E-Prints – DigitalKoans

"The Transformation of the Green Road to Open Access"

(1) Background: The 2002 Budapest Open Access Initiative recommended on self-archiving of scientific articles in open repositories as the "green road" to open access. Twenty years later, only one part of the researchers deposits their publications in open repositories; moreover, one part of the repositories’ content is not based on self-archived deposits but on mediated nonfaculty contributions. The purpose of the paper is to provide more empirical evidence on this situation and to assess the impact on the future of the green road. (2) Methods: We analyzed the contributions on the French national HAL repository from more than 1,000 laboratories affiliated to the ten most important French research universities, with a focus on 2020, representing 14,023 contributor accounts and 166,939 deposits. (3) Results: We identified seven different types of contributor accounts, including deposits from nonfaculty staff and import flows from other platforms. Mediated nonfaculty contribution accounts for at least 48% of the deposits. We also identified difference between institutions and disciplines. (4) Conclusions: Our empirical results reveal a transformation of open repositories from self-archiving and direct scientific communication towards research information management. Repositories like HAL are somewhere in the middle of the process. The paper describes data quality as the main issue and major challenge of this transformation.

https://doi.org/10.20944/preprints202302.0268.v1

Only 10% Fully Understand "Preprint": "Framing COVID-19 Preprint Research as Uncertain: A Mixed-Method Study of Public Reactions"

Unlike hedging, preprint disclosure had no impact on audience message evaluations, nor vaccine attitudes and intentions. In one sense, this is a positive finding in that transparency about preprint status is unlikely to produce negative public reactions. Yet a likely explanation for the null effects is that most participants lacked the knowledge to differentiate between preprints and peer-reviewed research and did not understand this disclosure as an indicator of preliminary science. The qualitative data supported this explanation. When asked how they interpret the term "preprint" when they see it in a scientific news article, participants’ responses indicated that most had a limited understanding of the concept, even among those who received the preprint disclosure message with a brief explanation of the term. In total, only 10% of participants provided definitions of preprint that aligned with those accepted by the scholarly community. Only 15% described the term as an indicator of uncertain or preliminary evidence.

https://doi.org/10.1080/10410236.2023.2164954

"PreprintMatch: A Tool for Preprint to Publication Detection Shows Global Inequities in Scientific Publication"

Preprints, versions of scientific manuscripts that precede peer review, are growing in popularity. They offer an opportunity to democratize and accelerate research, as they have no publication costs or a lengthy peer review process. Preprints are often later published in peer-reviewed venues, but these publications and the original preprints are frequently not linked in any way. To this end, we developed a tool, PreprintMatch, to find matches between preprints and their corresponding published papers, if they exist. This tool outperforms existing techniques to match preprints and papers, both on matching performance and speed. PreprintMatch was applied to search for matches between preprints (from bioRxiv and medRxiv), and PubMed. The preliminary nature of preprints offers a unique perspective into scientific projects at a relatively early stage, and with better matching between preprint and paper, we explored questions related to research inequity. We found that preprints from low income countries are published as peer-reviewed papers at a lower rate than high income countries (39.6% and 61.1%, respectively), and our data is consistent with previous work that cite a lack of resources, lack of stability, and policy choices to explain this discrepancy. Preprints from low income countries were also found to be published quicker (178 vs 203 days) and with less title, abstract, and author similarity to the published version compared to high income countries. Low income countries add more authors from the preprint to the published version than high income countries (0.42 authors vs 0.32, respectively), a practice that is significantly more frequent in China compared to similar countries. Finally, we find that some publishers publish work with authors from lower income countries more frequently than others.

https://doi.org/10.1371/journal.pone.0281659

"Lack of Sustainability Plans for Preprint Services Risks Their Potential to Improve Science"

Despite successfully building a revenue model that shares the burden between Cornell University, the Simons Foundation and several members and supporters, arXiv’s “funding is still outpaced by [their] growth” – the server hosts over 2 million preprints already and is growing by 10% each year. And while arXiv has been supporting more and more scholars to share and discover preprints, the team behind it has been through significant changes in leadership and is dealing with the urgent need to modernize their 30-year-old technology. As a former Executive Director of arXiv noted, “[arXiv’s success] may not last forever”. Similarly, the recent news that Chan Zuckerberg Initiative has renewed its financial support for the leading preprint servers in biology and medicine, bioRxiv and medRxiv is welcome relief, but this support is temporary, and the team must find a way to continue in the long run.

