Long-term availability of data associated with articles in PLOS ONE

Author : Lisa M. Federer

The adoption of journal policies requiring authors to include a Data Availability Statement has helped to increase the availability of research data associated with research articles. However, having a Data Availability Statement is not a guarantee that readers will be able to locate the data; even if provided with an identifier like a uniform resource locator (URL) or a digital object identifier (DOI), the data may become unavailable due to link rot and content drift. :

To explore the long-term availability of resources including data, code, and other digital research objects associated with papers, this study extracted 8,503 URLs and DOIs from a corpus of nearly 50,000 Data Availability Statements from papers published in PLOS ONE between 2014 and 2016.

These URLs and DOIs were used to attempt to retrieve the data through both automated and manual means. Overall, 80% of the resources could be retrieved automatically, compared to much lower retrieval rates of 10–40% found in previous papers that relied on contacting authors to locate data.

Because a URL or DOI might be valid but still not point to the resource, a subset of 350 URLs and 350 DOIs were manually tested, with 78% and 98% of resources, respectively, successfully retrieved.

Having a DOI and being shared in a repository were both positively associated with availability. Although resources associated with older papers were slightly less likely to be available, this difference was not statistically significant, suggesting that URLs and DOIs may be an effective means for accessing data over time.

These findings point to the value of including URLs and DOIs in Data Availability Statements to ensure access to data on a long-term basis.

URL : Long-term availability of data associated with articles in PLOS ONE

DOI : https://doi.org/10.1371/journal.pone.0272845

Reading Peer Review : PLOS ONE and Institutional Change in Academia

Authors : Martin Paul Eve, Cameron Neylon, Daniel Paul O’Donnell, Samuel Moore, Robert Gadie, Victoria Odeniyi, Shahina Parvin

This Element describes for the first time the database of peer review reports at PLOS ONE, the largest scientific journal in the world, to which the authors had unique access.

Specifically, this Element presents the background contexts and histories of peer review, the data-handling sensitivities of this type of research, the typical properties of reports in the journal to which the authors had access, a taxonomy of the reports, and their sentiment arcs.

This unique work thereby yields a compelling and unprecedented set of insights into the evolving state of peer review in the twenty-first century, at a crucial political moment for the transformation of science.

It also, though, presents a study in radicalism and the ways in which PLOS’s vision for science can be said to have effected change in the ultra-conservative contemporary university.

URL : Reading Peer Review : PLOS ONE and Institutional Change in Academia

Original location : https://www.cambridge.org/core/elements/reading-peer-review/42F027E4C67D246DD8C3AC440A68C7A7

Megajournal mismanagement: Manuscript decision bias and anomalous editor activity at PLOS ONE

Author : Alexander M. Petersen

Since their emergence just a decade ago, nearly 2% of scientific research is now published by megajournals, representing a major industrial shift in the production of knowledge. Such high-throughput production stresses several aspects of the publication process, including the editorial oversight of peer-review.

As the largest megajournal, PLOS ONE has relied on a single-tier editorial board comprised of ∼7000 active academics, who thereby face conflicts of interest relating to their dual roles as both producers and gatekeepers of peer-reviewed literature.

While such conflicts of interest are also a factor for editorial boards of smaller journals, little is known about how the scalability of megajournals may introduce perverse incentives for editorial service.

To address this issue, we analyzed the activity of PLOS ONE editors over the journal’s inaugural decade (2006–2015) and find highly variable activity levels. We then leverage this variation to model how editorial bias in the manuscript decision process relates to two editor-specific factors: repeated editor-author interactions and shifts in the rates of citations directed at editors – a form of citation remuneration that is analogue to self-citation.

Our results indicate significantly stronger manuscript bias among a relatively small number of extremely active editors, who also feature relatively high self-citation rates coincident in the manuscripts they handle.

These anomalous activity patterns are consistent with the perverse incentives and the temptations they offer at scale, which is theoretically grounded in the “slippery-slope” evolution of apathy and misconduct in power-driven environments.

By applying quantitative evaluation to the gatekeepers of scientific knowledge, we shed light on various ethics issues crucial to science policy – in particular, calling for more transparent and structured management of editor activity in megajournals that rely on active academics.

