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

“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….”

Innovating editorial practices: academic publishers at work | Research Integrity and Peer Review | Full Text

“Journals independent of large commercial publishers tend to have less hierarchically structured processes, report more flexibility to implement innovations, and to a greater extent decouple commercial and editorial perspectives….

This is in line with the dominant view on the changing status of publishers, which requires the publishers to take considerable action. Part of this action, driven by the shift towards more open access publishing, consists of a changing focus on ‘what the community wants’. While previously librarians would be the main source and spokesmen of ‘what the community wants’, publishers are quickly shifting their attention towards needs and desires of researchers, either in their role as authors or as reviewers, as exemplified in initiatives such as Publons, the use of the Journal Impact Factor to advertise to authors, publisher-facilitated preprint servers, or the appearance of mega-journals. This aligns with the publishers’ business needs: in the subscription-model, librarians were involved in deciding which subscriptions to buy, but in the open access model researchers themselves are more directly involved in deciding where to publish and hence where to spend money on publishing.

A stronger focus on transparency constitutes another trend among publishers that is fueled by external changes in the publishing landscape. By being more transparent about publishing work, for instance by showing how many reviewers had to be invited, publishers can demonstrate the effort that goes into the review process, thereby showing their added value: “We need to do a better job in showing how we have added value. Being open about review and the system is a way of doing this” (senior manager)….”

Systematize information on journal policies and practices – A call to action – Leiden Madtrics

In most research fields, journals play a dominant role in the scholarly communication system. However, the availability of systematic information on the policies and practices of journals, for instance with respect to peer review and open access publishing, is surprisingly limited and scattered. Of course we have the journal impact factor, as well as a range of other citation-based journal metrics (e.g., CiteScore, SNIP, SJR, and Eigenfactor), but these metrics provide information only on one very specific aspect of a journal. As is widely recognized, there is a strong need for a wider range of information on journals (see for instance here and here). Such information is for instance needed to facilitate responsible evaluation practices, to promote open access publishing, and to improve journal peer review.

Open and Reproducible Research Group (ORRG)

“Open Science is better science. Research benefits from sharing data and scientific knowledge which is publicly available, making open science essential. The Open and Reproducible Research Group (ORRG) uses evidence-based and computational approaches to make research cultures more open, transparent and participatory through new practices and technologies. In our interdisciplinary team we combine competences in philosophy, sociology, and information science with computer science and life science. We research services, policies, and tools to investigate and foster the uptake and evaluation of Open Science practices in the following areas: …”

 

Help me redesign the scientific paper | Dynamic Ecology

“If scientists spend taxpayer money to generate irreproducible results, the public’s logical response should be to either withhold funds or demand a new process that emphasizes reproducibility….

Collaborative Independent Review is one way that funders, journals and scientists could implement a more reproducible paper….

The perils of preprints | The BMJ

“Preprints—manuscripts that have not undergone peer review—were first embraced in physics, catalysed by the creation in the early 1990s of arXiv.org, an open online repository for scholarly papers.1 It was not until 2013 that similar initiatives were embraced by the biological and then medical sciences,2 and novel publishing platforms continue to emerge. Some commentators believe the potential for harm is outweighed by the benefits,134 but others have raised specific concerns regarding medical preprints and mitigating the risk of harm to the public.2 These discussions need to be revisited in the context of the covid-19 pandemic, which has been accompanied by an explosion of preprint publications….”

 

The perils of preprints | The BMJ

“Preprints—manuscripts that have not undergone peer review—were first embraced in physics, catalysed by the creation in the early 1990s of arXiv.org, an open online repository for scholarly papers.1 It was not until 2013 that similar initiatives were embraced by the biological and then medical sciences,2 and novel publishing platforms continue to emerge. Some commentators believe the potential for harm is outweighed by the benefits,134 but others have raised specific concerns regarding medical preprints and mitigating the risk of harm to the public.2 These discussions need to be revisited in the context of the covid-19 pandemic, which has been accompanied by an explosion of preprint publications….”

 

Ars Inveniendi Analytica | Published by Ars Inveniendi Analytica

“we believe that the mathematical community could and should engage into the creation of a line of arXiv overlay journals, covering the various areas of Mathematics, and publishing papers of the highest quality. We are thus launching, with the support of a group of colleagues who have accepted our invitation to serve as editors, an arXiv overlay journal in Mathematical Analysis, called Ars Inveniendi Analytica. This journal will benefit from the financial support of the University of Texas Libraries, and has been assisted in these initial stages by the Harvard Library, a member of the Confederation of Open Access Repositories….”

Communiqué: Meeting participants agree to work together on a technical architecture for distributed peer review on repository resources – COAR

“On January 23-24, 2020, COAR (Confederation of Open Access Repositories) convened a meeting to investigate the potential for a common, distributed architecture that would connect peer review with resources in repositories. The aim of the meeting, hosted by Inria in Paris, France, was to share the current workflows of various projects and systems that are managing or developing overlay peer review on a variety of different repository types (institutional, preprint, data, etc.), and assess whether there is sufficient interest in defining a set of common protocols and vocabularies that would allow interoperability across different systems.

Meeting participants reviewed and discussed a number of different use cases. While each case has its own unique attributes, it was clear that there are significant similarities in terms of functionalities and objectives. A draft architecture for distributed peer review on repositories, applying existing web technologies and standards such as Linked Data Notifications and Activity Streams 2.0, was presented by Herbert Van de Sompel of DANS and prototyped by Martin Klein of Los Alamos National Laboratory. By the end of the meeting, there was a consensus by participants that it would be worthwhile to further specify the proposed architecture, through detailing the use cases, developing a common model, and further profiling the technologies. This work will be undertaken in the coming weeks and months.

The outcome of this work could be extremely powerful. It would allow us to move away from the current ‘system to system’ approach to a highly distributed, technically efficient overlay peer review architecture, which would enable any compatible repository and peer review service to participate in the network. This profiling builds on previous work of COAR such as Next Generation Repositories and Pubfair. COAR will provide regular updates about the progress of this work and all results will be widely shared once stable outcomes are available….”

Modelling Overlay Peer Review Processes with Linked Data Notifications

In November 2017, the Confederation of Open Access Repositories (COAR) published a report outlining the technologies and behaviours of the Next Generation Repository (NGR). In the report, the NGR Working Group argues that repositories must take their place in a resource-centric network, where the individual resources (metadata and actual content) within the repositories are interconnected on the Web both with each other and, more importantly with resource-oriented networked services. These links between resources and overlay services can bring many new opportunities for broadening the scope of the services offered by repositories and 3rd party initiatives. The emphasis on moving to a fully resource-centric paradigm presented in the vision for the Next Generation Repository offers an opportunity to exploit what programmers call “pass by reference” – a notion which underlies the fundamental function of the Web.

One specific use case related to this vision is the linking of repository resources with services providing commentary, annotation and peer reviews; a use case that is currently being considered by several different initiatives in the scholarly communications landscape. The wide distribution of resources (typified by articles) in repositories, coupled with the growing interest in overlay journals, introduces the possibility of adopting an asynchronous notification paradigm to achieve interoperability between repositories and peer review systems….”