Enabling preprint discovery, evaluation, and analysis with Europe PMC

Authors : Mariia Levchenko, Michael Parkin, Johanna McEntyre, Melissa Harrison

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.

URL : Enabling preprint discovery, evaluation, and analysis with Europe PMC

DOI : https://doi.org/10.1101/2024.04.19.590240

An analysis of the effects of sharing research data, code, and preprints on citations

Authors : Giovanni Colavizza, Lauren Cadwallader, Marcel LaFlamme, Grégory Dozot, Stéphane Lecorney, Daniel Rappo, Iain Hrynaszkiewicz

Calls to make scientific research more open have gained traction with a range of societal stakeholders. Open Science practices include but are not limited to the early sharing of results via preprints and openly sharing outputs such as data and code to make research more reproducible and extensible. Existing evidence shows that adopting Open Science practices has effects in several domains.

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. 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.

Arxiv : https://arxiv.org/abs/2404.16171

To preprint or not to preprint: A global researcher survey

Authors : Rong Ni, Ludo Waltman

Open science is receiving widespread attention globally, and preprinting offers an important way to implement open science practices in scholarly publishing. To develop a systematic understanding of researchers’ adoption of and attitudes toward preprinting, we conducted a survey of authors of research papers published in 2021 and early 2022. Our survey results show that the United States and Europe led the way in the adoption of preprinting.

The United States and European respondents reported a higher familiarity with and a stronger commitment to preprinting than their colleagues elsewhere in the world. The adoption of preprinting is much stronger in physics and astronomy as well as mathematics and computer science than in other research areas. Respondents identified free accessibility of preprints and acceleration of research communication as the most important benefits of preprinting.

Low reliability and credibility of preprints, sharing results before peer review and premature media coverage are the most significant concerns about preprinting, emphasized in particular by respondents in the life and health sciences. According to respondents, the most crucial strategies to encourage preprinting are integrating preprinting into journal submission workflows and providing recognition for posting preprints.

URL : To preprint or not to preprint: A global researcher survey

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

The experiences of COVID-19 preprint authors: a survey of researchers about publishing and receiving feedback on their work during the pandemic

Authors : Narmin Rzayeva, Susana Oliveira Henriques, Stephen Pinfield, Ludo Waltman

The COVID-19 pandemic caused a rise in preprinting, triggered by the need for open and rapid dissemination of research outputs. We surveyed authors of COVID-19 preprints to learn about their experiences with preprinting their work and also with publishing their work in a peer-reviewed journal.

Our research had the following objectives: 1. to learn about authors’ experiences with preprinting, their motivations, and future intentions; 2. to consider preprints in terms of their effectiveness in enabling authors to receive feedback on their work; 3. to compare the impact of feedback on preprints with the impact of comments of editors and reviewers on papers submitted to journals. In our survey, 78% of the new adopters of preprinting reported the intention to also preprint their future work.

The boost in preprinting may therefore have a structural effect that will last after the pandemic, although future developments will also depend on other factors, including the broader growth in the adoption of open science practices. A total of 53% of the respondents reported that they had received feedback on their preprints. However, more than half of the feedback was received through “closed” channels–privately to the authors.

This means that preprinting was a useful way to receive feedback on research, but the value of feedback could be increased further by facilitating and promoting “open” channels for preprint feedback. Almost a quarter of the feedback received by respondents consisted of detailed comments, showing the potential of preprint feedback to provide valuable comments on research.

Respondents also reported that, compared to preprint feedback, journal peer review was more likely to lead to major changes to their work, suggesting that journal peer review provides significant added value compared to feedback received on preprints.

URL : The experiences of COVID-19 preprint authors: a survey of researchers about publishing and receiving feedback on their work during the pandemic

DOI : https://doi.org/10.7717/peerj.15864

Comparison of effect estimates between preprints and peer-reviewed journal articles of COVID-19 trials

Authors : Mauricia Davidson, Theodoros Evrenoglou, Carolina Graña, Anna Chaimani, Isabelle Boutron

Background

Preprints are increasingly used to disseminate research results, providing multiple sources of information for the same study. We assessed the consistency in effect estimates between preprint and subsequent journal article of COVID-19 randomized controlled trials.