bit.ly/3y745Ji

2.6 Billion Total Downloads: arXiv Annual Report 2022

Our critical priorities during 2022 were to secure additional funding, hire technical and program directors, and ramp up our efforts to modernize arXiv’s software by moving it to the cloud, which will provide better stability, scalability and maintainability. I’m pleased to report that we were able to make significant progress on all of these fronts. arXiv brought in more funding than expected in the form of grants, memberships, and donations, and we hired Stephanie Orphan as program director and Charles Frankston as technical director. Both bring strong and complementary expertise to the team. Moving the technical operations of arXiv—a service with a 30 year history—off of Cornell’s on-premises servers is a major, complicated task. The move to the cloud is currently in progress and on track

bit.ly/41exRsX

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"The Preprint Revolution — Implications for Bibliographic Databases"

In the box below, we present six recommendations for optimizing the indexing of preprints in bibliographic databases. As we will discuss later, implementing these recommendations requires close collaboration between bibliographic databases and other actors in the scholarly publishing system.

Recommendation 1: Cover all relevant preprint servers.

A bibliographic database should index preprints from all relevant preprint servers. A disciplinary database (e.g., PubMed and Europe PMC) should index preprints from all preprint servers relevant in a particular discipline. A multidisciplinary database (e.g., Dimensions, the Lens, Scopus, and Web of Science) should index preprints from all preprint servers across all disciplines.

Recommendation 2: Provide comprehensive preprint metadata.

A bibliographic database should provide metadata for preprints that is as comprehensive as metadata for journal articles. The metadata should at least include the title and abstract of a preprint, the names and affiliations of the authors, the reference list, and funding information. It should also include a version history.

Recommendation 3: Provide links between preprints and journal articles.

If an article has been published both on a preprint server and in a journal, a bibliographic database should provide a link between the preprint and the journal article. The link establishes that the preprint and the journal article are different versions of the same article. The preprint and the journal article belong to the same publication family.

Recommendation 4: Provide links between preprints and peer reviews.

If a preprint has been peer reviewed and the reviews have been made openly available, a bibliographic database should index the reviews and should provide links between the preprint and the reviews.

Recommendation 5: Provide deduplicated citation links between publication families.

A bibliographic database should provide deduplicated citation links at the level of publication families. If there are multiple citation links from publications in one publication family (e.g., from a preprint and from a journal article) to publications in another publication family, these citation links should be deduplicated.

Recommendation 6: Do not make arbitrary distinctions between publication types (preprints, journal articles, and others).

A bibliographic database should not make arbitrary distinctions between preprints, journal articles, and other publication types. A database may inform its users about relevant differences between publications of different types (e.g., whether publications have been peer reviewed or not), but otherwise it should treat all publications in the same way, regardless of their publication type.

bit.ly/3KtuWXl

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Clarivate: "The Preprint Citation Index: Linking Preprints to the Trusted Web of Science Ecosystem"

After many months of planning, we are launching the Preprint Citation Index, a multidisciplinary collection of preprints from leading repositories that helps researchers stay current with the newest research while maintaining confidence in the resources they rely on. . . . The Preprint Citation Index currently provides nearly two million preprints from arXiv, bioRxiv, chemRxiv, medRxiv and Preprints.org. We plan to add preprints from a dozen additional repositories as well as display open peer reviews on Preprint Citation Index throughout 2023.

bit.ly/3YxPcuw

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"Outside the Library: Early Career Researchers and Use of Alternative Information Sources in Pandemic Times"

Presents findings from a study into the attitudes and practices of pandemic-era early career researchers (ECRs) in regard to obtaining access to the formally published scholarly literature, which focused on alternative providers, notably ResearchGate and Sci-Hub. . . . Findings show that alternative providers, as represented by ResearchGate and Sci-Hub, have become established and appear to be gaining ground. However, there are considerable country- and discipline-associated differences.

https://doi.org/10.1002/leap.1522

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"One Size Does Not Fit All: Self-Archiving Personas Based on Federally Funded Researchers at a Mid-Sized Private Institution"

Introduction: This mixed-method study analyzes the self-archiving behaviors and underlying motivations of researchers at an institution very recently recategorized by the Carnegie Classification system from "Doctoral– High Research Activity (R2)" to "Doctoral–Very High Research Activity (R1)." Methods: A quantitative analysis of data provided by CHORUS, a multi-institutional open access (OA) infrastructure project designed to minimize the administrative costs of complying with federal public access mandates, was followed by semi-structured qualitative interviews with researchers to determine the underlying motivations for self-archiving research papers resulting from federal grant support. Results: Fifty-one authors with federal research funding published 71 journal articles; 139 OA versions of these 71 articles were intentionally made available by researchers across nine types of platforms, including and in addition to those provided by publishers. Interviews with 11 investigators revealed motivators such as a dedication to public access to knowledge, learned behaviors in specific disciplines, and enlightened self-interest. Challenges included concern regarding confidentiality, confusion about intellectual property and funder requirements, administrative overhead, and integrity of the scholarly record. Discussion: Despite concerns and a lack of an OA mandate and other drivers more commonly present at larger, more research-intensive universities, several researchers interviewed actively engaged in self-archiving article versions, not always with clear motivations. These findings have implications for both scholarly communications and collection development services. Conclusion: These quantitative and qualitative data informed the creation of three distinct personas intended to help librarians at similar universities design services in a manner that aligns with investigator motivations.

