E-Prints – DigitalKoans

“Making the Connection: An Examination of Institutional Repositories and Scholarly Communication Crosslinking Practices”

Institutional repositories (IRs) remain a powerful tool for opening, sharing, and preserving scholarship. Scholarly communication (SC) services and resources are essential to promoting and supporting IRs. Linking SC services within an IR offers support to users at their point of need. This study investigates the prevalence of web linking between IR and SC services in 145 Association of Research Libraries and Carnegie R1 libraries. This quantitative analysis identifies gaps and offers practical recommendations for developing connections between SC and IR websites at academic libraries. . . .

[T]he authors expected a comparable number of SC pages at institutions that had IRs. However, over 30 percent of the study’s library websites did not feature a dedicated SC web page. Furthermore, it is noteworthy that between spring 2021 and spring 2022 there was a 10 percent decrease in the number of institutions that offer SC services information to their user community. . . .

It is reassuring that the number of IRs remained consistent. Another bright spot is the nearly 14 percent increase in links made from the IR to SC services between spring 2021 and spring 2022. . . .

The few IRs in the study that did crosslink back to SC pages (9.1% in spring 2021; 23.0% in spring 2022) often included the SC link directly on the repository’s homepage.

https://tinyurl.com/mrxdj59j

“Open Repositories Are Being Profoundly Impacted By AI Bots and Other Crawlers: Results of a COAR Survey”

The results of the survey found that over 90% of respondents are encountering AI bots, usually more than once a week, and often leading to service disruptions. Respondents also reported using a variety of measures to minimize or stop AI bots from accessing the repository applying a mix of approaches such as rate-limiting, firewall rules, robots.txt rules and shared white-lists.

https://tinyurl.com/vh38m8a7

“Accelerating Access to Research Results: New Implementation Date for the 2024 NIH Public Access Policy”

I am excited to announce that one of my first actions as NIH Director is pushing the accelerator on policies to make NIH research findings freely and quickly available to the public. The 2024 Public Access Policy, originally slated to go into effect on December 31, 2025, will now be effective as of July 1, 2025.

To be clear, maximum transparency regarding the research we support is our default position. Since the release of NIH’s 2008 Public Access Policy, more than 1.5 million articles reporting on NIH-supported research have been made freely available to the public through PubMed Central. While the 2008 Policy allowed for an up to 12-month delay before such articles were required to be made publicly available, in 2024, NIH revised the Public Access Policy to remove the embargo period so that researchers, students, and members of the public have rapid access to these findings.

https://tinyurl.com/nudx2rej

“Effect of Perceived Preprint Effectiveness and Research Intensity on Posting Behaviour”

Open science is increasingly recognised worldwide, with preprint posting emerging as a key strategy. This study explores the factors influencing researchers’ adoption of preprint publication, particularly the perceived effectiveness of this practice and research intensity indicators such as publication and review frequency. Using open data from a comprehensive survey with 5,873 valid responses, we conducted regression analyses to control for demographic variables. Researchers’ productivity, particularly the number of journal articles and books published, greatly influences the frequency of preprint deposits. The perception of the effectiveness of preprints follows this. Preprints are viewed positively in terms of early access to new research, but negatively in terms of early feedback. Demographic variables, such as gender and the type of organisation conducting the research, do not have a significant impact on the production of preprints when other factors are controlled for. However, the researcher’s discipline, years of experience and geographical region generally have a moderate effect on the production of preprints. These findings highlight the motivations and barriers associated with preprint publication and provide insights into how researchers perceive the benefits and challenges of this practice within the broader context of open science.

https://arxiv.org/abs/2504.18896

“Making Your Repository (More) Accessible”

Introduction: As colleges and universities make increasing and overdue efforts under the auspices of access, equity, and inclusion to make their resources accessible to all users, these efforts must extend to the institution’s online presence, including its institutional repository. IR managers must first ask what “accessible” means for compliance with university policies as well as the Americans with Disability Act (ADA), immediately followed by plans for both remediating existing content and imposing best practices on new content, amid current workflows and budgetary restraints.

