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Digital Editions and Version Numbering

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Author : Paul A. Broyles

Digital editions are easily modified after they are first published — a state of affairs that poses challenges both for long-term scholarly reference and for various forms of electronic distribution and analysis.

This article argues that producers of digital editions should assign meaningful version numbers to their editions and update those version numbers with each change, allowing both humans and computers to know when resources have been modified and how significant the changes are.

As an examination of versioning practices in the software industry reveals, version numbers are not neutral descriptors but social products intended for use in specific contexts, and the producers of digital editions must consider how version numbers will be used in developing numbering schemes.

It may be beneficial to version different parts of an edition separately, and in particular to version the data objects or content of an edition independently from the environment in which it is displayed.

The article concludes with a case study of the development of a versioning policy for the Piers Plowman Electronic Archive, and includes an appendix surveying how a selection of digital editions handle the problem of recording and communicating changes.

URL : http://www.digitalhumanities.org/dhq/vol/14/2/000455/000455.html

Research methodology and characteristics of journal articles with original data, preprint articles and registered clinical trial protocols about COVID-19

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Authors : Mahir Fidahic, Danijela Nujic, Renata Runjic, Marta Civljak, Zvjezdana Lovric Makaric, Livia Puljak

Background

The research community reacted rapidly to the emergence of COVID-19. We aimed to assess characteristics of journal articles, preprint articles, and registered trial protocols about COVID-19 and its causal agent SARS-CoV-2.

Methods

We analyzed characteristics of journal articles with original data indexed by March 19, 2020, in World Health Organization (WHO) COVID-19 collection, articles published on preprint servers medRxiv and bioRxiv by April 3, 2010.

Additionally, we assessed characteristics of clinical trials indexed in the WHO International Clinical Trials Registry Platform (WHO ICTRP) by April 7, 2020.

Results

Among the first 2118 articles on COVID-19 published in scholarly journals, 533 (25%) contained original data. The majority was published by authors from China (75%) and funded by Chinese sponsors (75%); a quarter was published in the Chinese language.

Among 312 articles that self-reported study design, the most frequent were retrospective studies (N = 88; 28%) and case reports (N = 86; 28%), analyzing patients’ characteristics (38%). Median Journal Impact Factor of journals where articles were published was 5.099.

Among 1088 analyzed preprint articles, the majority came from authors affiliated in China (51%) and were funded by sources in China (46%). Less than half reported study design; the majority were modeling studies (62%), and analyzed transmission/risk/prevalence (43%).

Of the 927 analyzed registered trials, the majority were interventional (58%). Half were already recruiting participants. The location for the conduct of the trial in the majority was China (N = 522; 63%).

The median number of planned participants was 140 (range: 1 to 15,000,000). Registered intervention trials used highly heterogeneous primary outcomes and tested highly heterogeneous interventions; the most frequently studied interventions were hydroxychloroquine (N = 39; 7.2%) and chloroquine (N = 16; 3%).

Conclusions

Early articles on COVID-19 were predominantly retrospective case reports and modeling studies. The diversity of outcomes used in intervention trial protocols indicates the urgent need for defining a core outcome set for COVID-19 research.

Chinese scholars had a head start in reporting about the new disease, but publishing articles in Chinese may limit their global reach. Mapping publications with original data can help finding gaps that will help us respond better to the new public health emergency.

URL : Research methodology and characteristics of journal articles with original data, preprint articles and registered clinical trial protocols about COVID-19

DOI : https://doi.org/10.1186/s12874-020-01047-2

Problematizing ‘predatory publishing’: A systematic review of factors shaping publishing motives, decisions, and experiences

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Authors : David Mills, K. Inouye

This article systematically reviews recent empirical research on the factors shaping academics’ knowledge about, and motivations to publish work in, so‐called ‘predatory’ journals. Growing scholarly evidence suggests that the concept of ‘predatory’ publishing’ – used to describe deceptive journals exploiting vulnerable researchers – is inadequate for understanding the complex range of institutional and contextual factors that shape the publication decisions of individual academics.

This review identifies relevant empirical studies on academics who have published in ‘predatory’ journals, and carries out a detailed comparison of 16 papers that meet the inclusion criteria. While most start from Beall’s framing of ‘predatory’ publishing, their empirical findings move the debate beyond normative assumptions about academic vulnerability.

