Frontiers | The Academic, Societal and Animal Welfare Benefits of Open Science for Animal Science | Veterinary Science

Abstract:  Animal science researchers have the obligation to reduce, refine, and replace the usage of animals in research (3R principles). Adherence to these principles can be improved by transparently publishing research findings, data and protocols. Open Science (OS) can help to increase the transparency of many parts of the research process, and its implementation should thus be considered by animal science researchers as a valuable opportunity that can contribute to the adherence to these 3R-principles. With this article, we want to encourage animal science researchers to implement a diverse set of OS practices, such as Open Access publishing, preprinting, and the pre-registration of test protocols, in their workflows.

 

Why preprints are good for patients | Nature Medicine

“Rapid communication of clinical trial results has likely saved lives during the COVID-19 pandemic and should become the new norm….

But during health emergencies, there are many tensions, one of which is the mismatch between the urgent need for information and evidence and the much longer time frames of scientific peer review and publication. The COVID-19 pandemic is the first global health emergency of the new information age, with data and results widely shared via social media. This has resulted in very real difficulties in distinguishing important information from noise, and real news from fake news. How should the research and medical community best manage this new reality?…

Some may argue that the speed advantage of preprints does not outweigh the risks of poor-quality, misleading or even fraudulent research being published and acted upon. I would counter that clinicians should not rely solely on peer review to assess the validity and meaningfulness of research findings. This is because dubious, perhaps fraudulent data can still get through peer review, as was seen with early COVID papers published and then retracted from two of the most prestigious medical journals. In addition, even valid data can be misleading. There has been an avalanche of observational data that passed peer review and was then used to justify treatments, most notably with hydroxychloroquine, but the susceptibility of observational methodology to moderate biases means that such data should not be the basis of patient care.

I take two lessons from our experience running the largest COVID-19 clinical trial over the last two years. The first is that that the preprint system has come of age, demonstrating huge value in rapidly communicating important research findings. Almost daily I am alerted through social media alerts from trusted sources and colleagues of important new findings published as preprints. A degree of immediate peer review is also available by means of the preprint comments section and from colleagues via social media. The full peer-reviewed manuscripts usually appear many weeks or even months later. I cannot envisage a future without such rapid dissemination of new evidence.

 

Given this new reality, the second lesson is that we must ensure that the medical community and policy makers are sufficiently skilled in critical thinking and scientific methods that they can make sensible decisions, regardless of whether an article is peer reviewed or not.”

Need for universal acceptance of preprinting by editors of journals of health professional education | SpringerLink

“While publishers in multiple fields are adopting preprints [2], we have discovered a great deal of confusion about the pros and cons of preprinting as well as disparity in publishers’ policies regarding preprinting in health professions education (HPE). In seeking to resolve this confusion, we documented preprint policies at 74 journals within HPE (e.g. nursing, medicine, pharmacy, dentistry, rehabilitation sciences, nutrition). We culled preprint policies for 43 (58%) journals using journal websites, JISC’s Sherpa Romeo tool, and Wikipedia’s list of academic publishers by preprint policy. We then obtained information from email solicitations for an additional 27 (36%), leaving us without information for 4 (5%). Of the 70 journals for which we have information, 53 (76%) will review/accept preprinted manuscripts; 11 (16%) do not, and 6 (9%) are unclear or make decisions on a case-by-case basis. (For a link to our list of HPE journals and our understanding of their policies regarding preprinted manuscripts, see https://jahse.med.utah.edu/submission/ and select “Where to Publish”.) No wonder there is confusion.

We encourage our colleagues across the health professions to join our call to eliminate this confusion by encouraging all HPE journals to support and promote preprinting. The value of preprinting has only become more important during the COVID-19 pandemic [3]. Being able to preprint scholarship prior to formal submission enhances formative review and revision, augments the benefits of peer coaching, and promotes higher quality publications. Preprinting also makes work available to others more quickly, which can enhance collaboration and uptake of new ideas without compromising the eventual copyright of the final published product.”

Interviews with the lab protocol community – insights from an Academic Editor and a reviewer – EveryONE

“What do you think are the benefits of lab protocols for open science?

RK: PLOS ONE journal in collaboration with protocols.io has developed a unique and state-of-the-art platform for publishing lab protocols. This is a well-timed and useful innovation. The development of scientific knowledge is based on a variety of methodological approaches bordering on art. Because of the increasing complexity of scientific methods and their diversity, an appropriate forum or open science platform is needed, where the research community can present the best solution and point out the problems that may be encountered in other laboratories. Such a platform should of course be open, and in this form, it is really effective.

