E-Prints – DigitalKoans

"An Analysis of the Effects of Sharing Research Data, Code, and Preprints on Citations"

In this study, we investigate whether adopting one or more Open Science practices leads to significantly higher citations for an associated publication, which is one form of academic impact. We use a novel dataset known as Open Science Indicators, produced by PLOS and DataSeer, which includes all PLOS publications from 2018 to 2023 as well as a comparison group sampled from the PMC Open Access Subset. In total, we analyze circa 122’000 publications. We calculate publication and author-level citation indicators and use a broad set of control variables to isolate the effect of Open Science Indicators on received citations. We show that Open Science practices are adopted to different degrees across scientific disciplines. We find that the early release of a publication as a preprint correlates with a significant positive citation advantage of about 20.2% (±.7) on average. We also find that sharing data in an online repository correlates with a smaller yet still positive citation advantage of 4.3% (±.8) on average. However, we do not find a significant citation advantage for sharing code. Further research is needed on additional or alternative measures of impact beyond citations. Our results are likely to be of interest to researchers, as well as publishers, research funders, and policymakers.

https://doi.org/10.1371/journal.pone.0311493

"Enabling Preprint Discovery, Evaluation, and Analysis with Europe PMC"

Preprints provide an indispensable tool for rapid and open communication of early research findings. Preprints can also be revised and improved based on scientific commentary uncoupled from journal-organised peer review. The uptake of preprints in the life sciences has increased significantly in recent years, especially during the COVID-19 pandemic, when immediate access to research findings became crucial to address the global health emergency. With ongoing expansion of new preprint servers, improving discoverability of preprints is a necessary step to facilitate wider sharing of the science reported in preprints. To address the challenges of preprint visibility and reuse, Europe PMC, an open database of life science literature, began indexing preprint abstracts and metadata from several platforms in July 2018. Since then, Europe PMC has continued to increase coverage through addition of new servers, and expanded its preprint initiative to include the full text of preprints related to COVID-19 in July 2020 and then the full text of preprints supported by the Europe PMC funder consortium in April 2022. The preprint collection can be searched via the website and programmatically, with abstracts and the open access full text of COVID-19 and Europe PMC funder preprint subsets available for bulk download in a standard machine-readable JATS XML format. This enables automated information extraction for large-scale analyses of the preprint corpus, accelerating scientific research of the preprint literature itself. This publication describes steps taken to build trust, improve discoverability, and support reuse of life science preprints in Europe PMC. Here we discuss the benefits of indexing preprints alongside peer-reviewed publications, and challenges associated with this process.

https://doi.org/10.1371/journal.pone.0303005

"’Does It Feel like a Scientific Paper?’: A Qualitative Analysis of Preprint Servers’ Moderation and Quality Assurance Processes"

In recent years, preprints—i.e., scholarly manuscripts that have not been peer reviewed or published in a journal—have emerged as a major source of research communication and a critical component of open science. However, concerns have been raised about preprints’ potential to facilitate the spread of flawed or misleading research due to the lack of quality control performed by preprint servers. Yet, there is limited knowledge of how servers currently vet incoming content and how this impacts the openness and diversity of scholarly content. In this paper, we examine preprint servers’ moderation processes, the intentions underpinning them, and their potential effects through a qualitative analysis of in-depth interviews with 14 key preprint server personnel. We find a wide range of moderation processes, which vary depending on specific server contexts and needs and are motivated by a desire to prevent the spread of misinformation and protect trust in preprints and servers. Participants repeatedly emphasized the difference between their moderation processes and peer review, but in practice often applied similar criteria for delineating scientific from unscientific content. Moreover, moderation processes often relied on trust cues, such as article formats or author affiliations, as proxies for research quality, potentially introducing similar biases as have been found in traditional journal peer review. We discuss implications for the diversity of preprint content and authors, as well as the future of preprint servers within an evolving scholarly communication ecosystem.

https://doi.org/10.31222/osf.io/mp6ky

"Open Access Is Shaping Scientific Communication"

