Converting Access Microbiology to an open research platform: focus group and AI review tool research results | Microbiology Society

Abstract:  The Microbiology Society will be launching an open research platform in October 2021. Developed using funding from the Wellcome Trust and the Howard Hughes Medical Institute (HHMI), the platform will combine our current sound-science journal, Access Microbiology, with artificial intelligence (AI) review tools and many of the elements of a preprint server. In an effort to improve the rigour, reproducibility and transparency of the academic record, the Access Microbiology platform will host both preprints of articles and their Version of Record (VOR) publications, as well as the reviewer reports, Editor’s decision, authors’ response to reviewers and the AI review reports. To ensure the platform meets the needs of our community, in February 2020 we conducted focus group meetings with various stakeholders. Using articles previously submitted to Access Microbiology, we undertook testing of a range of potential AI review tools and investigated the technical feasibility and utility of including these tools as part of the platform. In keeping with the open and transparent ethos of the platform, we present here a summary of the focus group feedback and AI review tool testing.

 

AAAS Plan S Compliance Policy: Staying Committed to Subscriptions – The Scholarly Kitchen

“Back in January, the American Association for the Advancement of Science (AAAS) announced a pilot to allow authors funded by cOAlition S organizations that have adopted the Plan S Rights Retention Strategy to place a CC BY or a CC BY-ND license on their accepted manuscripts and to share them without embargo. 

Specifically, the AAAS License to Publish states that 

“AAAS licenses back the following rights to the Author in the version of the cOAlition S Funded Work that has been peer-reviewed and accepted for publication, (the “Accepted Version”) but not the final, copyedited and proofed version published by AAAS (the “Final Published Version”): The right to self-archive and distribute the Accepted Version under either a CC BY 4.0 license or a CC BY-ND license, including on the Author’s personal website, in the Author’s company/institutional repository or archive, and in not for profit subject-based repositories such as PubMed Central, without embargo but only following publication of the Final Published Version.” …

The announcement of the pilot policy was widely reported on and was welcomed by cOAlition S in a special statement. Since that time, representatives of cOAlition S have repeatedly praised the AAAS policy in webinars and the like. This celebratory response has been a bit puzzling to me. Plan S aims to flip the publishing system to gold open access, with its various leaders often decrying the lack of progress in the two decades since the Budapest Open Access Initiative statement. Specifically, Plan S states that, “the subscription-based model of scientific publishing, including its so-called ‘hybrid’ variants, should therefore be terminated.” 

Yet in this case, cOAlition S is praising a publisher that is holding fast to the subscription-based model of closed publishing. And doing so even though this AAAS pilot policy is not a comprehensive route to compliance for Plan S since not all funders in the coalition have adopted the Rights Retention Strategy. Elsewhere I’ve observed that, over time, the implementation of Plan S has been marked by policies that “rehabilitate” journals into compliance. Is this another case of rehabilitation? …”

 

 

Public feedback on preprints can unlock their full potential to accelerate science.

“Public preprint review can help authors improve their paper, find new collaborators, and gain visibility. It also helps readers find interesting and relevant papers and contextualize them with the reactions of experts in the field. Never has this been more apparent than in COVID-19, where rapid communication and expert commentary have both been in high demand. Yet, most feedback on preprints is currently exchanged privately.

Join ASAPbio in partnership with DORA, HHMI, and the Chan Zuckerberg Initiative to discuss how to create a culture of constructive public review and feedback on preprints….”

Guest Post – Open and Faster Scholarly Communication in a Post-COVID World – The Scholarly Kitchen

“The pandemic presented an urgency for effective science to inform decision-making and has shown just how fast and open scholarly communication can be. Researchers shared their preliminary results on preprint servers and institutional repositories at unprecedented rates, inspiring various preprint peer-review initiatives. Journal publishers processed manuscripts from submission to publication in record time. And much of what we know about Covid-19 has been learned through data sharing and cooperation at the international level, with the use of critical data-sharing infrastructure.

While the research community has responded with an extraordinary level of openness, speed, and collaboration, it has also brought to the fore some of the key challenges we still face in the transition to open research – and the opportunities they represent….”

 

Incorporating Preprints into Academic Assessment | DORA

“Join DORA and ASAPbio on Tuesday Day, June 29, for a joint webinar on preprints and academic assessment….

Speakers will discuss important topics surrounding the incorporation of preprints into academic assessment: the value of considering preprints in academic assessment, how preprints can be included in existing assessment processes, and what challenges may arise along the way. Participants will have the opportunity to engage in the dialogue and ask questions of the speakers in the last section of the webinar.