AF: Improving data reproducibility in research is one of today’s most important issues to address. Providing clear and detailed protocols, without limitation of words or space, is an effective way to communicate optimized protocols. This will directly help to improve data reproducibility between labs, as well as provide a thorough record of procedures that have been published in parallel. Improving communication of optimized protocols helps to drive robust research, allowing people to build their own research on already thorough studies, and not spend excessive time optimizing protocols based on poorly executed or explained protocols. …”

Benefits of publishing with us | About UCL Open: Environment

“UCL Open: Environment is committed to using its position and unique set of strengths to develop and disseminate original knowledge, not only for its own inherent value but also to address the significant challenges facing the world today and those that will arise in the future.

Drawing on these founding values, we want to stimulate disruptive thinking across the research landscape to showcase radical and critical thinking applied to real world problems that benefit humanity. We believe that the future of scientific and scholarly pursuit is best served by an open science agenda and fully open access publishing because knowledge should be accessible to all, regardless of location or financial means. We want to transform the way new knowledge is shared openly and without barriers….”

How research is being transformed by open data and AI | Popular Science

“How iNaturalist can correctly recognize (most of the time, at least) different living organisms is thanks to a machine-learning model that works off of data collected by its original app, which first debuted in 2008 and is simply called iNaturalist. Its goal is to help people connect to the richly animated natural world around them. 

The iNaturalist platform, which boasts around 2 million users, is a mashup of social networking and citizen science where people can observe, document, share, discuss, learn more about nature, and create data for science and conservation. Outside of taking photos, the iNaturalist app has extended capabilities compared to the gamified Seek. It has a news tab, local wildlife guides, and organizations can also use the platform to host data collection “projects” that focus on certain areas or certain species of interest. 

When new users join iNaturalist, they’re prompted to check a box that allows them to share their data with scientists (although you can still join if you don’t check the box). Images and information about their location that users agree to share are tagged with a creative commons license, otherwise, it’s held under an all-rights reserved license. About 70 percent of the app’s data on the platform is classified as creative commons. “You can think of iNaturalist as this big open data pipe that just goes out there into the scientific community and is used by scientists in many ways that we’re totally surprised by,” says Scott Loarie, co-director of iNaturalist. …

But with an ever-growing amount of data, our ability to wrangle these numbers and stats manually becomes virtually impossible. “You would only be able to handle these quantities of data using very advanced computing techniques. This is part of the scientific world we live in today,” Durant adds….

Another problem that researchers have to consider is maintaining the quality of big datasets, which can impinge on the effectiveness of analytics tools. This is where the peer-review process plays an important role….”

 

What are the benefits of open access? TIB study confirms advantages and dispels reservations – Technische Informationsbibliothek (TIB)

“Open access – free access to scholarly publications – offers many advantages. As surveys show, however, some researchers still have reservations. In the past decade, numerous empirical studies have been published providing substantiated results on the hopes and concerns regarding open access….

To conduct this review, TIB identified a total of 318 scientific studies that empirically examine various effects of open access. From this corpus, the authors selected 61 particularly relevant studies for a systematic comparison; these were then analysed thoroughly and the various results were compared in detail.

The effects studied relate to seven major aspects of open access:

Attention in the scientific community
Quality of scientific publications
Knowledge transfer
Productivity of the publishing system
Use of publications
Inequality in the science system
Economic impact on the publishing system…

Dr. David Hopf, lead author of the study, reported the key findings: “The literature reviewed confirms several advantages of open access: open access leads to increased usage and to a professionally and geographically more diverse readership. At the same time, open access publications make a greater contribution to knowledge transfer than traditionally published research results, and the publishing process – the time between the submission and acceptance or publication of articles – is shorter. What is more, a number of negative concerns assumed in relation to the effects of open access – for example, that open access publications are of an inferior quality and lead to disadvantages in print edition sales – have been dispelled.”

However, one partial result came as a surprise: the fact that open access publications are cited more frequently than publications that are not freely available is often mentioned as an advantage of open access – and is also confirmed by most empirical studies. However, a substantial proportion of the empirical literature deviates from this result, which means that an OA citation advantage cannot be conclusively confirmed empirically. In light of a high level of plausibility and methodological difficulties in this area, however, it can still be assumed that such an advantage exists.

Just one finding indicates a negative effect of open access: where so-called article processing charges (APCs) – publication costs incurred by many open access publications – exist, authors with fewer resources may be discouraged from publishing open access, e.g. due to low income levels in some regions of the world or a lack of institutional funding. However, this is not an effect of open access per se, but rather an effect of a particular business model for financing open access publications….”