It seems likely that OA and traditional reader-pay journals will coexist in the immediate future, and probably should in the long run. In this context, the OSTP OA mandate will neither undermine the gatekeeping role of scientific journals nor much perturb the future evolution of scientific communication. The widespread adoption of TAs was already underway; if anything, the mandate reinforces that path. In an environment where both readers pay and OA journals operate alongside preprint platforms, it is natural to ask whether preprints might constrain subscription prices and APCs. If preprints and their peer-reviewed counterparts were close substitutes, then APCs for most OA journals would decline considerably.

https://doi.org/10.1126/science.adp8882

"Effects of Research Paper Promotion via ArXiv and X"

In the evolving landscape of scientific publishing, it is important to understand the drivers of high-impact research, to equip scientists with actionable strategies to enhance the reach of their work, and to understand trends in the use of modern scientific publishing tools to inform their further development. Here, we study trends in the use of early preprint publications and revisions on ArXiv and the use of X (formerly Twitter) for promotion of such papers in computer science and physics. We find that early submissions to ArXiv and promotion on X have soared in recent years. Estimating the effect that the use of each of these modern affordances has on the number of citations of scientific publications, we find that peer-reviewed conference papers in computer science that are submitted early to ArXiv gain on average 21.1±17.4 more citations, revised on ArXiv gain 18.4±17.6 more citations, and promoted on X gain 44.4±8 more citations in the first 5 years from an initial publication. In contrast, journal articles in physics experience comparatively lower boosts in citation counts, with increases of 3.9±1.1, 4.3±0.9, and 6.9±3.5 citations respectively for the same interventions. Our results show that promoting one’s work on ArXiv or X has a large impact on the number of citations, as well as the number of influential citations computed by Semantic Scholar, and thereby on the career of researchers. These effects are present also for publications in physics, but they are relatively smaller. The larger relative effect sizes, effects of promotion accumulating over time, and elevated unpredictability of the number of citations in computer science than in physics suggest a greater role of world-of-mouth spreading in computer science than in physics.

https://arxiv.org/abs/2401.11116v2

Updated Report to the U.S. Congress on Financing Mechanisms for Open Access Publishing of Federally Funded Research

This current report elaborates on:

Implementation to advance federal public access policies. Updated agency public access policies will go into effect by December 31, 2025, in accordance with the 2022 Memorandum.

Trends in scholarly publishing since the release of the November 2023 Report, including further discussion of business models to enable public access to federally funded research, as well as domestic and global developments in advancing public access to research results.

An expansion of the analysis of estimated article processing charges paid to publish federally funded research from 2016 to 2022, with further discussion of limitations associated with calculating these charges.

Efforts to advance research integrity, including through implementation of federal public access policies and open science practices.

Continuing trends in peer review as they relate to research integrity, equity, and sustainability.

https://tinyurl.com/yryw9ejv

"Analyzing Research Data Repositories (RDR) from BRICS Nations: A Comprehensive Study"

As of March 2, 2024, re3data.org indexes a total of 3,192 Research Data Repositories (RDRs) worldwide, with BRICS nations contributing 195. China leads among BRICS nations, followed by India, Russia, and Brazil. . . . "House, tailor-made " software is widely used for creating RDRs, followed by Dataverse and DSpace. . . . Most repositories are disciplinary, followed by institutional ones. Most repositories specify data upload types, with "restricted " being the most common, followed by closed types. Open access is predominant in data access, followed by restricted access and embargo periods, while a small number restrict access entirely.

https://doi.org/10.1108/LM-04-2024-0040

"Accelerated Acceptance Time for Preprint Submissions: A Comparative Analysis Based on Pubmed"

This study compared the differences in acceptance time between 100,077 preprint papers from the platforms arXiv, bioRxiv, and medRxiv, and 1,314,973 non-preprint papers submitted to the same journal within the same year and month. . . . The findings demonstrate that manuscripts released as preprints before journal submission experience significantly shorter acceptance time compared to those without preprints. However, if preprints are posted after submitting to a journal, they do not confer an advantage in terms of acceptance time.