Literature Review: Literature on the topic of accessibility in IRs has mostly focused on the need to make collections accessible and the challenges for doing so. Advice on how to navigate the actual process is harder to come by.

Description of Service: The University of Mississippi established a goal that everything going into its IR would use OCR software to convert images of text into searchable text and create a process by which patrons could request remediation of older content from the IR, whether documents or recordings. A combination of shared tools (including Equidox and SensusAccess) and interdepartmental partnerships has made a significant difference in making these digital collections proactively accessible.

Next Steps: We continue to maintain partnerships with units around campus, made challenging by frequent turnover as in demand specialists take positions at other institutions. Despite our efforts to provide searchable text as a minimum level of service, OCR correction provides tags but not necessarily headings or alt-text. Hopefully future versions of OCR editors will include such features.

https://doi.org/10.31274/jlsc.18308

“openRxiv Launch to Sustain and Expand Preprint Sharing in Life and Health Sciences”

Since their launches in 2013 and 2019, respectively, preprint servers bioRxiv and medRxiv have transformed how scientific findings are communicated. They have hosted more than 325,000 reports of new discoveries, enabling scientists worldwide to collaborate, iterate, and build upon each other’s work at an unprecedented pace. . . .

Establishing openRxiv aims to accelerate the value of these preprint servers, making it easier for these resources to grow and adapt. Created as services of Cold Spring Harbor Laboratory in partnership with other institutions, bioRxiv and medRxiv now move under openRxiv’s researcher-driven governance, ensuring that preprint sharing remains independent, sustainable, and responsive to researchers’ evolving needs.

https://tinyurl.com/2auerw5t

“Open But Hidden: Open Access Gaps in the National Science Foundation Public Access Repository”

Introduction: In 2022, the U.S. government released new guidelines for making publicly funded research open and available. For the National Science Foundation (NSF), these policies reinforce requirements in place since 2016 for supported research to be submitted to the Public Access Repository (PAR).

Methods: To evaluate the public access compliance of research articles submitted to the NSF-PAR, this study searched for NSF-PAR records published between 2017 and 2021 from two research intensive institutions. Records were reviewed to determine whether the PAR held a deposited copy, as required by the 2016 policies, or provided a link out to publisher-held version(s).

Results: A total of 841 unique records were identified, all with publicly accessible versions. Yet only 42% had a deposited PDF version available in the repository as required by the NSF 2016 Public Access Policy. The remaining 58% directed instead to publisher-held versions. In total, only 55% of record links labeled “Full Text Available” directed users to a publicly accessible version with a single click.

Discussion: Records within PAR do not clearly direct users to the publicly accessible full text. In almost half of records, the most prominently displayed link directed users to a paywall version, even when a publicly available version existed. Records accessible only through the CHORUS (Clearing House for the Open Research of the United States) initiative were further obscured by requiring specialized navigation of publisher-owned sites.

Conclusion: Despite having a repository mandate since 2016, NSF compliance rates remain low. Additional support and/or oversight is needed to address the additional requirements introduced under the 2022 memo.

https://doi.org/10.31274/jlsc.17767

“Moving Open Repositories out of the Blind Spot of Initiatives to Correct the Scholarly Record”

Open repositories were created to enhance access and visibility of scholarly publications, driven by open science ideals emphasising transparency and accessibility. However, they lack mechanisms to update the status of corrected or retracted publications, posing a threat to the integrity of the scholarly record. To explore the scope of the problem, a manually verified corpus was examined: we extracted all the entries in the Crossref × Retraction Watch database for which the publication date of the corrected or retracted document ranged from 2013 to 2023. This corresponded to 24,430 entries with a DOI, which we use to query Unpaywall and identify their possible indexing in HAL, an open repository (second largest institutional repository worldwide). In most cases (91%), HAL does not mention corrections. While the study needs broader scope, it highlights the necessity of improving the role of open repositories in correction processes with better curation practices. We discuss how harvesting operations and the interoperability of platforms can maintain the integrity of the entire scholarly record. Not only will the open repositories avoid damaging its reliability through ambiguous reporting, but on the contrary, they will also strengthen it.

https://doi.org/10.1002/leap.1655

"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