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

Data Management Plans: Implications for Automated Analyses

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Authors : Ngoc-Minh Pham, Heather Moulaison-Sandy, Bradley Wade Bishop, Hannah Gunderman

Data management plans (DMPs) are an essential part of planning data-driven research projects and ensuring long-term access and use of research data and digital objects; however, as text-based documents, DMPs must be analyzed manually for conformance to funder requirements.

This study presents a comparison of DMPs evaluations for 21 funded projects using 1) an automated means of analysis to identify elements that align with best practices in support of open research initiatives and 2) a manually-applied scorecard measuring these same elements.

The automated analysis revealed that terms related to availability (90% of DMPs), metadata (86% of DMPs), and sharing (81% of DMPs) were reliably supplied. Manual analysis revealed 86% (n = 18) of funded DMPs were adequate, with strong discussions of data management personnel (average score: 2 out of 2), data sharing (average score 1.83 out of 2), and limitations to data sharing (average score: 1.65 out of 2).

This study reveals that the automated approach to DMP assessment yields less granular yet similar results to manual assessments of the DMPs that are more efficiently produced. Additional observations and recommendations are also presented to make data management planning exercises and automated analysis even more useful going forward.

URL : Data Management Plans: Implications for Automated Analyses

DOI : http://doi.org/10.5334/dsj-2023-002

Creating research ethics and integrity country report cards: Case study from Europe

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Authors : Andrijana Perković Paloš, Rea Roje, Vicko Tomić, Ana Marušić

Structures for and practices of research integrity (RI) and research ethics (RE) differ among countries. This study analyzed the processes and structures for RI and RE in Europe, following the framework developed at the World Conferences on Research Integrity.

We present RI and RE Country Report Cards for 16 European countries, which included the information on RI and RE structures, processes and outcomes. While some of the countries are front-runners when it comes to RI and RE, with well-established and continually developing policies and structures, others are just starting their journey in RI and RE.

Although RI and RE contextual divergences must be taken into account, a level of harmonization among the countries is necessary so that researchers working in the European area can similarly handle RI and RE issues and have similar expectations regardless of the organization in which they work. RI and RE Country Report Cards can be a tool to monitor, compare, and strengthen RE and integrity across countries through empowerment and inspiration by examples of good practices and developed systems.

URL : Creating research ethics and integrity country report cards Case study from Europe

DOI : https://doi.org/10.1080/08989621.2022.2163632

Do academic inventors have diverse interests?

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Authors : Shuo Xu, Ling Li, Xin An

Academic inventors bridge science and technology, and have attracted increasing attention. However, little is known about whether they have more diverse research interests than researchers with a single role, and whether their important position for science–technology interactions correlates with their diverse interests.

For this purpose, we describe a rule-based approach for matching and identifying academic inventors, and an author interest discovery model with credit allocation schemes is utilized to measure the diversity of each researcher’s interests.

Finally, extensive empirical results on the DrugBank dataset provide several valuable insights. Contrary to our intuitive expectation, the research interests of academic inventors are the least diverse, while those of authors are the most.

In addition, the important position of the researchers has a certain relation with the diversity of research interests. More specifically, the degree of centrality has a significant positive correlation with the diversity of interests, and the constraint presents a significant negative correlation.

A significant weaker negative correlation can also be observed between the diversity of research interests of academic inventors and their closeness centrality. The normalized betweenness centrality seems be independent from interest diversity.

These conclusions help understand the mechanisms of the important position of academic inventors for science–technology interactions, from the perspective of research interests.

URL : Do academic inventors have diverse interests?

DOI : https://doi.org/10.1007/s11192-022-04587-0

Scholarly publishing and peer review in the Global South: the role of the reviewer

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Author : Peter Lor

Peer review is an integral part of contemporary scholarly publishing, especially journal publishing. Work submitted by scholars from all parts of the world is subjected to it. This includes submissions by scholars from the Global South, who wish to publish in “international” journals or in local journals which follow the same model.

These authors may not be native English speakers and may be unfamiliar with the conventions of Western scholarship. Many of them conduct research and write their manuscripts under challenging circumstances.

They may find it difficult to comply with the requirements of the journals to which they submit their articles. Their manuscripts quite often pose challenges to the peer reviewers.

The purpose of this article is to provide some background on scholarly publishing in the Global South and the challenges those colleagues face, and to outline what this may mean for the role of the reviewer.

URL : Scholarly publishing and peer review in the Global South: the role of the reviewer

DOI : https://doi.org/10.36253/jlis.it-512

Global Trends in Knowledge Production and the Evolving Peer Review Process

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Author : Steven Witt

This essay thus seeks to provide further critique and clarity to the peer review process and the ways in which management of peer review is evolving. These changes occur within a context of massive growth in the knowledge production process: global trends, information technologies, and policies that encourage more people globally to take part in the research process.

Associated with these global changes are stressors on the peer review process and particularly questions about who gets to be a peer reviewer and who has the right to produce knowledge under these processes.

Less a formal review and analysis of peer review across LIS, this essay takes the form of an autoethnographic narrative that that seeks to draw upon the researcher’s personal observations, experience, and reflections to critically examine changes to the peer review system that are taking place.

URL : Global Trends in Knowledge Production and the Evolving Peer Review Process

DOI : https://doi.org/10.36253/jlis.it-515

Neither Computer Science, nor Information Studies, nor Humanities Enough: What Is the Status of a Digital Humanities Conference Paper?

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Authors : Laura Estill, Jennifer Guiliano

This paper explores the disciplinary and regional conventions that surround the status of conference papers throughout their lifecycle from submission/abstract, review, presentation, and in some cases, publication.

Focusing on national and international Digital Humanities conferences, while also acknowledging disciplinary conferences that inform Digital Humanities, this paper blends close readings of conference calls for papers with analysis of conference practices to reckon with what constitutes a conference submission and its status in relationship to disciplinary conventions, peer review, and publication outcomes.

Ultimately, we argue that the best practice for Digital Humanities conferences is to be clear on the review and publication process so that participants can gauge how to accurately reflect their contributions.

URL : Neither Computer Science, nor Information Studies, nor Humanities Enough: What Is the Status of a Digital Humanities Conference Paper?

DOI : https://doi.org/10.16995/dscn.8090