https://doi.org/10.1007/s11192-024-05056-6

"A Census of Institutional Repositories at Regional Public Universities"

This study reports on the implementation of institutional repositories (IRs) at regional public universities (RPUs) in the United States and its territories. The author investigated repository platform choice, operation style, and content. More than half of RPUs have implemented an IR. The author discusses how these findings align with trends in previous research and explores the unique aspects of IRs at RPUs—particularly the prevalence of student works and special collections materials. For over two decades, institutional repositories (IRs) have been used at institutions of higher education to collect, preserve, and share the scholarly works of an institution. During that same time there have been an increasing number of studies looking at who has implemented an IR, the most popular IR platforms, and type and number of objects deposited in IRs. While some studies have looked at small or teaching-focused institutions, most of these studies have focused on IR implementations at large research-focused institutions.

https://tinyurl.com/yc2fs4r2

"Developing Open Access Resource Management Principles in a Consortial Environment: A University of California Model"

In the summer of 2021, the University of California (UC) migrated to a new integrated library system, called the Systemwide Integrated Library System project (SILS), which for the first time brought all ten UC campuses, two regional storage facilities, and the California Digital Library (CDL) together into one shared library system. With new potential for increased collaboration and cooperation, SILS leadership groups identified consortial open access (OA) resource management as a key opportunity in the new system, in alignment with UC’s priorities around discovery and access to library collections, as well as UC’s commitment to open access and transforming the scholarly communication landscape. This article discusses the formation of the UC Open Access Resource Management Task Force (OARMTF), a group charged to investigate what it would mean to consortially manage OA resources. Specifically, this article focuses on the OARMTF’s work setting out principles for OA resource management, which the authors hope may serve as a useful case study for other institutions or consortia interested in developing principles around OA resource management, as well as encourage more discussion and research into best practices for consortial management of OA resources.

https://doi.org/10.5860/lrts.68n1.8216

"Opening Up: A Global Context for Local Open Access Initiatives in Higher Education"

Open access policies and mandates can be a useful tool in persuading faculty at higher education institutions around the globe to produce and share open scholarship. But are such policies widely written, accepted, and adopted? Leveraging information found on the Registry of Open Access Repositories Mandatory Archiving Policies, this paper analyzes open access policies at higher education institutions worldwide. The data indicate that Europe holds the most policies, while fewer policies have been enacted in the Americas, Africa, Oceania, and Asia due to a myriad of barriers. Overall, better strategies to promote open access are needed, and such strategies may not necessarily take the form of an open access policy. My own investigation of global open access policies has informed my practices with respect to open access. In this paper, I demonstrate how librarians acting as policy entrepreneurs can assist with the promotion of open access at their institutions and then conclude with suggestions, solutions, and pathways beyond policy adoption to promote and advocate for open access.

https://tinyurl.com/2h3uz5n4

"An Analysis of the Effects of Sharing Research Data, Code, and Preprints on Citations"

In this study, we investigate whether adopting one or more Open Science practices leads to significantly higher citations for an associated publication, which is one form of academic impact. We use a novel dataset known as Open Science Indicators, produced by PLOS and DataSeer, which includes all PLOS publications from 2018 to 2023 as well as a comparison group sampled from the PMC Open Access Subset. In total, we analyze circa 122’000 publications. We calculate publication and author-level citation indicators and use a broad set of control variables to isolate the effect of Open Science Indicators on received citations. We show that Open Science practices are adopted to different degrees across scientific disciplines. We find that the early release of a publication as a preprint correlates with a significant positive citation advantage of about 20.2% on average. We also find that sharing data in an online repository correlates with a smaller yet still positive citation advantage of 4.3% on average. However, we do not find a significant citation advantage for sharing code.

https://arxiv.org/abs/2404.16171

The Open Access Tracking Project Is Now 15 Years Old

Peter Suber has announced that the Open Access Tracking Project is now 15 years old. This project has made an invaluable contribution to the Open Access and Open Science movements. Readers are encouraged to considering joining it and posting new works of interest to it. Even occasional contributions are meaningful.