 

This webinar is free to attend and open to everyone interested in improving research assessment. In particular, this webinar will aim to equip early career researchers, faculty, and academic leadership with the knowledge to advocate for the use of preprints at their institutions.”

Attitudes and practices of open data, preprinting, and peer-review—A cross sectional study on Croatian scientists

Baždari? K, Vrki? I, Arh E, Mavrinac M, Gligora Markovi? M, Bili?-Zulle L, et al. (2021) Attitudes and practices of open data, preprinting, and peer-review—A cross sectional study on Croatian scientists. PLoS ONE 16(6): e0244529. https://doi.org/10.1371/journal.pone.0244529

Abstract: Attitudes towards open peer review, open data and use of preprints influence scientists’ engagement with those practices. Yet there is a lack of validated questionnaires that measure these attitudes. The goal of our study was to construct and validate such a questionnaire and use it to assess attitudes of Croatian scientists. We first developed a 21-item questionnaire called Attitudes towards Open data sharing, preprinting, and peer-review (ATOPP), which had a reliable four-factor structure, and measured attitudes towards open data, preprint servers, open peer-review and open peer-review in small scientific communities. We then used the ATOPP to explore attitudes of Croatian scientists (n = 541) towards these topics, and to assess the association of their attitudes with their open science practices and demographic information. Overall, Croatian scientists’ attitudes towards these topics were generally neutral, with a median (Md) score of 3.3 out of max 5 on the scale score. We also found no gender (P = 0.995) or field differences (P = 0.523) in their attitudes. However, attitudes of scientist who previously engaged in open peer-review or preprinting were higher than of scientists that did not (Md 3.5 vs. 3.3, P<0.001, and Md 3.6 vs 3.3, P<0.001, respectively). Further research is needed to determine optimal ways of increasing scientists’ attitudes and their open science practices.

What We Learned Doing Fast Grants – Future

“And so, in early April, we decided to start Fast Grants, which we hoped could be one of the faster sources of emergency science funding during the pandemic. We had modest hopes given our inexperience and lack of preparation, but we felt that the opportunity to provide even small accelerations would be worthwhile given the scale of the disaster. 

The original vision was simple: an application form that would take scientists less than 30 minutes to complete and that would deliver funding decisions within 48 hours, with money following a few days later….

The first round of grants were given out within 48 hours. Later rounds of grants, which often required additional scrutiny of earlier results, were given out within two weeks. These timelines were much shorter than the alternative sources of funding available to most scientists. Grant recipients were required to do little more than publish open access preprints and provide monthly one-paragraph updates….”

Editorial: Can Journals, as Trusted Intermediaries, Cut Through the Signal-to-Noise Problem in Medical Publishing?

“Although open-access publication has its upsides, for purposes of this essay, I am going to lump publishing in open-access journals in with posting to preprint servers as potentially problematic. My reason for doing so is that both make it harder for clinicians to separate helpful research from distracting, unhelpful, and in the case of preprint servers, unvetted material. In previous editorials, I’ve highlighted some redeeming qualities of open-access publication [17, 18]; I also note that open access is a publication option here at CORR®. But from where I sit today, it’s becoming clear to me that the distortion of publication incentives that are inherent to fully open-access journals does not serve readers (or their patients) very well….”

eLife announces new approach to publishing in medicine | For the press | eLife

eLife is excited to announce a new approach to peer review and publishing in medicine, including public health and health policy.

One of the most notable impacts of the COVID-19 pandemic has been the desire to share important results and discoveries quickly, widely and openly, leading to rapid growth of the preprint server medRxiv. Despite the benefits of rapid, author-driven publication in accelerating research and democratising access to results, the growing number of clinical preprints means that individuals and institutions may act quickly on new information before it is adequately scrutinised.

To address this challenge, eLife is bringing its system of editorial oversight by practicing clinicians and clinician-investigators, and rigorous, consultative peer review to preprints. The journal’s goal is to produce ‘refereed preprints’ on medRxiv that provide readers and potential users with a detailed assessment of the research, comments on its potential impact, and perspectives on its use. By providing this rich and rapid evaluation of new results, eLife hopes peer-reviewed preprints will become a reliable indicator of quality in medical research, rather than journal impact factor.

Preprints 101 for authors

“Preprints enable researchers to rapidly share their work publicly before the formal peer review process. In this webinar you will learn more about preprints and their benefits for the research community from ASAPbio; will hear an author’s perspective on posting preprints from Sumeet Pal Singh, a group leader at IRIBHM, ULB; and will find out how to incorporate preprints in your literature search routine by using the preprint discovery tools developed by Europe PMC.”

