How the world is adapting to preprints

“A certain trend emerged from the preprint discussions. Praise for preprints and their virtues was reliably bracketed by an acknowledgement that the medium was a bit green and a bit untamed: the Wild West of scientific publishing, where anything can happen.

Similar analogies from the publishing community have been abundant. At a talk organized by the Society for Scholarly Publishing, Shirley Decker-Lucke, Content Director at SSRN, likened preprints to raw oysters: They’re generally safe, but sometimes you get a bad one. On the same panel, Lyle Ostrow, Assistant Professor of Neurology at Johns Hopkins, compared the adoption of preprints to the shift from horse-drawn buggies to automobiles: They’re faster, they’re better, but they will require education to use safely. The following week, a Scholarly Kitchen article about preprints drew a parallel with unruly teenagers: “tremendous promise, but in need of more adult supervision to achieve their potential”….

As it is, most preprint servers have not been agnostic about the papers they post. Generally, they restrict passage of content that is clearly unscientific, unethical, potentially harmful or not representative of a novel, empirically derived finding. That is, they already impose some editorial standards.

Preprint platforms offer authors a legitimate place to host their work with unprecedented speed, for free. In time, they could be in a position to enforce, or at least strongly incentivize, standards that are widely acknowledged to support research integrity, like data and code availability, details of randomization and blinding, study limitations and lay summaries for findings that are consequential to human health….”

PLAN S and other progress for Open Access to knowledge

Abstract:  The principle of Open Access (OA) is about the breaking of any paywall to the knowledge coming from research funded by public monies. After twenty years of statements not much has changed and the market of scientific journals is still in the hands of oligopolistic companies. Plan S is a disruptive initiative created by research funders in Europe and US which aims to foster the transition to Open Access by acting against hybrid journals and citation index. The Italian Institute for Nuclear Physics (INFN) has signed Plan S and, in close relationship with the Universities, the Conference of Rectors (CRUI), and the National Research Council (CNR), is outreaching the academic communities to discuss strengths, weaknesses, opportunities and threats.  In this work both a description of Plan S and a brief status report of other initiatives are given.

 

Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods | bioRxiv

Abstract:  The reproducibility crisis in science is a multifaceted problem involving practices and incentives, both in the laboratory and in publication. Fortunately, some of the root causes are known and can be addressed by scientists and authors alike. After careful consideration of the available literature, the National Institutes of Health identified several key problems with the way that scientists conduct and report their research and introduced guidelines to improve the rigor and reproducibility of pre-clinical studies. Many journals have implemented policies addressing these same criteria. We currently have, however, no comprehensive data on how these guidelines are impacting the reporting of research. Using SciScore, an automated tool developed to review the methods sections of manuscripts for the presence of criteria associated with the NIH and other reporting guidelines, e.g., ARRIVE, RRIDs, we have analyzed ~1.6 million PubMed Central papers to determine the degree to which articles were addressing these criteria. The tool scores each paper on a ten point scale identifying sentences that are associated with compliance with criteria associated with increased rigor (5 pts) and those associated with key resource identification and authentication (5 pts). From these data, we have built the Rigor and Transparency Index, which is the average score for analyzed papers in a particular journal. Our analyses show that the average score over all journals has increased since 1997, but remains below five, indicating that less than half of the rigor and reproducibility criteria are routinely addressed by authors. To analyze the data further, we examined the prevalence of individual criteria across the literature, e.g., the reporting of a subject’s sex (21-37% of studies between 1997 and 2019), the inclusion of sample size calculations (2-10%), whether the study addressed blinding (3-9%), or the identifiability of key biological resources such as antibodies (11-43%), transgenic organisms (14-22%), and cell lines (33-39%). The greatest increase in prevalence for rigor criteria was seen in the use of randomization of subjects (10-30%), while software tool identifiability improved the most among key resource types (42-87%). We further analyzed individual journals over time that had implemented specific author guidelines covering rigor criteria, and found that in some journals, they had a big impact, whereas in others they did not. We speculate that unless they are enforced, author guidelines alone do little to improve the number of criteria addressed by authors. Our Rigor and Transparency Index did not correlate with the impact factors of journals.

 

 

The changing role of funders in responsible research assessment: progress, obstacles and the way ahead

“This working paper explores what RRA [Responsible Research Assessment] is, and where it comes from, by outlining fifteen initiatives that have influenced the shape and direction of current RRA debates. It goes on to describe the responses that these have elicited, with a particular focus on the role and contribution of research funders, who have more freedom and agency to experiment and initiate change than other actors in research systems.