Here is a description of the project from its home page:

OATP is a crowd-sourced social-tagging project running on free software to capture news and comment on open access to research.

Its mission is (1) to create real-time alerts for OA-related news and comment, and (2) to organize knowledge of the field, by tag or subtopic, for easy searching and sharing.

OATP publishes a comprehensive primary feed of new OA developments, and hundreds of smaller secondary feeds on subtopics or subsets, for example, one feed for each project tag, one for each search, and one for each user-created boolean combination of its other feeds.

OATP runs on TagTeam, open-source software developed specifically for OATP and now available for open, tag-based research projects on any topic. See the OATP hub within TagTeam. TagTeam stores all OATP tag records for deduping, export, preservation, modification, and search. OATP started on Connotea and moved to TagTeam in September 2012.

Peter Suber launched OATP in April 2009, and wrote a full-length description of it in the SPARC Open Access Newsletter for May 2009. In mid-2011 OATP became part of the Harvard Open Access Project (HOAP).

https://tinyurl.com/m5ku5mxh

"Preprints, Journals and Openness: Disentangling Goals and Incentives "

I would argue that private funders such as the Gates Foundation or the Howard Hughes Medical Institute (HHMI) could provide material support through grants and policies for quality peer review, baking peer review into selection of grantees. Such an approach will require careful structures and mechanisms for reviewer selection, and measures of success, or we may run the risk of creating further inequities. Mind you, in many fields it is just hard to find good reviewers prepared to put in the effort required for a considered, thoughtful review. Societies, such as my own, could also consider material ways to support peer review more actively — a philosophical and practical approach to raising the profile of peer review at an early stage in the life of a researcher.

https://tinyurl.com/ymckyb9x

"Gates Open Access Policy Refresh Increases Compliance Burden and Eliminates Financial Support "

Broadly considered, the only grantees who are genuinely free to publish where they wish are those with other funding sources besides Gates with which to pay publication fees. Grantees who do not have other funds will not be able to publish in subscription journals that charge publishing fees or in fully open access journals that charge an APC. . . .

Grantees who do not have other funding sources to pay publication fees will need to identify journals that do not charge a fee to publish open or that do not charge any fees to publish a non-open article. But, it cannot be assumed that such journals will consider a manuscript that asserts the mandated rights retention statement (RRS): "Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 License has already been assigned to the Author Accepted Manuscript version that might arise from this submission."

https://tinyurl.com/4mjctu2u

"Is the Bill and Melinda Gates Foundation’s New OA Policy the Start of a Shift towards Preprints?"

Whether a more decoupled ecosystem emerges will depend on other funders. Will key funders like Howard Hughes Medical Institute (HHMI) and Wellcome Trust follow Gates? Up until now they have made supportive noises about preprints but stopped short of mandates. Both are supporters of Plan S though, and frankly Plan S 2.0 looks a lot like Plan U. And what of the elephant in the room, National Institutes of Health (NIH)? The recent OSTP memo requires US-government-funded articles to be made free, but does not provide additional funds. If government agencies like NIH were to decide preprints qualify, as bioRxiv and arXiv have suggested, authors would have an easy path to making articles free that doesn’t require them to find an extra $5-10K behind the couch to cover APCs.

https://tinyurl.com/2t7z39vf

"Life Scientists’ Experience with Posting Preprints during the COVID-19 Pandemic"