They offer particular insights into the academic pressures on scholars at the periphery of a global research economy. This systematic review shows the value of a holistic approach to studying individual publishing decisions within specific institutional, economic and political contexts.

Rather than assume that scholars publishing in ‘questionable’ journals are naïve, gullible or lacking in understanding, fine‐grained empirical research provides a more nuanced conceptualization of the pressures and incentives shaping their decisions. The review suggests areas for further research, especially in emerging research systems in the global South.

URL : Problematizing ‘predatory publishing’: A systematic review of factors shaping publishing motives, decisions, and experiences

DOI : https://doi.org/10.1002/leap.1325

Global Flow of Scholarly Publishing and Open Access

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Author : Olivier Pourret

Open access is not a new topic for Elements. The topic was addressed by Alex Speer, Kevin Murphy, and Sharon Tahirkheliin 2013 (Speer et al. 2013) and, later, by Christian Chopin in 2018 (Chopin 2018). I fully agree that there is a strong imperative for the geochemistry, mineralogy, and petrology communities to ensure that the research it produces is widely accessible, especially in the increasingly important context of the United Nations Sustainable Development Goals.

Indeed, according to the STM Report 2018 (Johnson et al. 2018), two thirds of the scholarly literature in 2016 remains inaccessible to the public because it is hidden behind a paywall. Scholars have been making various cases for wider public access to published research, known as open access (OA), since the late 1980s.

Scientific publishing is currently undergoing a major transformation,with a move towards OA marking a major shift in the financial models of the major publishers. This opens up greater diversity in publishing routes and raises wider issues around publishing ethics.

URL : https://hal.archives-ouvertes.fr/hal-02496933/

Genuine semantic publishing

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Authors : Tobias Kuhn, Michel Dumontier

Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers.

This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm.

We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications.

We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead.

This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points.

URL : Genuine semantic publishing

Original location : https://content.iospress.com/articles/data-science/ds010

Open Science and Its Enemies: Challenges for a Sustainable Science–Society Social Contract

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Author : Venni V. Krishna

Science as a social institution has evolved as the most powerful, highly influential, and sought out institution after the conflicts between science and religion following Galileo. Knowledge as a public good, scientific peer review of science, the prominence of open publications, and the emphasis on professional recognition and scientific autonomy have been the hallmark of science in the past three centuries.

According to this scientific spirit, the scientific social system and society formed a unique social contract. This social contract drew considerable institutional and state legitimacy for the openness and public good of science in the service of state and society, all through the post-war period.

Openness and public good of science are recognized and legitimized by the scientific community and science agencies at the global level. This paradigm of open science, in varying forms and manifestations, contributed to the progress of systematic knowledge at the service of humankind over the last three centuries.

Entering the third decade of the 21st century, the social contract between science and society is undergoing major changes. In fact, the whole paradigm of open science and its social contract is being challenged by various “enemies” or adversaries such as (a) market-based privatized commercial science, (b) industry 4.0 advanced technologies, and (c) a “new iron curtain” on the free flow of science data and information.

What is at stake? Are there major changes? Is the very social institution of science transforming? What impact will this have on our contemporary and future sustainable society? These are some important issues that will be addressed in this article.

URL : Open Science and Its Enemies: Challenges for a Sustainable Science–Society Social Contract

DOI : https://doi.org/10.3390/joitmc6030061

Changing how we evaluate research is difficult, but not impossible

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Authors : Anna Hatch, Stephen Curry

The San Francisco Declaration on Research Assessment (DORA) was published in 2013 and described how funding agencies, institutions, publishers, organizations that supply metrics, and individual researchers could better evaluate the outputs of scientific research.

Since then DORA has evolved into an active initiative that gives practical advice to institutions on new ways to assess and evaluate research. This article outlines a framework for driving institutional change that was developed at a meeting convened by DORA and the Howard Hughes Medical Institute.

The framework has four broad goals: understanding the obstacles to changes in the way research is assessed; experimenting with different approaches; creating a shared vision when revising existing policies and practices; and communicating that vision on campus and beyond.

URL : Changing how we evaluate research is difficult, but not impossible

DOI : https://doi.org/10.7554/eLife.58654