Preprints: a Timely Counterbalance for Big Data-Driven Research

Commentary on "Preliminary Species Hypotheses" in Entomological Taxonomy: A Global Data and FAIR Infrastructure Perspective

What if early taxonomic findings were treated like preprints, open to iterative improvement or managed with practices from the open-source community, such as Git branching, merging and patch management? Prompted by Buckley's article Charting a Future for Entomological Taxonomy in New Zealand (2024), this commentary explores these possibilities in the context of biodiversity informatics. In response to the need for rapid, scalable biodiversity monitoring, Buckley introduces preliminary species hypotheses (PSH) as a bridge between quick identification tools and the rigorous Linnaean system, leveraging DNA barcoding and AI-assisted image recognition to produce provisional classifications that can later be validated. Expanding on Buckley's framework, this commentary emphasises the critical role of data linking, versioning and integration to support evolving taxonomic data. Borrowing from software and open-source practices, I explore the idea of managing PSH with an infrastructure that treats each taxonomic update as a versioned "commit", which can be tracked, refined and integrated over time. Drawing insights from FAIR (Findable, Accessible, Interoperable, Reusable) principles and Digital Extended Specimens, I identify infrastructure requirements for PSH, including robust data standards, persistent identifiers and interoperability to support global biodiversity repositories. Additionally, Taxonomic Data Objects offer a model for dynamically integrating PSH into adaptable taxonomies that can evolve with new data and tools. By positioning PSH within an open, infrastructure-focused framework, this commentary advocates for scalable, hypothesis-driven biodiversity data that meets modern conservation needs, bridging traditional and emerging practices in taxonomy.

The use and acceptability of preprints in health and social care settings: A scoping review

BACKGROUND

Preprints are open and accessible scientific manuscript or report that is shared publicly, through a preprint server, before being submitted to a journal. The value and importance of preprints has grown since its contribution during the public health emergency of the COVID-19 pandemic. Funders and publishers are establishing their position on the use of preprints, in grant applications and publishing models. However, the evidence supporting the use and acceptability of preprints varies across funders, publishers, and researchers. The scoping review explored the current evidence on the use and acceptability of preprints in health and social care settings by publishers, funders, and the research community throughout the research lifecycle.

METHODS

A scoping review was undertaken with no study or language limits. The search strategy was limited to the last five years (2017-2022) to capture changes influenced by COVID-19 (e.g., accelerated use and role of preprints in research). The review included international literature, including grey literature, and two databases were searched: Scopus and Web of Science (24 August 2022).

RESULTS

379 titles and abstracts and 193 full text articles were assessed for eligibility. Ninety-eight articles met eligibility criteria and were included for full extraction. For barriers and challenges, 26 statements were grouped under four main themes (e.g., volume/growth of publications, quality assurance/trustworthiness, risks associated to credibility, and validation). For benefits and value, 34 statements were grouped under six themes (e.g., openness/transparency, increased visibility/credibility, open review process, open research, democratic process/systems, increased productivity/opportunities).

CONCLUSIONS

Preprints provide opportunities for rapid dissemination but there is a need for clear policies and guidance from journals, publishers, and funders. Cautionary measures are needed to maintain the quality and value of preprints, paying particular attention to how findings are translated to the public. More research is needed to address some of the uncertainties addressed in this review.

Counterpoint: Preprints and the Future of Scientific Publishing-In Favor of Relevance

Peer-reviewed journals provide an invaluable but inadequate vehicle for scientific communication. Preprints are now an essential complement to peer-reviewed publications. Eschewing preprints will slow scientific progress and reduce the public health impact of epidemiologic research. The coronavirus disease 2019 (COVID-19) pandemic highlighted long-standing limitations of the peer-review process. Preprint servers, such as bioRxiv and medRxiv, served as crucial venues to rapidly disseminate research and provide detailed backup to sound-bite science that is often communicated through the popular press or social media. The major criticisms of preprints arise from an unjustified optimism about peer review. Peer review provides highly imperfect sorting and curation of research and only modest improvements in research conduct or presentation for most individual papers. The advantages of peer review come at the expense of months to years of delay in sharing research methods or results. For time-sensitive evidence, these delays can lead to important missteps and ill-advised policies. Even with research that is not intrinsically urgent, preprints expedite debate, expand engagement, and accelerate progress. The risk that poor-quality papers will have undue influence because they are posted on a preprint server is low. If epidemiology aims to deliver evidence relevant for public health, we need to embrace strategic uses of preprint servers.

