Publishing – DigitalKoans

"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

"Harvard Library is Launching Harvard Open Journals Program"

Harvard Library is launching a new initiative called the Harvard Open Journals Program (HOJP), which will help researchers advance scholarly publishing that is open access, sustainable, and equitable. HOJP will provide publishing services, resources, and seed funding to participating Harvard researchers for new academic journals. All journal articles will be entirely free for authors and readers, with no barriers to publish or to access.. . . Yuan Li, University Scholarly Communication Officer and Director of Open Scholarship and Research Data Services at Harvard Library, pointed out the innovative nature of the program, "It is new for an institution to support faculty in seeking out an academic press to publish a no-fee open access journal and to provide assistance in securing its long-term funding. And offering a repository overlay journal model provides an alternative that appeals to some editorial boards and is gaining traction through initiatives such as Episciences. As we implement and refine this program on our campus, we hope it will inspire other universities to adopt such approaches to supporting barrier-free scholarly publishing."

https://tinyurl.com/ymkhs4db

Ithaka S+R: "Generative AI and Scholarly Publishing: Announcing a New Research Project"

To help, Ithaka S+R is launching a new study of the strategic implications of generative AI for scholarly publishing, with support from STM Solutions and a group of its members. The following key questions will guide our inquiry:

Will generative AI be integrated into the existing goals, processes, and infrastructures for scholarly publishing? Or, does this represent a transformative technology that will require fundamental restructuring of those goals, processes, and infrastructures?

Could generative AI effectively render our current assumptions about the role and purpose of publishers obsolete? What new roles could publishers play in a radically transformed information environment?

Which potential transformations should publishers encourage, and which risks require immediate coordinated responses while the technology is still taking root in the sector?

What new kinds of shared technical and/or social infrastructure are needed to support the ethical adoption of generative AI in support of the goals of scholarship and scholarly publishing? What systems and structures will be necessary to balance the needs of authors, readers, rights holders, publishers, and aggregators?

https://tinyurl.com/2s432pfh

"State of Open Science in Cancer Research"

This study has been focused on assessing the Open Science scenario of cancer research during the period 2011–2021, in terms of the derived scientific publications and raw data dissemination. . . .

50,822 papers were recovered, 71% of which belong to first and second quartile journals. 59% of the articles were published in Open Access (OA) journals. The Open Access model and international collaboration positively conditioned the number of citations received. Among the most productive journals stood out Plos One, Cancers, and Clinical and Translational Oncology. 2693 genomics, proteomics and metabolomics datasets were retrieved, being Gene Expression Omnibus the favoured repository.

https://doi.org/10.1007/s12094-024-03468-7

"Sorry We’re Open, Come in We’re Closed: Different Profiles in the Perceived Applicability of Open Science Practices to Completed Research Projects"

Open science is an increasingly important topic for research, politics and funding agencies. However, the discourse on open science is heavily influenced by certain research fields and paradigms, leading to the risk of generalizing what counts as openness to other research fields, regardless of its applicability. In our paper, we provide evidence that researchers perceive different profiles in the potential to apply open science practices to their projects, making a one-size-fits-all approach unsuitable. In a pilot study, we first systematized the breadth of open science practices. The subsequent survey study examined the perceived applicability of 13 open science practices across completed research projects in a broad variety of research disciplines. We were able to identify four different profiles in the perceived applicability of open science practices. For researchers conducting qualitative-empirical research projects, comprehensively implementing the breadth of open science practices is tendentially not feasible. Further, research projects from some disciplines tended to fit a profile with little opportunity for public participation. Yet, disciplines and research paradigms appear not to be the key factors in predicting the perceived applicability of open science practices. Our findings underscore the case for considering project-related conditions when implementing open science practices. This has implications for the establishment of policies, guidelines and standards concerning open science.

https://doi.org/10.1098/rsos.230595

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

"Benefits of Open Access to Researchers from Lower-Income Countries: A Global Analysis of Reference Patterns in 1980–2020"