https://doi.org/10.31274/jlsc.13886

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"arXiv Announces New Policy on ChatGPT and Similar Tools"

In view of this, we

continue to require authors to report in their work any significant use of sophisticated tools, such as instruments and software; we now include in particular text-to-text generative AI among those that should be reported consistent with subject standards for methodology.

remind all colleagues that by signing their name as an author of a paper, they each individually take full responsibility for all its contents, irrespective of how the contents were generated. If generative AI language tools generate inappropriate language, plagiarized content, errors, mistakes, incorrect references, or misleading content, and that output is included in scientific works, it is the responsibility of the author(s).

generative AI language tools should not be listed as an author; instead authors should refer to (1).

bit.ly/3wKlx5J

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"Model(s) of the Future? Overlay Journals as an Overlooked and Emerging Trend in Scholarly Communication"

Overlay journals, a potentially overlooked model of scholarly communication, have seen a resurgence due to the increasing number of preprint repositories and preprints on coronavirus disease 2019 (COVID-19) related topics. Overlay journals at various stages of maturity were examined for unique characteristics, including whether the authors submitted their article to the journal, whether the peer reviews of the article were published by the overlay journal, and whether the overlay journals took advantage of opportunities for increased discovery. As librarians and researchers seek new, futuristic models for publishing, overlay journals are emerging as an important contribution to scholarly communication.

https://doi.org/10.5206/cjils-rcsib.v45i2.14730

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"A Framework for Improving the Accessibility of Research Papers on arXiv.org"

The research content hosted by arXiv is not fully accessible to everyone due to disabilities and other barriers. This matters because a significant proportion of people have reading and visual disabilities, it is important to our community that arXiv is as open as possible, and if science is to advance, we need wide and diverse participation. In addition, we have mandates to become accessible, and accessible content benefits everyone. In this paper, we will describe the accessibility problems with research, review current mitigations (and explain why they aren’t sufficient), and share the results of our user research with scientists and accessibility experts. Finally, we will present arXiv’s proposed next step towards more open science: offering HTML alongside existing PDF and TeX formats. An accessible HTML version of this paper is also available at https://info.arxiv.org/about/accessibility_research_report.html

https://arxiv.org/abs/2212.07286

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"Phase 1 of the NIH Preprint Pilot: Testing the Viability of Making Preprints Discoverable in PubMed Central and PubMed"

Introduction: The National Library of Medicine (NLM) launched a pilot in June 2020 to 1) explore the feasibility and utility of adding preprints to PubMed Central (PMC) and making them discoverable in PubMed and 2) to support accelerated discoverability of NIH-supported research without compromising user trust in NLM’s widely used literature services. Methods: The first phase of the Pilot focused on archiving preprints reporting NIH-supported SARS-CoV-2 virus and COVID-19 research. To launch Phase 1, NLM identified eligible preprint servers and developed processes for identifying NIH-supported preprints within scope in these servers. Processes were also developed for the ingest and conversion of preprints in PMC and to send corresponding records to PubMed. User interfaces were modified for display of preprint records. NLM collected data on the preprints ingested and discovery of preprint records in PMC and PubMed and engaged users through focus groups and a survey to obtain direct feedback on the Pilot and perceptions of preprints. Results: Between June 2020 and June 2022, NLM added more than 3,300 preprint records to PMC and PubMed, which were viewed 4 million times and 3 million times, respectively. Nearly a quarter of preprints in the Pilot were not associated with a peer-reviewed published journal article. User feedback revealed that the inclusion of preprints did not have a notable impact on trust in PMC or PubMed. Discussion: NIH-supported preprints can be identified and added to PMC and PubMed without disrupting existing operations processes. Additionally, inclusion of preprints in PMC and PubMed accelerates discovery of NIH research without reducing trust in NLM literature services. Phase 1 of the Pilot provided a useful testbed for studying NIH investigator preprint posting practices, as well as knowledge gaps among user groups, during the COVID-19 public health emergency, an unusual time with heightened interest in immediate access to research results.

