Category Archives: oa.speed

News & Views: Preprints and COVID-19: Findings from our PRW Survey – Delta Think

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“In anticipation of Peer Review Week 2020, and in consideration of the theme ‘Trust in Peer Review’, Delta Think surveyed broadly across a two-week period in August to determine whether COVID-19 has impacted perceptions of preprints. The survey was open to everyone – from Publishers to Librarians to Researchers to the Lay Public with an interest in scientific output.

We entered into the survey with open minds, though a few recurring themes circulating in news outlets were on our minds including: the idea that both traditional journal submissions and articles posted to preprint servers have spiked in the last six months, owing to COVID-19; and the hunch that perhaps increased traffic indicated a correlated spike in trust, or conversely, that challenged findings making their way into mainstream news might have reduced trust. Was the reputation associated with preprints in jeopardy? Or could they play a critical role in speeding up science at a time so critical for the global health community? With these early loose hypotheses and questions, we launched the survey.

We explore the survey results below. In the spirit of transparency, we will make the data collected available within the next few weeks. It’s also important to note that while this was a quick survey, and is not meant to include a representative sample from the participating audiences, it provides interesting top-level findings and points to areas that may be ripe for a further investigation or a deeper dive in future….”

Preprints in the Public Eye – ASAPbio

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“Today, we’re pleased to announce the launch of a project on the use of preprints in the media with support from the Open Society Foundations. 

Premature media coverage was the top concern about preprints in our recent #biopreprints2020 survey, for both those who had published their research as preprints and for those who had not….

ASAPbio, with support from the Open Society Foundations, now aims to consolidate and expand on existing efforts to set best practice standards for preprints via the launch of our Preprints in the Public Eye project. We are calling for involvement from researchers, journalists, institutions, librarians, funding agencies, and more to work on the following three main aims or the project:

To improve the transparency and clarity of how preprints are labelled so that readers understand what checks have and have not been made on a preprint.
To agree a set of best practice guidelines for researchers and institutions on how to work with journalists on research reported as preprints.
To agree a set of best practice guidelines for journalists on how to assess and report on research posted as preprints….”

Viral Science: Masks, Speed Bumps, and Guard Rails: Patterns

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“With the world fixated on COVID-19, the WHO has warned that the pandemic response has also been accompanied by an infodemic: overabundance of information, ranging from demonstrably false to accurate. Alas, the infodemic phenomenon has extended to articles in scientific journals, including prestigious medical outlets such as The Lancet and NEJM. The rapid reviews and publication speed for COVID-19 papers has surprised many, including practicing physicians, for whom the guidance is intended….

The Allen Institute for AI (AI2) and Semantic Scholar launched the COVID-19 Open Research Dataset (CORD-19), a growing corpus of papers (currently 130,000 abstracts plus full-text papers being used by multiple research groups) that are related to past and present coronaviruses.

Using this data, AI2, working with the University of Washington, released a tool called SciSight, an AI-powered graph visualization tool enabling quick and intuitive exploration
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 of associations between biomedical entities such as proteins, genes, cells, drugs, diseases, and patient characteristics as well as between different research groups working in the field. It helps foster collaborations and discovery as well as reduce redundancy….

The research community and scientific publishers working together need to develop and make accessible open-source software tools to permit the dual-track submission discussed above. Repositories such as Github are a start….”

Balancing Scientific Rigor With Urgency in the Coronavirus Disease 2019 Pandemic | Open Forum Infectious Diseases | Oxford Academic

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“In the midst of the worst pandemic in a century, the medical community must contend with an unprecedented deluge of scientific information. Coronavirus disease 2019 (COVID-19) has stretched the capacity of journals to ensure rapid dissemination of studies to inform the response to the pandemic while maintaining quality standards. At the same time, the ecosystem of knowledge dissemination is changing, with the rise of nonpeer-reviewed pathways, including the use of preprint servers and the apparent trend of publication by press release. We argue that peer-reviewed journals are more critical than ever, and that it is imperative that journals not abandon principles of scientific rigor in favor of urgency….”

Coronavirus mapping in scientific publications: When science advances rapidly and collectively, is access to this knowledge open to society? | SpringerLink

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Abstract:  The COVID-19 pandemic is creating a global health emergency. Mapping this health emergency in scientific publications demands multiple approaches to obtain a picture as complete as possible. To progress in the knowledge of this pandemic and to control its effects, international collaborations between researchers are essentials, as well as having open and immediate access to scientific publications, what we called “coopetition”. Our main objectives are to identify the most productive countries in coronavirus publications, to analyse the international scientific collaboration on this topic, and to study the proportion and typology of open accessibility to these publications. We have analyzed 18,875 articles indexed in Web of Science. We performed the descriptive statistical analysis in order to explore the performance of the more prolific countries and organizations, as well as paying attention to the last 2 years. Registers have been analyzed separately via the VOSviewer software, drawing a network of links among countries and organizations to identify the starred countries and organizations, and the strongest links of the net. We have explored the capacity of researchers to generate scientific knowledge about a health crisis emergency, and their global capacity to collaborate among them in a global emergency. We consider that science is moving rapidly to find solutions to international health problems but access to this knowledge by society is not so quick due to several limitations (open access policies, corporate interests, etc.). We have observed that papers from China in the last 3 months (from January 2020 to March 2020) have a strong impact compared with papers published in years before. The United States and China are the major producers of documents of our sample, followed by all European countries, especially the United Kingdom, Germany, the Netherlands, and France. At the same time, the leading role of Saudi Arabia, Canada or South Korea should be noted, with a significant number of documents submitted but very different dynamics of international collaboration. The proportion of international collaboration is growing in all countries in 2019–2020, which contrasts with the situation of the last two decades. The organizations providing the most documents to the sample are mostly Chinese. The percentage of open access articles on coronavirus for the period 2001–2020 is 59.2% but if we focus in 2020 the figures increase up to 91.4%, due to the commitment of commercial publishers with the emergency.