The main objective of the open access (OA) movement is to make scientific literature freely available to everyone. This may be of particular importance to researchers in lower-income countries, who often face barriers due to high subscription costs. In this article, we address this issue by analysing over time the reference lists of scientific publications around the world. Our study focuses on key issues, including whether researchers from lower-income countries reference fewer publications in their research and how this trend evolves over time. We also investigate whether researchers from lower-income countries rely more on the literature that is openly available through different OA routes compared with other researchers. Our study revealed that the proportion of OA references has increased over time for all publications and country groups. However, publications from lower-income countries have seen a higher growth rate of OA-based references, suggesting that the emergence of OA publishing has been particularly advantageous to researchers in these countries.

https://doi.org/10.1177/01655515241245952

"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

"Better Together: BTAA [Big Ten Academic Alliance Libraries] Libraries, CDL and Lyrasis Commit to Strengthen Diamond Open Access in the United States"

Representatives from the Big Ten Academic Alliance Libraries (BTAA Libraries), California Digital Library (CDL) and Lyrasis attended the Global Summit on Diamond Open Access in Toluca, Mexico in October 2023. The Summit convened the international community to engage in dialog about how to advance Diamond Open Access (OA) to secure scholarly research as a public good and ensure equitable access to both the publishing and reading of that research. You can learn more from the recently released Report of the 2nd Diamond Open Access Conference.

https://tinyurl.com/39emttzk

Predatory Publishing: "The Publication Facts Label: A Public and Professional Guide for Research Articles"

These two questions—on public concerns over misinformation and academic apprehensions over journal and article quality—reflect a spirit of distrust that we, as former school teachers now involved in scholarly publishing, have felt was too important an instructional opportunity for us to leave to others. As a result, we are prototyping an educational strategy to help readers, both the "common reader, " as Virginia Woolf named them (1925) and researchers, learn a little more about what to make of work in the unfamiliar journals that come to their attention.

We [John Willinsky and Daniel Pimentel] are calling it a publication facts label (PFL). It is intended to appear with each research article. It emulates the look and feel of the Nutrition Facts label on food products in the United States. At this point in its development, the PFL draws data and links from the journal’s publishing platform on eight critical elements for scholarly publishing and presents to readers: (a) the publisher’s identity; (b) the journal’s scholarly editorial oversight; (c) the journal’s article acceptance rate; (d) the indexing of the journal; (e) the article’s number of peer reviewers and reviewer backgrounds; (f) the article authors’ competing interests; (g) the research study’s data availability; and (h) the funders of the research (Fig. 1).

https://doi.org/10.1002/leap.1599

"Launch of UPLOpen.com: Revolutionizing Access to Open Knowledge and Empowering Global Sustainability Goals"

In an ambitious move to democratize access to scholarly knowledge and advance the United Nations Sustainable Development Goals (UN SDGs), the De Gruyter eBound Foundation is thrilled to unveil UPLOpen.com, a product of University Press Library Open (UPLO), an innovative website that curates high-quality, open access scholarship from the world’s leading university presses. . . .

At launch, UPLOpen.com proudly hosts more than 350 open access books from over thirty university presses, including two landmark collections: Luminos, from the University of California Press, and TOME (Toward an Open Monograph Ecosystem), a pilot project of the Association of American Universities (AAU), Association of Research Libraries (ARL), and Association of University Presses (AUPresses), which concluded in 2022 but continues to release new titles. By mid-2024, the number of titles hosted on UPLOpen.com is expected to exceed 2,500, with further plans for significant growth already in motion for 2025 and beyond.

https://tinyurl.com/5ftcmx2p

"Researchers Need ‘Open’ Bibliographic Databases, New Declaration Says"

Some of the best known databases, such as the Web of Science and Scopus, are proprietary and offer pay-to-access data and services supporting these and other metrics, including university rankings and journal impact factors. But in a declaration posted today, more than 30 research and funding organizations call for the community to commit to platforms that instead are free for all, more transparent about their methods, and without restrictions about how the data can be used.

https://tinyurl.com/2nvzf9dh

Open Access Press: "UCL [University College London] Press Downloads Hit 10 Million"

UCL Press’s pioneering Open Access (OA) programme spans many of the major academic disciplines, from history to philosophy and the sciences to anthropology. The Press has published 339 books that have been downloaded more than 8.7 million times, while its 14 journals have attracted more than 2.6 million downloads. . . .

