its home country….

Such a comparatively low-key approach is in line with past precedent as Japanese funding bodies such as JST, have typically opted for a light-touch and iterative approach to open access policies – which for the most part have been developed in consultation with publishers – in contrast to counterparts in other countries that have put forward more radical and headline-generating open access initiatives such as the US OSTP “Holdren Memo”, Plan S, and UKRI’s open access policy announced in mid-2021. Previous versions of the JST open access policy issued in 2013 and 2017 went little remarked upon in many open science circles and were notable for their conciliatory approach, in contrast to the openly-stated ambition to disrupt and reform the world of scholarly publishing of many other funders. Following this consultative tradition, the current policy was circulated in draft form to publisher members of CHORUS, of which JST is a participating funder, for comment prior to publication….

The most noticeable difference between the new policy and previous iterations is the introduction of an embargo period which stipulates that at minimum the Accepted Manuscript (AM) of any paper arising from a project submitted for funding to JST after the go-live date of April 1, 2022, must be made publicly accessible in an institutional or public repository in Japan within 12 months of publication of the resultant journal article. Whilst cautious by European standards, this is the first time that an embargo of any type has been included in the JST policy. In addition to AMs of research articles, the policy covers those of review articles and conference papers. While the revised policy signals a preference for the green route and does not mandate that the VoR be made available open access, publication as an open access article is a “permitted” route and under the new policy, APCs are fully reimbursable from grant money….

Furthermore, it is notable that both the policy and its implementation guidelines are silent on the twin subjects of transformative journals and transformative agreements. …

Advocates of faster and more radical transformation will probably lament the lack of clarity or silence on certain issues – such as a ban on publishing in hybrid journals and gaps around CC BY licensing for the AM – that have become totemic in many open access circles and offer a more lukewarm response. Those in the latter group may find some consolation in the knowledge that in Japan, caution does not necessarily indicate disapproval and is often regarded as a virtue, encapsulated in the phrase: ???????? (Ishibashi wo tataite wataru) “to tap on a stone bridge before crossing.” Cautious progress may initially be slower than those who rush headlong, but caution helps avoids missteps. And you’re still going across the bridge.”

 

The future of research revealed | Elsevier.com | April 20, 2022

“The research ecosystem has been undergoing rapid and profound change, accelerated by COVID-19. This transformation is being fueled by many factors, including advances in technology, funding challenges and opportunities, political uncertainty, and new pressures on women in research. At Elsevier, we have been working with the global research community to better understand these changes and what the world of research might look like in the future. The results were published today in Elsevier’s new Research Futures Report 2.0. The report is free to read and download….”

Job: Preprint Community Manager | preLights

preLights is a preprint highlighting service that is centred around a community of early-career researchers. Launched in 2018, this initiative has gained significant attention from researchers as well as the publishing industry, being nominated for an ALPSP Award for Innovation in Publishing in 2019. We are now looking for the right person to join us for the next phase of community building and the site’s growth and development.

Joining an experienced and successful publishing team, this is an exciting opportunity for an enthusiastic and motivated team player to take a step into publishing or for someone already working in publishing to extend their interest in online communities.

Applicants will have relevant research experience, ideally a PhD in a field that features in preLights’ coverage. They should have a good understanding of the needs of scientists and the growing impact of preprints in biomedical research.