Opening Up to Open Science

“This way of sharing science has some benefits: peer review, for example, helps to ensure (even if it never guarantees) scientific integrity and prevent inadvertent misuse of data or code. But the status quo also comes with clear costs: it creates barriers (in the form of publication paywalls), slows the pace of innovation, and limits the impact of research. Fast science is increasingly necessary, and with good reason. Technology has not only improved the speed at which science is carried out, but many of the problems scientists study, from climate change to COVID-19, demand urgency. Whether modeling the behavior of wildfires or developing a vaccine, the need for scientists to work together and share knowledge has never been greater. In this environment, the rapid dissemination of knowledge is critical; closed, siloed knowledge slows progress to a degree society cannot afford. Imagine the consequences today if, as in the 2003 SARS disease outbreak, the task of sequencing genomes still took months and tools for labs to share the results openly online didn’t exist. Today’s challenges require scientists to adapt and better recognize, facilitate, and reward collaboration….

This tension between individual and institutional incentives and the progress of science must be recognized and resolved in a manner that contributes to solving the great challenges of today and the future. To change the culture, researchers must do more than take a pledge; they must change the game—the structures, the policies, and the criteria for success. In a word, open science must be institutionalized….

A powerful open science story can be found in the World Climate Research Programme’s Coupled Model Intercomparison Project (CMIP), established in 1995. Before CMIP, with the internet in its infancy, climate model results were scattered around the world and difficult to access and use. CMIP inspired 40 modeling groups and about 1,000 researchers to collaborate on advancing modeling techniques and setting guidelines for how and where to share results openly. That simple step led to an unexpected transformation: as more people were able to access the data, the community expanded, and more groups contributed data to CMIP. More people asking questions and pointing out issues in their results helped drive improvements. In its assessment reports, the Intergovernmental Panel on Climate Change relied on research publications using CMIP data to assess climate change. As a platform, CMIP enabled thousands of scientists to work together, self-correct their work, and create further ways to collaborate—a virtuous circle that attracted more scientists and more data, and increased the speed and usefulness of the work….

The most important message from these reports is that all parts of science, from individual researchers to universities and funding agencies, need to coordinate their efforts to ensure that early adopters aren’t jeopardizing their careers by joining the open science community. The whole enterprise has to change to truly realize the full benefits of open science. Creating this level of institutional adoption also requires updating policies, providing training, and recognizing and rewarding collaborative science….”

Opening up Science—to Skeptics – By Rohan Arcot & Hunter Gehlbach – Behavioral Scientist

“The research community is no stranger to skepticism. Its own members have been questioning the integrity of many scientific findings with particular intensity of late. In response, we have seen a swell of open science norms and practices, which provide greater transparency about key procedural details of the research process, mitigating many research skeptics’ misgivings. These open practices greatly facilitate how science is communicated—but only between scientists. 

Given the present historical moment’s critical need for science, we wondered: What if scientists allowed skeptics in the general public to look under the hood at how their studies were conducted? Could opening up the basic ideas of open science beyond scholars help combat the epidemic of science skepticism?  …”

University of Maryland’s Senate Approves Policy to Enhance Equitable Access to Scholarly Publications | UMD PACT

“At its meeting on April 6, 2022, University of Maryland’s Senate voted to approve a new institutional policy that will advance equitable, open access to the University’s research and scholarship. In alignment with the University’s land-grant mission and its social justice values, the new policy, entitled “Equitable Access to Scholarly Articles Authored by University Faculty,” aids in the removal of price and permission barriers related to discoverability and access for anyone seeking UMD’s peer-reviewed scholarly work. 

The policy was spearheaded by UMD PACT, a campus-wide working group sponsored by the University Library Council, the Office of the Provost, and the Division of Research. The benefits and features of the policy are summarized briefly below: …

Through the policy, faculty members grant certain nonexclusive rights over their scholarly articles to the University of Maryland. This grant of nonexclusive rights, called the Equitable Access License, allows the University to distribute peer-reviewed versions of the articles free-of-charge to the general public, through DRUM, the University of Maryland’s online institutional repository. Faculty members commit to depositing (self-archiving) peer-reviewed versions of their scholarly articles into DRUM. The policy includes waiver and embargo options to enhance author freedom and control over their work….”