https://doi.org/10.1101/2022.12.12.520156

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"Ten Recommended Practices for Managing Preprints in Generalist and Institutional Repositories"

Currently, there are numerous gaps in geographic and domain coverage and some authors will choose to deposit their research outputs into another type of repository, such as an institutional or generalist repository. . . . To address these gaps, a COAR-ASAPbio Working Group on Preprint in Repositories identified ten recommended practices for managing preprints across three areas: linking, discovery, and editorial processes. While we acknowledge that many of these practices are not currently in use by institutional and generalist repositories, we hope that these recommendations will encourage repositories around the world that collect preprints to begin to apply them locally.

https://cutt.ly/R0gursT

Full report

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"Comparison of Clinical Study Results Reported in medRxiv Preprints vs Peer-reviewed Journal Articles"

Most clinical studies posted as preprints on medRxiv and subsequently published in peer-reviewed journals had concordant study characteristics, results, and final interpretations. With more than three-fourths of preprints published in journals within 24 months, these results may suggest that many preprints report findings that are consistent with the final peer-reviewed publications.

https://cutt.ly/k0gyQOv

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"Evaluation of Publication of COVID-19–Related Articles Initially Presented as Preprints"

In this study, we identified 3343 COVID-19–related preprints posted on medRxiv in 2020. Our March 2022 search indicated that 1712 of those preprints (51.2%) were subsequently published in the peer-reviewed literature; this number increased to 1742 (52.1%) when we repeated the search in October 2022. Not considering January 2020, in which only 1 article on COVID-19 was posted, the rate of subsequent publication in a scientific journal ranged from 43.5% (94 of 216 preprints; observed in March 2020) to 60.6% (177 of 292 preprints posted in August 2020). The Table shows the top 25 of 579 peer-reviewed journals in which these preprints were published; 827 preprints (47.5%) were subsequently published in quartile 1 journals (Figure).

bit.ly/3HprhIq

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"Free and Open-Source Automated Open Access Preprint Harvesting"

Universities are attempting to ensure that all of their research is publicly accessible because of funding mandates. Many universities have established campus open access (OA) repositories but are struggling with how to upload millions of manuscripts under numerous license agreements while also linking metadata to make them discoverable. To do this manually requires around 15 minutes per manuscript from an experienced librarian. The time and cost to do this campus-wide is prohibitive. To radically reduce the time and costs of this process and to harvest all past work, this article reports on the development and testing of a free and open source (FOSS) JavaScript-based application, aperta-accessum, which does the following: 1) harvests names and emails from a department’s faculty webpage; 2) identifies scholars’ Open Researcher and Contributor Identifiers (ORCID iDs); 3) obtains digital object identifiers (DOIs) of publications for each scholar; 4) checks for existing copies in an institution’s OA repository; 5) identifies the legal opportunities to provide OA versions of all of the articles not already in the OA repository; 6) sends authors emails requesting a simple upload of author manuscripts; and 7) adds link-harvested metadata from DOIs with uploaded preprints into a bepress repository; the code can be modified for additional repositories. The results of this study show that, in the administrative time needed to make a single document OA manually, aperta-accessum can process approximately five entire departments worth of peer-reviewed articles. Following best practices discussed, it is clear that this open-source OA harvester enables institutional library’s stewardship of OA knowledge on a mass scale for radically reduced costs.

https://doi.org/10.31274/jlsc.14421

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"eLife Reviewed Preprints: Interview with Fiona Hutton"

How is the new publishing model similar to or different from older publishing models based on preprints combined with peer review (e.g. Copernicus, F1000)? There are three main differences. 1) Peer review and assessment at eLife continues to be organised by an editorial team made up of academic experts and led by an Editor-in-Chief, Deputy Editors, Senior Editors, and a Board of Reviewing Editors via a consultative peer-review model already known as one of the most constructive for authors in the industry. 2) The addition of an eLife assessment is a further crucial part of our model, distinctive from what others are doing—it is a key addition to our public peer reviews and it enables readers to understand the context of the work, the significance of the research and the strength of the evidence. 3) We are no longer making accept/reject decisions based on peer review—authors will choose if and when to produce a Version of Record at any point following the review process.

https://cutt.ly/gMPfonI

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"Motivations, Concerns and Selection Biases When Posting Preprints: A Survey of bioRxiv Authors"