In the COVID-19 pandemic, it was much more critical for many life science researchers to rapidly disseminate research results—so they used preprints as upstream publication opportunities. This was rather new to the life sciences where preprint servers had only appeared as early as 2013. With a mixed-methods-study we examined this development and investigated whether preprint posting is a temporary phenomenon or the beginning of a cultural shift in publishing behavior in the life sciences. First, we conducted a survey of researchers who have posted COVID-19 related preprints. We investigated experiences with posting preprints during the COVID-19 pandemic, motivations for and concerns about posting preprints, the role of research institutions or funders, and the future of preprint publishing. Answers were grouped to compare differences between respondents’ gender, career stage, region of origin (global south or global north) and experience with posting preprints before and during the COVID-19 pandemic. We further analyzed eight popular preprint repositories regarding the number of posted preprints and preprint characteristics, such as the number of authors and citations. Interestingly, survey and preprint server analysis have presented different, if not contradicting results: While the majority of surveyed researchers was willing to continue posting preprints, the numbers of preprints published, especially on servers for the life sciences, have stagnated or declined. Also, while certain preprints garnered substantial citations during the COVID-19 pandemic, this has not resulted in a significant shift in researchers’ publishing behavior, and the posting of preprints has not become a routine. We concluded that the sustainability of preprint publishing practices is more strongly influenced by disciplinary norms and practices than by external shocks as the COVID-19 pandemic.

https://doi.org/10.1007/s11192-024-04982-9

"VeriXiv Supports Gates-Funded Researchers to Comply with New Open Access Policy"

F1000 and the Bill & Melinda Gates Foundation have announced plans to launch a new verified preprint platform that will enable the rapid availability of new findings and promote research integrity. VeriXiv [pronounced very-kive] will support researchers in complying with the Gates Foundation’s refreshed open access policy that requires all their funded research to be made available as a preprint from January 2025. . . .

Twenty different ethics and integrity checks will assess a range of issues, including plagiarism, image manipulation, author verification and competing interests. In addition, open research transparency checks will check whether the data is available in an appropriate repository and that methods have been included to support reproducibility. Each preprint will have clear labelling so that readers know the level of verification conducted on the article, and which levels have been passed.

https://www.f1000.com/verixiv/

Bill & Melinda Gates Foundation Ends APC Support and Requires Preprints

For over a decade, our foundation has championed transparency, access, and equity in scholarly publishing by working with publishers and journals to develop more open and accessible research publishing practices. But our quest for a truly equitable and inclusive scholarly publishing ecosystem remains incomplete. Today, we’re announcing a refreshed policy for our grantees that we hope will help foundation-supported breakthroughs reach the field in the fastest and fairest way possible.

At its core, the policy will:

End the foundation’s payment of individual article publishing fees such as APCs—paving the way for more equitable publishing models

Require grantees to share preprints of their articles—breaking free from journal constraints while prioritizing access to research and preserving grantee publishing choices

https://tinyurl.com/mtba833c

"Support for OSF Preprint Infrastructure and Community Servers"

Numerous Ivy Plus Libraries Confederation (IPLC) partner institutions* will provide three years of financial support for the Center for Open Science’s OSF Preprints, an open source platform and infrastructure that enables the facilitation and discovery of scholarship. COS notes that submission and consumption of preprints continues to grow with "~150,000 preprints hosted across all of the current and prior preprint communities, and 1.7 million views on preprint pages since September 2023."

https://tinyurl.com/yn9nntvu

"To Preprint or Not to Preprint: A Global Researcher Survey"

Open science is receiving widespread attention globally, and preprinting offers an important way to implement open science practices in scholarly publishing. To develop a systematic understanding of researchers’ adoption of and attitudes toward preprinting, we conducted a survey of authors of research papers published in 2021 and early 2022. Our survey results show that the United States and Europe led the way in the adoption of preprinting. The United States and European respondents reported a higher familiarity with and a stronger commitment to preprinting than their colleagues elsewhere in the world. The adoption of preprinting is much stronger in physics and astronomy as well as mathematics and computer science than in other research areas. Respondents identified free accessibility of preprints and acceleration of research communication as the most important benefits of preprinting. Low reliability and credibility of preprints, sharing results before peer review and premature media coverage are the most significant concerns about preprinting, emphasized in particular by respondents in the life and health sciences. According to respondents, the most crucial strategies to encourage preprinting are integrating preprinting into journal submission workflows and providing recognition for posting preprints.

https://doi.org/10.1002/asi.24880

Advancing Ireland’s Open Repository Landscape: A Strategic Roadmap

This report presents an in-depth analysis and strategic roadmap for advancing the open repository landscape in Ireland. Drawing on comprehensive data from interviews, surveys, self-assessments, and both national and international initiatives, the document outlines the current status, challenges, and future prospects for open repositories in Ireland. Key findings highlight significant advancements in open access adherence. Despite these successes, persistent challenges such as metadata quality, resource limitations, and sustainability issues underscore the need for concerted effort and strategic planning.