URL : Megajournal mismanagement: Manuscript decision bias and anomalous editor activity at PLOS ONE

DOI : https://doi.org/10.1016/j.joi.2019.100974

How much research shared on Facebook is hidden from public view? A comparison of public and private online activity around PLOS ONE papers

Authors : Asura Enkhbayar, Stefanie Haustein, Germana Barata, Juan Pablo Alperin

Despite its undisputed position as the biggest social media platform, Facebook has never entered the main stage of altmetrics research. In this study, we argue that the lack of attention by altmetrics researchers is not due to a lack of relevant activity on the platform, but because of the challenges in collecting Facebook data have been limited to activity that takes place in a select group of public pages and groups.

We present a new method of collecting shares, reactions, and comments across the platform-including private timelines-and use it to gather data for all articles published between 2015 to 2017 in the journal PLOS ONE.

We compare the gathered data with altmetrics collected and aggregated by Altmetric. The results show that 58.7% of papers shared on the platform happen outside of public view and that, when collecting all shares, the volume of activity approximates patterns of engagement previously only observed for Twitter.

Both results suggest that the role and impact of Facebook as a medium for science and scholarly communication has been underestimated. Furthermore, they emphasise the importance of openness and transparency around the collection and aggregation of altmetrics.

URL : https://arxiv.org/abs/1909.01476

Highly cited references in PLOS ONE and their in-text usage over time

Authors : Wolfgang Otto, Behnam Ghavimi, Philipp Mayr, Rajesh Piryani, Vivek Kumar Singh

In this article, we describe highly cited publications in a PLOS ONE full-text corpus. For these publications, we analyse the citation contexts concerning their position in the text and their age at the time of citing.

By selecting the perspective of highly cited papers, we can distinguish them based on the context during citation even if we do not have any other information source or metrics.

We describe the top cited references based on how, when and in which context they are cited. The focus of this study is on a time perspective to explain the nature of the reception of highly cited papers.

We have found that these references are distinguishable by the IMRaD sections of their citation. And further, we can show that the section usage of highly cited papers is time-dependent.

The longer the citation interval, the higher the probability that a reference is cited in a method section.

URL : https://arxiv.org/abs/1903.11693

“No comment”?: A study of commenting on PLOS articles

Authors : Simon Wakeling, Peter Willett, Claire Creaser, Jenny Fry, Stephen Pinfield, Valerie Spezi, Marc Bonne, Christina Founti, Itzelle Medina Perea

Article commenting functionality allows users to add publically visible comments to an article on a publisher’s website. As well as facilitating forms of post-publication peer review, for publishers of open-access mega-journals (large, broad scope, OA journals that seek to publish all technically or scientifically sound research) comments are also thought to serve as a means for the community to discuss and communicate the significance and novelty of the research, factors which are not assessed during peer review.

In this paper we present the results of an analysis of commenting on articles published by the Public Library of Science (PLOS), publisher of the first and best-known mega-journal PLOS ONE, between 2003 and 2016.

We find that while overall commenting rates are low, and have declined since 2010, there is substantial variation across different PLOS titles. Using a typology of comments developed for this research we also find that only around half of comments engage in an academic discussion of the article, and that these discussions are most likely to focus on the paper’s technical soundness.

Our results suggest that publishers have yet to encourage significant numbers of readers to leave comments, with implications for the effectiveness of commenting as a means of collecting and communicating community perceptions of an article’s importance.

DOI : https://doi.org/10.1177%2F0165551518819965

Data sharing in PLOS ONE: An analysis of Data Availability Statements

Authors : Lisa M. Federer, Christopher W. Belter, Douglas J. Joubert, Alicia Livinski, Ya-Ling Lu, Lissa N. Snyders, Holly Thompson

A number of publishers and funders, including PLOS, have recently adopted policies requiring researchers to share the data underlying their results and publications. Such policies help increase the reproducibility of the published literature, as well as make a larger body of data available for reuse and re-analysis.

In this study, we evaluate the extent to which authors have complied with this policy by analyzing Data Availability Statements from 47,593 papers published in PLOS ONE between March 2014 (when the policy went into effect) and May 2016.

Our analysis shows that compliance with the policy has increased, with a significant decline over time in papers that did not include a Data Availability Statement. However, only about 20% of statements indicate that data are deposited in a repository, which the PLOS policy states is the preferred method.

More commonly, authors state that their data are in the paper itself or in the supplemental information, though it is unclear whether these data meet the level of sharing required in the PLOS policy.

These findings suggest that additional review of Data Availability Statements or more stringent policies may be needed to increase data sharing.

URL : Data sharing in PLOS ONE: An analysis of Data Availability Statements

DOI : https://doi.org/10.1371/journal.pone.0194768