Since 2013, the usage of preprints as a means of sharing research in biology has rapidly grown, in particular via the preprint server bioRxiv. Recent studies have found that journal articles that were previously posted to bioRxiv received a higher number of citations or mentions/shares on other online platforms compared to articles in the same journals that were not posted. However, the exact causal mechanism for this effect has not been established, and may in part be related to authors’ biases in the selection of articles that are chosen to be posted as preprints. We aimed to investigate this mechanism by conducting a mixed-methods survey of 1,444 authors of bioRxiv preprints, to investigate the reasons that they post or do not post certain articles as preprints, and to make comparisons between articles they choose to post and not post as preprints. We find that authors are most strongly motivated to post preprints to increase awareness of their work and increase the speed of its dissemination; conversely, the strongest reasons for not posting preprints centre around a lack of awareness of preprints and reluctance to publicly post work that has not undergone a peer review process. We additionally find evidence that authors do not consider quality, novelty or significance when posting or not posting research as preprints, however, authors retain an expectation that articles they post as preprints will receive more citations or be shared more widely online than articles not posted.

https://doi.org/10.1371/journal.pone.0274441

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Australia: "Chief Scientist Plan for Free Research Access for All"

The nation’s chief scientist will this year recommend to government a radical departure from the way research is distributed in Australia, proposing a world-first model that shakes up the multi-billion-dollar publishing business so Australian readers don’t pay a cent. . . .The model goes much further than open access schemes in the US and Europe by including existing research libraries and has been designed specifically for Australia’s own challenges.

https://cutt.ly/UNBM1Cy

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ARL: "Two-Page Table Compares 2013 and 2022 Public-Access Guidance from US Office of Science and Technology Policy"

In an effort to highlight the significant differences between the 2013 [OSTP] memorandum and the 2022 guidance, the Association of Research Libraries (ARL) has published a comparison table of the two documents. This table breaks down the 2013 and 2022 OSTP public-access guidance into sections for a quick side-by-side comparison of 10 key components, including embargo period, data policies, formats, and metadata expectations.

https://cutt.ly/jNm0OeT

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"The Challenging State of University Campus and Library Open Access Policies"

Introduction: This study investigates whether United States university libraries’ commitment to increasing open access (OA) to scholarly outputs as demonstrated by their support of campus level OA policies translates into adoption of OA policies that apply specifically to library employees. Method: This mixed-methods study used an anonymous survey and optional open-ended interviews of scholarly communications librarians at Carnegie Classification Doctoral Universities (Very High Research [R1] and High Research [R2]) to gather information about OA policies or statements at their institutions and/or within their libraries. Results & Discussion: Variation in campus culture and governance structure meant the path from creation to adoption to implementation of a campus and/or library OA policy was similarly varied. The research reveals librarians’ motivations for and contributions to advancement of OA on their campuses, and sometimes also within their libraries. Conclusion: Many of the rationales driving adoption of campus OA policies similarly drive adoption of library-specific OA policies. Those surveyed whose institutions did have library-based OA policies referenced both the importance of leading by example and alignment with institutional mission and values.

https://doi.org/10.31274/jlsc.13049

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"What Does Open Research Look Like in My Field? New Researcher Case Studies Show How It’s Done"

Today UKRN releases both an updated version of its primer on open research in different disciplines, and a new set of accompanying case studies, hosted on dedicated UKRN pages for each discipline.

The case studies—23 so far—are based on interviews conducted during summer 2022 with active researchers across the UK and beyond. They describe a wide range of research practices across diverse fields of research, from art and design to condensed matter physics, and outline both why and how openness is relevant.

They cover topics such as open access and open data and software, but also co-production, pre-registration, preprints, ethics, the roles of infrastructure, and of other actors such as funders, standards bodies and community groups.

https://cutt.ly/zNpjQM1

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"eLife Ends Accept/Reject Decisions Following Peer Review"

eLife is pleased to announce a major change in editorial practice. Building on its 2021 shift to exclusively reviewing preprints, the organisation is ending the practice of making accept/reject decisions following peer review.

From January 31, 2023, eLife will instead publish every paper it reviews as a Reviewed Preprint, a new type of research output that combines the manuscript with eLife’s detailed peer reviews and a concise assessment of the significance of the findings and quality of the evidence.

https://cutt.ly/2B9tiCx

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"Overlay Journals: A Study of the Current Landscape"

Overlay journals are characterised by their articles being published on open access repositories, often already starting in their initial preprint form as a prerequisite for submission to the journal prior to initiating the peer-review process. In this study we aimed to identify currently active overlay journals and examine their characteristics. We utilised an explorative web search and contacted key service providers for additional information. . . . They may also rank highly within the traditional journal citation metrics. None of the investigated journals required fees from authors, which is likely related to the cost-effective aspects of the overlay publishing model.

https://doi.org/10.1177/09610006221125208

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