The role of software in science: a knowledge graph-based analysis of software mentions in PubMed Central

Science across all disciplines has become increasingly data-driven, leading to additional needs with respect to software for collecting, processing and analysing data. Thus, transparency about software used as part of the scientific process is crucial to understand provenance of individual research data and insights, is a prerequisite for reproducibility and can enable macro-analysis of the evolution of scientific methods over time. However, missing rigor in software citation practices renders the automated detection and disambiguation of software mentions a challenging problem. In this work, we provide a large-scale analysis of software usage and citation practices facilitated through an unprecedented knowledge graph of software mentions and affiliated metadata generated through supervised information extraction models trained on a unique gold standard corpus and applied to more than 3 million scientific articles. Our information extraction approach distinguishes different types of software and mentions, disambiguates mentions and outperforms the state-of-the-art significantly, leading to the most comprehensive corpus of 11.8 M software mentions that are described through a knowledge graph consisting of more than 300 M triples. Our analysis provides insights into the evolution of software usage and citation patterns across various fields, ranks of journals, and impact of publications. Whereas, to the best of our knowledge, this is the most comprehensive analysis of software use and citation at the time, all data and models are shared publicly to facilitate further research into scientific use and citation of software.

CITATION PRACTICES IN RESEARCH ARTICLES IN INDONESIA-BASED JOURNALS AND INTERNATIONAL JOURNALS Udi Samanhudi, Aisling O’Boyle

This paper examines the similarities and differences in the use of rhetorical citations in research articles in two journal publication contexts in the field of Applied Linguistics, namely Indonesian Journals aimed at a local audience, and International Journals aimed at a global audience. Fifty Discussion Sections from published research articles were taken from the two publication contexts. Results of the analysis indicate a dominant use of integral citations especially verb-controlling type in the Indonesian local corpus. It is suggested that this citation type requires less demand on synthesising various sources cited while Discussion Sections in the International corpus make greater use of non-integral citations which indicates a succinct synthesis of various sources. In terms of function, referring to literature is the most salient function in Indonesian local corpus while attribution is the most dominant function found in the International corpus. Accompanying the textual analysis of citation practices in these journals, Indonesian academics as part of the community of the discipline were interviewed. Their perspectives indicate urgency for results of genre analysis studies to be transformed into teaching materials to assist especially novice writers in the field of Applied Linguistics in understanding English research article writing conventions better.

A Proposed Method for Residual Citation Allocation Based on Citation Contexts’ Similarity

This article proposes an approach for allocating residual citations to scientific publications and demonstrating this proposed approach with a sample of biomedical publications. Residue citations (i.e., citations that are lost due to citation practices termed “Obliteration by Incorporation” and the “Palimpsestic Syndrome”) in consequent citations in the second, third or nth generations are then reconstituted. The proposed approach takes into account citation contexts (i.e., the contribution of a cited publication) for allocating residual citation. The proposed method for allocating residual citation is based on the similarity between the citation contexts of a publication and those of its nth generation citations in their n+1th generation citations. The proposed method was demonstrated using a sample with ten base articles and their five generations of citations, from which 5,272 citation context pairs were obtained. The proposed indirect citation weighting was compared with the existing cascading citation weighting method using one T-test. Statistical tests were also performed to understand the differences in the residual citations from one generation to the other. Like the cascading citation system, residual citations from articles to their generations of citations decreased as the number of generations increased. However, residue citations accrued to publications at all the generations were statistically different between the proposed residual citation and the cascading citation system. This study proposes a method for assessing scientific communication based on the contribution of scientific publications beyond the conventional direct citation.

Naming is Power

Citing is a political act. It is a practice that can work both sides of the same coin: it can give voice, and it can silence. Through this research, we call for those contributing to the scholarship of teaching and learning (SoTL) to attend to this duality explicitly and intentionally. In this multidisciplinary field, SoTL knowledge-producers bring the citation norms of their home disciplines, a habit that calls for interrogation and negotiation of the citation practices used in this shared space. The aim of our study was to gather data about how citation is practiced within the SoTL community: who we cite, how we cite, and what values, priorities, and politics are conveyed in these practices. We were also interested in whether any self-selected categories of identity (e.g., gender, career stage) related to self-described citation practices and priorities. Findings suggest several statistically significant relationships did emerge, which we identify as important avenues for further research and writing. We conclude with 10 principles of citation practices in SoTL.

Foreign judges of the Pacific as agents of global constitutionalism

Studies of global constitutionalism have focused on the transnational movement of constitutional law through the citation of foreign judgments. However, little attention has been paid to the movement of constitutional judges themselves. This article considers how the foreign judges who sit on courts of constitutional jurisdiction in Pacific island states can be understood as part of the phenomenon of global constitutionalism. It identifies three ways in which foreign judges can be agents of global constitutionalism: as mechanisms for the diffusion of constitutional ideas, as expressions of global constitutional values and as objects of transnational legal transfer. An empirical analysis comparing the citation practices of local and foreign judges in constitutional cases in nine Pacific states suggests that the use of foreign judges on constitutional courts does contribute to the international movement of constitutional ideas. However, a critical analysis of foreign judges as expressions and objects of global constitutionalism sheds light on a range of tensions in the role of constitutional judges and understandings of global constitutionalism.

Introducing Reproducibility to Citation Analysis: a Case Study in the Earth Sciences

Objectives: Replicate methods from a 2019 study of Earth Science researcher citation practices. Calculate programmatically whether researchers in Earth Science rely on a smaller subset of literature than estimated by the 80/20 rule. Determine whether these reproducible citation analysis methods can be used to analyze open access uptake. Methods: Replicated methods of a prior citation study provide an updated transparent, reproducible citation analysis protocol that can be replicated with Jupyter Notebooks. Results: This study replicated the prior citation study’s conclusions, and also adapted the author’s methods to analyze the citation practices of Earth Scientists at four institutions. We found that 80% of the citations could be accounted for by only 7.88% of journals, a key metric to help identify a core collection of titles in this discipline. We then demonstrated programmatically that 36% of these cited references were available as open access. Conclusions: Jupyter Notebooks are a viable platform for disseminating replicable processes for citation analysis. A completely open methodology is emerging and we consider this a step forward. Adherence to the 80/20 rule aligned with institutional research output, but citation preferences are evident. Reproducible citation analysis methods may be used to analyze open access uptake, however, results are inconclusive. It is difficult to determine whether an article was open access at the time of citation, or became open access after an embargo.

‘As It Is Written’ … Where? Examining Generic Citations of Scripture in the New Testament

This article examines 33 ‘generic’ citations of Israel’s scriptures in the NT, defined as passages containing an introductory formula or other overt reference to a source, but lacking any actual quoted text. Each passage (from the gospels, Acts and Pauline epistles) is examined in terms of its citation form and particular meaning in context, and then this broader pattern of ‘generic’ citation is compared with Second Temple citation practices. Having rarely been studied collectively, these citations provide interesting insight into how the NT authors draw upon the whole of the OT – without reference to specific prooftexts – to make assertions about Israel’s history, Christology, and the church. They should be given more consideration in the broader field of biblical intertextuality.