Paul Ayris, Pro-Vice-Provost at UCL LCCOS (Library, Culture, Collections and Open Science), commented: "Started in 2015, UCL Press continues to get better and better. 10,000,000 downloads and consultations underline the transformative effect that Open Access can have, particularly in the OA monograph space. UCL is proud to be developing a sustainable model for institutional OA publishing in Europe."

https://tinyurl.com/ym76wmbh

"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

COMMUNIA: "New Policy Paper on Access to Publicly Funded Research"

Today, COMMUNIA is releasing Policy Paper #17 on access to publicly funded research (also available as a PDF file), in which we propose a targeted intervention in European copyright law to improve access to publicly funded research. . ..

We recommend a three-tiered approach to open publicly funded research outputs to the public, immediately upon publication, where a secondary publication obligation co-exists with a secondary publication right. We consider that an obligation by the funding recipients to republish is a more consequential approach to protect the public interest, as it makes Open Access (OA) mandatory, ultimately ensuring that publicly funded research outputs are republished in OA repositories. A right is, however, necessary to ensure that the authors, and subsequently the funding recipients, retain the rights necessary to comply with the obligation. A right also provides a legal framework for the dissemination in OA repositories of publicly funded research outputs published before the entry into force of a secondary publication obligation.

In addition, we recommend the introduction of a copyright exception for the benefit of knowledge institutions, such as libraries and archives, to further support the task of making available research outputs published before the entry into force of secondary publication rights and obligations.

https://tinyurl.com/5yuaet4v

"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

"Is ChatGPT Corrupting Peer Review? Telltale Words Hint at AI Use"

A study that identified buzzword adjectives that could be hallmarks of AI-written text in peer-review reports suggests that researchers are turning to ChatGPT and other artificial intelligence (AI) tools to evaluate others’ work. . . .

Their analysis suggests that up to 17% of the peer-review reports have been substantially modified by chatbots — although it’s unclear whether researchers used the tools to construct reviews from scratch or just to edit and improve written drafts.

https://www.nature.com/articles/d41586-024-01051-2

"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

"PubTator 3.0: An AI-Powered Literature Resource for Unlocking Biomedical Knowledge"

PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly. PubTator 3.0’s online interface and API utilize these precomputed entity relations and synonyms to provide advanced search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results. We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive set of features and tools that allow researchers to navigate the ever-expanding wealth of biomedical literature, expediting research and unlocking valuable insights for scientific discovery.

https://doi.org/10.1093/nar/gkae235

"Transitional Agreements Aren’t Working: What Comes Next?"

Most important is the question of whether TAs deliver on their promise of their name to be transitional and transformative. Overall, the rate of journal "flipping" is low (with the exception of some smaller publishers). Most shocking, if not entirely unsurprising, to me was the following finding: based on the journal flipping rates observed between 2018 -2022 it would take at least 70 years for the big five publishers to flip their TA titles to OA.

https://tinyurl.com/n2ukvxr6

"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/

"New Report on the Sustainability of Diamond OA in Europe"

A new report from the DIAMAS work package that SPARC Europe looks at understanding how institutional publishing is sustained today. Institutional publishers and service providers are diverse due to their missions, size and service provision. In addition, there is no definitive set of tasks that all institutional publishers share. These characteristics influence the sustainability options available to them and the choices they make. . . .

Diamond OA publishing needs more stable and long-term funding. IPSPs utilise diverse funding models, and 40% depend on time-limited grants to support their operations and many are burdened by the administration that these grants demand. They rely primarily on parent organisations for basic support, especially in-kind support, such as personnel, and services. Personnel are more central to IPSPs’ financial sustainability than revenue streams, but they are often employed outside the boundary of the IPSP itself, which means that IPSPs have to negotiate for resources.

https://tinyurl.com/yw9ythtx

Report