The paper also presents the findings of a survey of RRA policies and practices in the participant organisations of the Global Research Council (GRC)—mainly national public funding agencies—with responses from 55 organisations worldwide….”

The changing role of funders in responsible research assessment: progress, obstacles and the way ahead

“This working paper explores what RRA [Responsible Research Assessment] is, and where it comes from, by outlining fifteen initiatives that have influenced the shape and direction of current RRA debates. It goes on to describe the responses that these have elicited, with a particular focus on the role and contribution of research funders, who have more freedom and agency to experiment and initiate change than other actors in research systems.

The paper also presents the findings of a survey of RRA policies and practices in the participant organisations of the Global Research Council (GRC)—mainly national public funding agencies—with responses from 55 organisations worldwide….”

The changing role of funders in responsible research assessment: progress, obstacles and the way ahead | DORA

“In partnership with the Research on Research Institute (RoRI), CWTS-Leiden, and National Research Foundation of South Africa, DORA published a position paper providing a state-of-play of responsible research assessment (RRA) practices from funders. The paper’s release coincided with the 2020 Global Research Council (GRC) virtual conference on RRA practices. It also presents the findings of a survey of RRA policies and practices in the participant GRC organizations, which are mainly national public funding agencies.”

The changing role of funders in responsible research assessment: progress, obstacles and the way ahead | DORA

“In partnership with the Research on Research Institute (RoRI), CWTS-Leiden, and National Research Foundation of South Africa, DORA published a position paper providing a state-of-play of responsible research assessment (RRA) practices from funders. The paper’s release coincided with the 2020 Global Research Council (GRC) virtual conference on RRA practices. It also presents the findings of a survey of RRA policies and practices in the participant GRC organizations, which are mainly national public funding agencies.”

Watching preprints evolve | Nature Reviews Immunology

“In February 2021, Nature Reviews Immunology launches the first of its monthly ‘Preprint Watch’ columns. Here, we explain the rationale for our coverage of preprints and the precautions we have taken to guard against their improper use….

There is no doubt that the COVID-19 pandemic, which necessitated the rapid dissemination of results, has fuelled some of this increase, with approximately one-quarter (463) of the 2020 ‘immunology’ preprints on bioRxiv containing the search term ‘COVID-19’ or ‘SARS-CoV-2’. It also seems clear from these numbers that even in non-pandemic times, preprints are here to stay. At Nature Reviews Immunology, we anticipate that the accelerated acceptance of the value of preprints that has occurred in 2020 will translate to long-term changes in their use, and we are well placed to respond to these changes….

[I]n April 2020 Nature Reviews Immunology began a collaboration with the Precision Immunology Institute at the Icahn School of Medicine, New York, USA (the Sinai Immunology Review Project; SIRP)2, to publish short ‘In Brief’ summaries (for example, ref.3) on a weekly basis of the most relevant, new COVID-19-related preprints (for example, ref.4), many of which have since been published in high-profile journals (for example, ref.5). We were mindful of the potential dangers of highlighting and publicizing non-peer-reviewed results, but we were reassured by the system that SIRP had established to scan, filter and review preprints, involving both early career researchers (ECRs) and faculty members. This curation of the preprint literature at a time when journals and editors were overwhelmed with submissions was an essential service to the community, and the training in peer review for ECRs who were shut out of the lab should pay future dividends. In June 2020, a second group from the University of Oxford, UK (the OxImmuno Literature Initiative), operating under a similar system, also began to contribute regular preprint summaries (for example, refs6,7)….

We share your concerns about media reporting of incomplete or misleading data that might damage public trust in science. For this reason, we are maintaining a cautious approach to preprints, covering only a few select papers picked by experts after careful review. …”

 

10 Years of Open Access Society Publishing – Novara – – ChemistryOpen – Wiley Online Library

“Let’s take a step back. Why was ChemistryOpen launched in the first place? In the first decade of the new century, some of the European governments part of ChemPubSoc Europe (now Chemistry Europe Chemistry Europe) have started to recommend that all the research conducted with their funding be freely accessible for all readers, irrespective of socioeconomic or geographical considerations. As a response, and with the endorsement of the owner societies, ChemPubSoc Europe has launched ChemistryOpen. Back then, there was quite some skepticism regarding the open access publishing model. However, the involvement of the societies has been crucial in promoting the journal and its high ethical and quality standards among the chemistry community in Europe and worldwide. And 10 years later ChemistryOpen is one of the leading open access chemistry journals! …

Once again this year, ChemistryOpen has receive the highest number yearly submissions to date, and has achieved a record?breaking number of downloads. A big thanks to all of our authors for sending us your fascinating research from all over the world, and enabling the journal to reach a strong positioning in the everchanging and expanding publishing landscape. …”

OA Switchboard initiative: progress report December 2020 – OASPA

“Although many may want to forget all about 2020, I will remember it as a catalyst year, in which inspiring collaboration prepared for the OA Switchboard to go live as an operational solution in 2021. This progress report marks the end of the 2020 OA Switchboard project, and preludes the structural set-up for 2021 and beyond.