Open Science in Kenya: Where Are We? | Research Metrics and Analytics

“According to the United Nations Educational, Scientific, and Cultural Organization (UNESCO), Open Science is the movement to make scientific research and data accessible to all. It has great potential for advancing science. At its core, it includes (but is not limited to) open access, open data, and open research. Some of the associated advantages are promoting collaboration, sharing and reproducibility in research, and preventing the reinvention of the wheel, thus saving resources. As research becomes more globalized and its output grows exponentially, especially in data, the need for open scientific research practices is more evident — the future of modern science. This has resulted in a concerted global interest in open science uptake. Even so, barriers still exist. The formal training curriculum in most, if not all, universities in Kenya does not equip students with the knowledge and tools to subsequently practice open science in their research. Therefore, to work openly and collaboratively, there is a need for awareness and training in the use of open science tools. These have been neglected, especially in most developing countries, and remain barriers to the cause. Moreover, there is scanty research on the state of affairs regarding the practice and/or adoption of open science. Thus, we developed, through the OpenScienceKE framework, a model to narrow the gap. A sensitize-train-hack-collaborate model was applied in Nairobi, the economic and administrative capital of Kenya. Using the model, we sensitized through seminars, trained on the use of tools through workshops, applied the skills learned in training through hackathons to collaboratively answer the question on the state of open science in Kenya. While the former parts of the model had 20–50 participants, the latter part mainly involved participants with a bioinformatics background, leveraging their advanced computational skills. This model resulted in an open resource that researchers can use to publish as open access cost-effectively. Moreover, we observed a growing interest in open science practices in Kenya through literature search and data mining and that lack of awareness and skills may still hinder the adoption and practice of open science. Furthermore, at the time of the analyses, we surprisingly found that out of the 20,069 papers downloaded from BioRXiv, only 18 had Kenyan authors, a majority of which are international (16) collaborations. This may suggest poor uptake of the use of preprints among Kenyan researchers. The findings in this study highlight the state of open science in Kenya and challenges facing its adoption and practice while bringing forth possible areas for primary consideration in the campaign toward open science. It also proposes a model (sensitize-train-hack-collaborate model) that may be adopted by researchers, funders and other proponents of open science to address some of the challenges faced in promoting its adoption in Kenya….”

 

Preprints 101 for authors | EMBL-EBI Training

“Preprints enable researchers to rapidly share their work publicly before the formal peer review process. In this webinar you will learn more about preprints and their benefits for the research community from ASAPbio (Accelerating Science and Publication in biology); will hear an author’s perspective on posting preprints from Sumeet Pal Singh, a group leader at IRIBHM, ULB; and will find out how to incorporate preprints in your literature search routine by using the preprint discovery tools developed by Europe PMC….”

What are preprints? [Originally published in DADOS’ blog in May/2021] | SciELO in Perspective

“In 2020, DADOS began accepting the submission of manuscripts from preprint servers. However, there are still many concerns from the academic community, especially in the Social Sciences, about what preprints are and what changes they bring to the traditional framework of scientific assessment and publication. Our goal here is to answer these questions briefly, in addition to explaining in a simple way how to submit a preprint to DADOS. To this end, we have prepared a schematic of how manuscripts are evaluated in the traditional double-blind review system and how it has been modified in the preprint model. Next, we have a video and a podcast episode (both available in Portuguese only) about how DADOS will incorporate preprints, followed by a text summarizing this material….”

Is rapid scientific publication also high quality? Bibliometric analysis of highly disseminated COVID?19 research papers – Khatter – – Learned Publishing – Wiley Online Library

Abstract:  The impact of COVID-19 has underlined the need for reliable information to guide clinical practice and policy. This urgency has to be balanced against disruption to journal handling capacity and the continued need to ensure scientific rigour. We examined the reporting quality of highly disseminated COVID-19 research papers using a bibliometric analysis examining reporting quality and risk of bias (RoB) amongst 250 top scoring Altmetric Attention Score (AAS) COVID-19 research papers between January and April 2020. Method-specific RoB tools were used to assess quality. After exclusions, 84 studies from 44 journals were included. Forty-three (51%) were case series/studies, and only one was an randomized controlled trial. Most authors were from institutions based in China (n =?44, 52%). The median AAS and impact factor was 2015 (interquartile range [IQR] 1,105–4,051.5) and 12.8 (IQR 5–44.2) respectively. Nine studies (11%) utilized a formal reporting framework, 62 (74%) included a funding statement, and 41 (49%) were at high RoB. This review of the most widely disseminated COVID-19 studies highlights a preponderance of low-quality case series with few research papers adhering to good standards of reporting. It emphasizes the need for cautious interpretation of research and the increasingly vital responsibility that journals have in ensuring high-quality publications.