 

 

Science at Warp Speed: Medical Research, Publication, and Translation During the COVID-19 Pandemic | SpringerLink

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“In response to the COVID-19 pandemic, there has been a rapid growth in research focused on developing vaccines and therapies. In this context, the need for speed is taken for granted, and the scientific process has adapted to accommodate this. On the surface, attempts to speed up the research enterprise appear to be a good thing. It is, however, important to consider what, if anything, might be lost when biomedical innovation is sped up. In this article we use the case of a study recently retracted from the Lancet to illustrate the potential risks and harms associated with speeding up science. We then argue that, with appropriate governance mechanisms in place (and adequately resourced), it should be quite possible to both speed up science and remain attentive to scientific quality and integrity….”

Preliminary analysis of COVID-19 academic information patterns: a call for open science in the times of closed borders | SpringerLink

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Abstract:  The Pandemic of COVID-19, an infectious disease caused by SARS-CoV-2 motivated the scientific community to work together in order to gather, organize, process and distribute data on the novel biomedical hazard. Here, we analyzed how the scientific community responded to this challenge by quantifying distribution and availability patterns of the academic information related to COVID-19. The aim of this study was to assess the quality of the information flow and scientific collaboration, two factors we believe to be critical for finding new solutions for the ongoing pandemic. The RISmed R package, and a custom Python script were used to fetch metadata on articles indexed in PubMed and published on Rxiv preprint server. Scopus was manually searched and the metadata was exported in BibTex file. Publication rate and publication status, affiliation and author count per article, and submission-to-publication time were analysed in R. Biblioshiny application was used to create a world collaboration map. Preliminary data suggest that COVID-19 pandemic resulted in generation of a large amount of scientific data, and demonstrates potential problems regarding the information velocity, availability, and scientific collaboration in the early stages of the pandemic. More specifically, the results indicate precarious overload of the standard publication systems, significant problems with data availability and apparent deficient collaboration. In conclusion, we believe the scientific community could have used the data more efficiently in order to create proper foundations for finding new solutions for the COVID-19 pandemic. Moreover, we believe we can learn from this on the go and adopt open science principles and a more mindful approach to COVID-19-related data to accelerate the discovery of more efficient solutions. We take this opportunity to invite our colleagues to contribute to this global scientific collaboration by publishing their findings with maximal transparency.

 

 

Advocacy for an open and responsible scientific culture in our society

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“In a recent editorial, we called for information, which had become urgent, of Plan S, which was initially to apply from January 2020 and fortunately postponed until next year with a transitional phase, which may run until 20244. We insisted more generally on this notion of “open science”, and on the necessary involvement of researchers. We prejudged it necessary so that innovative awareness would precede theoretical rules, sometimes, if not often, judged disappointing a posteriori, and proposed a participatory methodology unlike decisions asserted and decreed by the Institutions.

We are continuing our reflection here aroused by the letter of “The Conversation” of last February 25 by Xin Xu5 which is entitled: “The threat of Covid-19 forces researchers to share their discoveries, and it is a revolution for science !”. In the preamble, let us say that we are delighted with this plea which reveals an awareness of the “bottom up” type. …”

Manifesto for EU COVID-19 Research | European Commission

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“By endorsing the manifesto you commit to

Make the generated results, whether tangible or intangible, public and accessible without delay, for instance on the Horizon Results Platform, on an existing IP sharing platform, or through an existing patent pool.

Make scientific papers and research data available in open access without delay and following the FAIR principles via preprint servers or public repositories, with rights for others to build upon the publications and data and with access to the tools needed for their validation.In particular, make COVID-19 research data available through the European COVID-19 Data Platform

Where possible, grant for a limited time, non-exclusive royalty free licences on the intellectual property resulting from EU-funded research. These non-exclusive royalty free licenses shall be given in exchange for the licensees’ commitment to rapidly and broadly distribute the resulting products and services under fair and reasonable conditions to prevent, diagnose, treat and contain COVID-19.

These non-exclusive royalty free licenses shall be given in exchange for the licensees’ commitment to rapidly and broadly distribute the resulting products and services under fair and reasonable conditions to prevent, diagnose, treat and contain Covid-19….”

The Acceleration of Science – Harvard Political Review

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“Despite his criticism of the Stanford preprint, Gelman agrees with Resnik and also does not believe preprints are the root of the problem. “In general, I’m a proponent of open post-publication review rather than secret pre-publication review,” he said. “So I don’t have any problem with preprint servers. People put stuff into a preprint server and they also send stuff into a journal for peer-review. I’ve done that [too].”

After weighing the costs and benefits of preprints, Dr. Resnik concludes, “Ethically, I think most people would agree that the emergency situation does justify trying to speed up the process as much as you can, without introducing unacceptable levels of error.” 

At this point, the question we should be asking is not whether to abolish preprint servers in the hopes of curtailing misinformation. The more relevant question lies in how can we reform the preprint system — and, more broadly, the interactions between the scientific community and the public — to minimize the risk of misinformation while sustaining the life-saving accelerated rate of research. Where do we find this balance? …”