Open access publishing - noble intention, flawed reality

For two decades, the international scholarly publishing community has been embroiled in a divisive debate about the best model for funding the dissemination of scientific research. Some may assume that this debate has been thoroughly resolved in favour of the Open Access (OA) model of scientific publishing. Recent commentaries reveal a less settled reality. This narrative review aims to lay out the nature of these deep divisions among the sector's stakeholders, reflects on their systemic drivers and considers the future prospects for actualising OA's intended benefits and surmounting its risks and costs. In the process, we highlight some of inequities OA presents for junior or unfunded researchers, and academics from resource-poor environments, for whom an increasing body of evidence shows clear evidence of discrimination and injustice caused by Article Processing Charges. The authors are university-appointed researchers working the UK and South Africa, trained in disciplines ranging from medicine and epidemiology to social science and digital science. We have no vested interest in any particular model of scientific publication, and no conflicts of interest to declare. We believe the issues we identify are pertinent to almost all research disciplines.

Preprint Servers in Kidney Disease Research: A Rapid Review

Preprint servers, such as arXiv and bioRxiv, have disrupted the scientific communication landscape by providing rapid access to research before peer review. medRxiv was launched as a free online repository for preprints in the medical, clinical, and related health sciences in 2019. In this review, we present the uptake of preprint server use in nephrology and discuss specific considerations regarding preprint server use in medicine. Distribution of kidney-related research on preprint servers is rising at an exponential rate. Survey of nephrology journals identified that 15 of 17 (88%) are publishing original research accepted submissions that have been uploaded to preprint servers. After reviewing 52 clinically impactful trials in nephrology discussed in the online Nephrology Journal Club (NephJC), an average lag of 300 days was found between study completion and publication, indicating an opportunity for faster research dissemination. Rapid review of papers discussing benefits and risks of preprint server use from the researcher, publisher, or end user perspective identified 53 papers that met criteria. Potential benefits of biomedical preprint servers included rapid dissemination, improved transparency of the peer review process, greater visibility and recognition, and collaboration. However, these benefits come at the risk of rapid spread of results not yet subjected to the rigors of peer review. Preprint servers shift the burden of critical appraisal to the reader. Media may be especially at risk due to their focus on "late-breaking" information. Preprint servers have played an even larger role when late-breaking research results are of special interest, such as during the global coronavirus disease 2019 pandemic. Coronavirus disease 2019 has brought both the benefits and risks of preprint servers to the forefront. Given the prominent online presence of the nephrology community, it is poised to lead the medicine community in appropriate use of preprint servers.

Preprint manuscripts and servers in the era of coronavirus disease 2019

RATIONALE, AIMS, AND OBJECTIVES

To both examine the impact of preprint publishing on health sciences research and survey popular preprint servers amidst the current coronavirus disease 2019 (COVID-19) pandemic.

METHODS

The authors queried three biomedical databases (MEDLINE, Web of Science, and Google Scholar) and two preprint servers (MedRxiv and SSRN) to identify literature pertaining to preprints. Additionally, they evaluated 12 preprint servers featuring COVID-19 research through sample submission of six manuscripts.

RESULTS

The realm of health sciences research has seen a dramatic increase in the presence and importance of preprint publications. By posting manuscripts on preprint servers, researchers are able to immediately communicate their findings, thereby facilitating prompt feedback and promoting collaboration. In doing so, they may also reduce publication bias and improve methodological transparency. However, by circumventing the peer-review process, academia incurs the risk of disseminating erroneous or misinterpreted data and suffering the downstream consequences. Never have these issues been better highlighted than during the ongoing COVID-19 pandemic. Researchers have flooded the literature with preprint publications as stopgaps to meet the desperate need for knowledge about the disease. These unreviewed articles initially outnumbered those published in conventional journals and helped steer the mainstream scientific community at the start of the pandemic. In surveying select preprint servers, the authors discovered varying usability, review practices, and acceptance polices.

CONCLUSION

While vital in the rapid dispensation of science, preprint manuscripts promulgate their conclusions without peer review and possess the capacity to misinform. Undoubtedly part of the future of science, conscientious consumers will need to appreciate not only their utility, but also their limitations.