The OA Switchboard journey started way before the December 2018 initial stakeholder meeting which marked the inception of a shared vision. For a breakthrough in the transformation of the market such that OA is supported as the predominant model of publication, a joint challenge had to be addressed: the complexity around the implementation of multi-lateral OA publication-level arrangements. A solution had already been defined: an intermediary – The OA Switchboard – a central information exchange hub, connecting parties and systems, streamlining communication and the neutral exchange of OA related publication-level information, and ensuring a financial settlement can be done….”

Open and Shut?: Open Access: “Information wants to be free”?

“Please note that what I say in the attached document is built on an interview. It is not intended to be any kind of prediction of the future; it is more an extended reflection after 20 years reporting on the OA movement, coupled with a heavy dose of speculation. Who knows, perhaps this will be the last thing I ever write on open access. Maybe this will prove my swan song.

I would also like to stress upfront that in the critique of the OA movement I make I don’t claim that my knowledge, or predictions, are superior to anyone else’s. This is just what I have concluded after many years observing the movement and reflects my current view on where I think we are today. It does also include a lot of factual data, as well as links and footnotes for those who like them. 

Importantly, while I do not consider myself to be an OA advocate, I admit that I was as naïve as anyone else about what the movement might be able to achieve.

Finally, while what I say might be slightly overweight in European developments, it may not matter if (as I believe is possible) events in Europe end up determining how open access develops globally. 

I say this because it seems possible that European OA initiatives will reconfigure the international scholarly communication system, and in ways that OA advocates will not be comfortable with. …”

Sustaining the Commons

“Humanities Commons — now three years old and serving nearly 25,000 users around the world — has become a key piece of online scholarly infrastructure. In order to ensure that the Commons becomes and remains sustainable, we have established some strategic plans for the network’s technical, financial, and governance future. Read our brief overview and visit the areas below for a deeper dive….”

AfricArXiv – the African preprint repository – Open Collective

“In April 2018, the seed for AfricArXiv was planted during the 2nd AfricaOSH summit in Kumasi, Ghana with this historic tweet

In June that same year, we joined forces with The Center for Open Science and launched a branded preprint service. Early in 2020 we extended our Open Access platform to a community

collection on Zenodo and initiated a partnership with ScienceOpen, with whom we are running AfricArXiv preprints and curating a collection of COVID-19 research from and about Africa.

Shortly after that and as an innovative and immediate response to the pandemic, we partnered with Knowledge Futures Group to provide a platform for audio/visual preprints on PubPub. Next, we plan to add Figshare and PKP/OPS to the list of our partner repositories. 

Since we work to foster community among African researchers, we were excited to launch a petition in 2019 to sign the African Principles for Open Access in Scholarly Communication https://info.africarxiv.org/african-oa-principles/. The petition is ongoing, so you can still add your name to it. Published under CC-BY licence, anyone can Share and Adapt the principles while giving appropriate credit ‘African Principles for Open Access in Scholarly Communication as agreed upon by the signatories‘, provide a link to the principles, and indicate if changes were made.

We announced our strategic partnerships with the Institute for Globally Distributed Open Research and Education (IGDORE), Open Knowledge Map and ScienceOpen. ORCID and AfricArXiv initiated joint efforts to assist African scientists in advancing their careers through unique identifiers. 

Since the beginning of the pandemic in March, we collect, create and disseminate a wealth of resources, ideas and guidelines around COVID-19 in Africa. 

We have received and accepted around 200 submissions in total across our partner repositories….”

TSPOA: What have we been up to? – Transitioning Society Publications to OA

“In February of 2018, we founded Transitioning Society Publications to Open Access (TSPOA) to provide support, advocacy, and referral services for societies and publishers of society journals. Our overarching aim has been to assist learned societies in transitioning their publications to open access (OA). In our first year-and-a-half the world has grappled with public health, socio-political, and environmental crises that have only underscored the critical need for public access to research and scholarship. This has been an extraordinarily challenging period for everyone, both within and outside of scholarly publishing. We’d like to take the opportunity to highlight a few of our efforts that we believe are bringing some positive change and impact in such uncertain times….”