Archives des mots-clés : scientific communication

Researchers and their data: A study based on the use of the word data in scholarly articles

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Authors : Frédérique Bordignon, Marion Maisonobe

Data is one of the most used terms in scientific vocabulary. This article focuses on the relationship between data and research by analyzing the contexts of occurrence of the word data in a corpus of 72,471 research articles (1980–2012) from two distinct fields (Social sciences, Physical sciences).

The aim is to shed light on the issues raised by research on data, namely the difficulty of defining what is considered as data, the transformations that data undergo during the research process, and how they gain value for researchers who hold them.

Relying on the distribution of occurrences throughout the texts and over time, it demonstrates that the word data mostly occurs at the beginning and end of research articles. Adjectives and verbs accompanying the noun data turn out to be even more important than data itself in specifying data.

The increase in the use of possessive pronouns at the end of the articles reveals that authors tend to claim ownership of their data at the very end of the research process. Our research demonstrates that even if data-handling operations are increasingly frequent, they are still described with imprecise verbs that do not reflect the complexity of these transformations.

URL : Researchers and their data: A study based on the use of the word data in scholarly articles

DOI : https://doi.org/10.1162/qss_a_00220

How do journals deal with problematic articles. Editorial response of journals to articles commented in PubPeer

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Authors : José-Luis Ortega, Lorena Delgado-Quirós

The aim of this article is to explore the editorial response of journals to research articles that may contain methodological errors or misconduct. A total of 17,244 articles commented on in PubPeer, a post-publication peer review site, were processed and classified according to several error and fraud categories.

Then, the editorial response (i.e., editorial notices) to these papers were retrieved from PubPeer, Retraction Watch, and PubMed to obtain the most comprehensive picture. The results show that only 21.5% of the articles that deserve an editorial notice (i.e., honest errors, methodological flaws, publishing fraud, manipulation) were corrected by the journal. This percentage would climb to 34% for 2019 publications.

This response is different between journals, but cross-sectional across all disciplines. Another interesting result is that high-impact journals suffer more from image manipulations, while plagiarism is more frequent in low-impact journals.

The study concludes with the observation that the journals have to improve their response to problematic articles.

URL : How do journals deal with problematic articles. Editorial response of journals to articles commented in PubPeer

DOI : https://doi.org/10.3145/epi.2023.ene.18

The Issues with Journal Issues: Let Journals Be Digital Libraries

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Author : C. Sean Burns

Science depends on a communication system, and today, that is largely provided by digital technologies such as the internet and web. Despite the fact that digital technologies provide the infrastructure for this communication system, peer-reviewed journals continue to mimic workflows and processes from the print era.

This paper focuses on one artifact from the print era, the journal issue, and describes how this artifact has been detrimental to the communication of science, and therefore, to science itself.

To replace the journal issue, this paper argues that scholarly publishing and journals could more fully embrace digital technologies by creating digital libraries to present and organize scholarly output.

URL : The Issues with Journal Issues: Let Journals Be Digital Libraries

DOI : https://doi.org/10.3390/publications11010007

The APC-Barrier and its effect on stratification in open access publishing

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Authors : Thomas Klebel, Tony Ross-Hellauer

Current implementations of Open Access (OA) publishing frequently involve Article Publishing Charges (APCs). Increasing evidence emerges that APCs impede researchers with fewer resources in publishing their research OA.

We analysed 1.5 million scientific articles from journals listed in the Directory of Open Access Journals to assess average APCs and their determinants for a comprehensive set of journal publications, across scientific disciplines, world regions and through time.

Levels of APCs were strongly stratified by scientific fields and the institutions’ countries, corroborating previous findings on publishing cultures and the impact of mandates of research funders.

After controlling for country and scientific field with a multilevel mixture model, however, we found small to moderate effects of levels of institutional resourcing on the level of APCs.

Effects were largest in countries with low GDP, suggesting decreasing marginal effects of institutional resources when general levels of funding are high. Our findings provide further evidence on how APCs stratify OA publishing and highlight the need for alternative publishing models.

URL : The APC-Barrier and its effect on stratification in open access publishing

DOI : https://doi.org/10.1162/qss_a_00245

Model(s) of the future? Overlay journals as an overlooked and emerging trend in scholarly communication

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Authors : Gail M. Thornton, Emily Kroeker

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.

URL : Model(s) of the future? Overlay journals as an overlooked and emerging trend in scholarly communication

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

Investigation of potential gender bias in the peer review system at Reproduction

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Authors : Marie Biolková, Tom Moore, Karen Schindler, Karl Swann, Andy Vail, Lindsay Flook, Helen Dick, Greg Fitzharris, Christopher A. Price, Norah Spears

This study examined whether publication outcome was affected by the gender of author, handling associate editor (AE), or reviewer, and whether there was gender bias in reviewer selection, in the journal Reproduction.

Analyses were carried out on 4289 original research manuscripts submitted to the journal between 2007 and 2019. Both female and male AEs appointed more male reviewers than female reviewers, but female AEs were significantly more likely to appoint female reviewers than male AEs were (p < 0.001).

When examining the gender of either first or last author manuscripts, those with female authors that were reviewed by female reviewers received better scores than those with male authors that were reviewed by female reviewers (p < 0.05): where the reviewer was male, no such effect was observed.

Acceptance rates of manuscripts were similar for both female and male authors, whether first or last, regardless of AE gender. Overall, there was no significant correlation between gender of first or last author, or of AE, on the likelihood of acceptance of a research paper.

These data suggest no bias against female authors during the peer review process in this reproductive biology journal.

URL : Investigation of potential gender bias in the peer review system at Reproduction

DOI : https://doi.org/10.1002/leap.1537

The Rise of GitHub in Scholarly Publications

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Authors : Emily Escamilla, Martin Klein, Talya Cooper, Vicky Rampin, Michele C. Weigle, Michael L. Nelson

The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs).

Similarly, the Software Heritage Foundation is working to archive public source code, but there is value in archiving the issue threads, pull requests, and wikis that provide important context to the code while maintaining their original URLs. In current implementations, source code and its ephemera are not preserved, which presents a problem for scholarly projects where reproducibility matters.

To understand and quantify the scope of this issue, we analyzed the use of GHP URIs in the arXiv and PMC corpora from January 2007 to December 2021. In total, there were 253,590 URIs to GitHub, SourceForge, Bitbucket, and GitLab repositories across the 2.66 million publications in the corpora.

We found that GitHub, GitLab, SourceForge, and Bitbucket were collectively linked to 160 times in 2007 and 76,746 times in 2021. In 2021, one out of five publications in the arXiv corpus included a URI to GitHub.

The complexity of GHPs like GitHub is not amenable to conventional Web archiving techniques. Therefore, the growing use of GHPs in scholarly publications points to an urgent and growing need for dedicated efforts to archive their holdings in order to preserve research code and its scholarly ephemera.

URL : https://arxiv.org/abs/2208.04895