UMD’s Senate Approves Policy to Enhance Equitable Access to Scholarly Publications – News | UMD Libraries

“At its meeting on April 6, 2022, University of Maryland’s Senate voted to approve a new institutional policy that will advance equitable, open access to the University’s research and scholarship. In alignment with the University’s land-grant mission and its social justice values, the new policy, entitled “Equitable Access to Scholarly Articles Authored by University Faculty,” aids in the removal of price and permission barriers related to discoverability and access for anyone seeking UMD’s peer-reviewed scholarly work. 

The policy was spearheaded by UMD PACT, a campus-wide working group sponsored by the University Library Council, the Office of the Provost, and the Division of Research. The benefits and features of the policy are summarized briefly below: …”

 

Demystifying teaching, learning and research through institutional repositories in higher learning institutions in Kenya | Emerald Insight

Abstract:  Purpose

The purpose of this paper is to provide an analysis of ways in which teaching, learning and research can be demystified in higher institutions of learning (HILs). Over the last decade, HILs around the world have faced various transformations to adapt to new opportunities for knowledge dissemination and utilization. Many benefits are gained from implementation of the platform including visibility, status and increased reputation. Despite the high uptake of institutional repositories (IRs) to guide teaching, learning and research of higher institutions learning’s digital resources more effectively, little has been written on how IRs can be used for effective teaching, learning and research in higher institutions of learning.

Design/methodology/approach

Using analytical method, this paper analysed and presented various thematical issues on IRs in relation to its efficacy, while proposing solutions for its sustainability.

Findings

The paper found that most universities have embraced IRs as an option for increasing their visibility, status and researchers’ relevance in the knowledge world. It is the conclusion of the study that IRs are currently recognized as an essential infrastructure to respond to the higher institutions of learning challenges in the digital world.

Practical implications

This paper provides higher institutions of learning an opportunity to prepare their IRs to demystify teaching, learning and research. Since IRs will make it possible to access variety of information at any time whenever required.

Social implications

Knowledge accessibility and utilization bring about social change in the society.

Originality/value

Little has been documented on how IRs can be used for effective teaching, teaching, learning and research in HILs. This paper provides an analysis of ways in which teaching, learning and research can be demystified in these institutions. Thus, it contributes new knowledge on demystifying teaching, learning and research through IRs in HILs.

Is it time to share qualitative research data?

Abstract:  Policies by the National Institutes of Health and the National Science Foundation and scandals surrounding failures to reproduce the findings of key studies in psychology have generated increased calls for sharing research data. Most of these discussions have focused on quantitative, rather than qualitative, research data. This article examines scientific, ethical, and policy issues surrounding sharing qualitative research data. We consider advantages of sharing data, including enabling verification of findings, promoting new research in an economical manner, supporting research education, and fostering public trust in science. We then examine standard procedures for archiving and sharing data, such as anonymizing data and establishing data use agreements. Finally, we engage a series of concerns with sharing qualitative research data, such as the importance of relationships in interpreting data, the risk of reidentifying participants, issues surrounding consent and data ownership, and the burden of data documentation and depositing on researchers. For each concern, we identify options that enable data sharing or describe conditions under which select data might be withheld from a data repository. We conclude by suggesting that the default assumption should be that qualitative data will be shared unless concerns exist that cannot be addressed through standard data depositing practices such as anonymizing data or through data use agreements.

 

benefits of data sharing and ensuring open sources of systematic review data | Journal of Public Health | Oxford Academic

Abstract:  Aims

The benefits of increasing public access to data from clinical trials are widely accepted. Such benefits extend to the sharing of data from high-quality systematic reviews, given the time and cost involved with undertaking reviews. We describe the application of open sources of review data, outline potential challenges and highlight efforts made to address these challenges, with the intent of encouraging publishers, funders and authors to consider sharing review data more broadly.

Results

We describe the application of systematic review data in: (i) advancing understanding of clinical trials and systematic review methods, (ii) repurposing of data to answer public health policy and practice relevant questions, (iii) identification of research gaps and (iv) accelerating the conduct of rapid reviews to inform decision making. While access, logistical, motivational and legal challenges exist, there has been progress made by systematic review, academic and funding agencies to incentivise data sharing and create infrastructure to support greater access to systematic review data.

Conclusion

There is opportunity to maximize the benefits of research investment in undertaking systematic reviews by ensuring open sources of systematic review data. Efforts to create such systems should draw on learnings and principles outlined for sharing clinical trial data.

The normalization of preprints – International Science Council

“The last few years have seen an explosive growth in the use of preprints and associated preprint servers by large sections of the scientific community. This ISC Occasional Paper addresses the history of the preprint, its advantages and potential disadvantages, and concludes with some recommendations for how the growing acceptance of preprint posting should be handled within academia, and the changes in cultural norms that this entails….”