Methods

The study utilized data from the COVID-NMA living systematic review of pharmacological treatments for COVID-19 (covid-nma.com) up to July 20, 2022. We identified randomized controlled trials (RCTs) evaluating pharmacological treatments vs. standard of care/placebo for patients with COVID-19 that were originally posted as preprints and subsequently published as journal articles.

Trials that did not report the same analysis in both documents were excluded. Data were extracted independently by pairs of researchers with consensus to resolve disagreements. Effect estimates extracted from the first preprint were compared to effect estimates from the journal article.

Results

The search identified 135 RCTs originally posted as a preprint and subsequently published as a journal article. We excluded 26 RCTs that did not meet the eligibility criteria, of which 13 RCTs reported an interim analysis in the preprint and a final analysis in the journal article. Overall, 109 preprint–article RCTs were included in the analysis.

The median (interquartile range) delay between preprint and journal article was 121 (73–187) days, the median sample size was 150 (71–464) participants, 76% of RCTs had been prospectively registered, 60% received industry or mixed funding, 72% were multicentric trials. The overall risk of bias was rated as ‘some concern’ for 80% of RCTs.

We found that 81 preprint–article pairs of RCTs were consistent for all outcomes reported. There were nine RCTs with at least one outcome with a discrepancy in the number of participants with outcome events or the number of participants analyzed, which yielded a minor change in the estimate of the effect. Furthermore, six RCTs had at least one outcome missing in the journal article and 14 RCTs had at least one outcome added in the journal article compared to the preprint. There was a change in the direction of effect in one RCT. No changes in statistical significance or conclusions were found.

Conclusions

Effect estimates were generally consistent between COVID-19 preprints and subsequent journal articles. The main results and interpretation did not change in any trial. Nevertheless, some outcomes were added and deleted in some journal articles.

URL : Comparison of effect estimates between preprints and peer-reviewed journal articles of COVID-19 trials

DOI : https://doi.org/10.1186/s12874-023-02136-8

Clickbait or conspiracy? How Twitter users address the epistemic uncertainty of a controversial preprint

Authors : Mareike Bauer, Maximilian Heimstädt, Carlos Franzreb, Sonja Schimmler

Many scientists share preprints on social media platforms to gain attention from academic peers, policy-makers, and journalists. In this study we shed light on an unintended but highly consequential effect of sharing preprints: Their contribution to conspiracy theories. Although the scientific community might quickly dismiss a preprint as insubstantial and ‘clickbaity’, its uncertain epistemic status nevertheless allows conspiracy theorists to mobilize the text as scientific support for their own narratives.

To better understand the epistemic politics of preprints on social media platforms, we studied the case of a biomedical preprint, which was shared widely and discussed controversially on Twitter in the wake of the coronavirus disease 2019 pandemic. Using a combination of social network analysis and qualitative content analysis, we compared the structures of engagement with the preprint and the discursive practices of scientists and conspiracy theorists.

We found that despite substantial engagement, scientists were unable to dampen the conspiracy theorists’ enthusiasm for the preprint. We further found that members from both groups not only tried to reduce the preprint’s epistemic uncertainty but sometimes deliberately maintained it.

The maintenance of epistemic uncertainty helped conspiracy theorists to reinforce their group’s identity as skeptics and allowed scientists to express concerns with the state of their profession.

Our study contributes to research on the intricate relations between scientific knowledge and conspiracy theories online, as well as the role of social media platforms for new genres of scholarly communication.

URL : Clickbait or conspiracy? How Twitter users address the epistemic uncertainty of a controversial preprint

DOI : https://doi.org/10.1177/20539517231180575