The report proposes a forward-looking roadmap spanning from 2025 to 2030 and beyond, prioritising the enhancement of repository infrastructures, metadata quality improvement, open mandates promotion, technological advancements, capacity building, and fostering collaborative partnerships. This strategic vision aims to develop and encourage Ireland’s transition to open research, leveraging innovative practices and collaborative efforts to facilitate a more open, inclusive, and sustainable research environment. By addressing current limitations and embracing future opportunities, the roadmap sets the stage for a transformative shift in Ireland’s scholarly communication landscape, with potential significant impacts on researchers, institutions, and society at large.

https://doi.org/10.5281/zenodo.10810233

"eLife’s New Model: One Year On"

On January 31 2023, we launched our new model for publishing, combining the speed and transparency of preprints with the expert scrutiny and evaluation of peer review. We committed to publish everything that we reviewed. We would publish preprints together with public reviews and assessments. By doing so we would reshape the purpose of a journal. . . .

More than 6,200 teams of researchers have submitted their research (fig.1), choosing our journal and publishing model. Our month-on-month submissions have been stable since launch, but this January marks the highest number so far with 615.

At present, 27.7% of submissions (fig. 2) to our new model are sent for review. This is compared to 31.4% of submissions sent for review in our legacy model (from February 1, 2022–January 31, 2023). . . .

Reviewed Preprints help researchers share their peer-reviewed and assessed research faster. For a Reviewed Preprint, the median time from submission to publication of the first version with reviews and eLife assessment is 91 days (fig. 3). This is over two and a half times faster than the median submission to publication time in the legacy model. . . .

By the end of January 2024 we had published 1332 Reviewed Preprints, and this figure rises to 1836 when we include revised versions. These articles have been viewed over 850,000 times by more than 320,000 readers.

https://tinyurl.com/yknkm2fn

"Platformisation of Science: Conceptual Foundations"

The digital platforms we are dealing with in this article are auxiliary tools that do not produce anything themselves but provide an infrastructure for service providers and users to meet. They have potentially unlimited scaling potential and have become the central places of exchange. In academia, we can also observe that research and its communication become more digital and that digital services are aiming to become platforms. In this article we explore the concept of digital platforms and their potential impact on academic research, firstly addressing the question: To what extent can digital platforms be understood as a specific type of research infrastructure? We draw from recent literature on platforms and platformisation from different streams of scholarship and relate them to the science studies concept of research infrastructures, to eventually arrive at a framework for science platforms. Secondly, we aim to assess how science platforms may affect scholarly practice. Thirdly, we aim to assess to what extent science is platformised and how this interferes with scientific understandings of quality and autonomy. At the end of this article, we argue that the potential benefits of platform infrastructure for academic pursuits cannot be ignored, but the commercialization of the infrastructure for scholarly communication is a cause for concern. Ultimately, a nuanced and well-informed perspective on the impact of platformisation on academia is necessary to ensure that the academic community can maximize the benefits of digital infrastructures while mitigating negative consequences.

http://dx.doi.org/10.53377/lq.16693

Inteview with Stevan Harnad: "Open and Impactful Scholarly Communication"

We posed selected questions to Stevan Harnad thirty years after his "subversive proposal" to self-archive online scholarly articles in university-hosted or disciplinary repositories to make them openly available and thus maximize research impact. A combination of factors including unfounded scepticism concerning open access, and bureaucratic access to the few institutional repositories launched by universities chiefly drove this outcome. The conclusions of the study may further inform educational efforts on scholarly communication in the digital era aimed at undergraduate students and researchers alike.

http://tinyurl.com/383u7nfe