A descriptive analysis of the data availability statements accompanying medRxiv preprints and a comparison with their published counterparts

Measuring data rot: An analysis of the continued availability of shared data from a Single University

To determine where data is shared and what data is no longer available, this study analyzed data shared by researchers at a single university. 2166 supplemental data links were harvested from the university's institutional repository and web scraped using R. All links that failed to scrape or could not be tested algorithmically were tested for availability by hand. Trends in data availability by link type, age of publication, and data source were examined for patterns. Results show that researchers shared data in hundreds of places. About two-thirds of links to shared data were in the form of URLs and one-third were DOIs, with several FTP links and links directly to files. A surprising 13.4% of shared URL links pointed to a website homepage rather than a specific record on a website. After testing, 5.4% the 2166 supplemental data links were found to be no longer available. DOIs were the type of shared link that was least likely to disappear with a 1.7% loss, with URL loss at 5.9% averaged over time. Links from older publications were more likely to be unavailable, with a data disappearance rate estimated at 2.6% per year, as well as links to data hosted on journal websites. The results support best practice guidance to share data in a data repository using a permanent identifier.

A study of search strategy availability statements and sharing practices for systematic reviews: Ask and you might receive

The literature search underpins data collection for all systematic reviews (SRs). The SR reporting guideline PRISMA, and its extensions, aim to facilitate research transparency and reproducibility, and ultimately improve the quality of research, by instructing authors to provide specific research materials and data upon publication of the manuscript. Search strategies are one item of data that are explicitly included in PRISMA and the critical appraisal tool AMSTAR2. Yet some authors use search availability statements implying that the search strategies are available upon request instead of providing strategies up front. We sought out reviews with search availability statements, characterized them, and requested the search strategies from authors via email. Over half of the included reviews cited PRISMA but less than a third included any search strategies. After requesting the strategies via email as instructed, we received replies from 46% of authors, and eventually received at least one search strategy from 36% of authors. Requesting search strategies via email has a low chance of success. Ask and you might receive-but you probably will not. SRs that do not make search strategies available are low quality at best according to AMSTAR2; Journal editors can and should enforce the requirement for authors to include their search strategies alongside their SR manuscripts.

Medicines and Healthcare products Regulatory Agency's "Consultation on proposals for legislative changes for clinical trials": a response from the Trials Methodology Research Partnership Adaptive Designs Working Group, with a focus on data sharing

In the UK, the Medicines and Healthcare products Regulatory Agency consulted on proposals "to improve and strengthen the UK clinical trials legislation to help us make the UK the best place to research and develop safe and innovative medicines". The purpose of the consultation was to help finalise the proposals and contribute to the drafting of secondary legislation. We discussed these proposals as members of the Trials Methodology Research Partnership Adaptive Designs Working Group, which is jointly funded by the Medical Research Council and the National Institute for Health and Care Research. Two topics arose frequently in the discussion: the emphasis on legislation, and the absence of questions on data sharing. It is our opinion that the proposals rely heavily on legislation to change practice. However, clinical trials are heterogeneous, and as a result some trials will struggle to comply with all of the proposed legislation. Furthermore, adaptive design clinical trials are even more heterogeneous than their non-adaptive counterparts, and face more challenges. Consequently, it is possible that increased legislation could have a greater negative impact on adaptive designs than non-adaptive designs. Overall, we are sceptical that the introduction of legislation will achieve the desired outcomes, with some exceptions. Meanwhile the topic of data sharing - making anonymised individual-level clinical trial data available to other investigators for further use - is entirely absent from the proposals and the consultation in general. However, as an aspect of the wider concept of open science and reproducible research, data sharing is an increasingly important aspect of clinical trials. The benefits of data sharing include faster innovation, improved surveillance of drug safety and effectiveness and decreasing participant exposure to unnecessary risk. There are already a number of UK-focused documents that discuss and encourage data sharing, for example, the Concordat on Open Research Data and the Medical Research Council's Data Sharing Policy. We strongly suggest that data sharing should be the norm rather than the exception, and hope that the forthcoming proposals on clinical trials invite discussion on this important topic.

The use and acceptability of preprints in health and social care settings: A scoping review

BACKGROUND

Preprints are open and accessible scientific manuscript or report that is shared publicly, through a preprint server, before being submitted to a journal. The value and importance of preprints has grown since its contribution during the public health emergency of the COVID-19 pandemic. Funders and publishers are establishing their position on the use of preprints, in grant applications and publishing models. However, the evidence supporting the use and acceptability of preprints varies across funders, publishers, and researchers. The scoping review explored the current evidence on the use and acceptability of preprints in health and social care settings by publishers, funders, and the research community throughout the research lifecycle.

METHODS

A scoping review was undertaken with no study or language limits. The search strategy was limited to the last five years (2017-2022) to capture changes influenced by COVID-19 (e.g., accelerated use and role of preprints in research). The review included international literature, including grey literature, and two databases were searched: Scopus and Web of Science (24 August 2022).

RESULTS

379 titles and abstracts and 193 full text articles were assessed for eligibility. Ninety-eight articles met eligibility criteria and were included for full extraction. For barriers and challenges, 26 statements were grouped under four main themes (e.g., volume/growth of publications, quality assurance/trustworthiness, risks associated to credibility, and validation). For benefits and value, 34 statements were grouped under six themes (e.g., openness/transparency, increased visibility/credibility, open review process, open research, democratic process/systems, increased productivity/opportunities).

CONCLUSIONS

Preprints provide opportunities for rapid dissemination but there is a need for clear policies and guidance from journals, publishers, and funders. Cautionary measures are needed to maintain the quality and value of preprints, paying particular attention to how findings are translated to the public. More research is needed to address some of the uncertainties addressed in this review.

A narrative review of recent tools and innovations toward automating living systematic reviews and evidence syntheses

Living reviews are an increasingly popular research paradigm. The purpose of a 'living' approach is to allow rapid collation, appraisal and synthesis of evolving evidence on an important research topic, enabling timely influence on patient care and public health policy. However, living reviews are time- and resource-intensive. The accumulation of new evidence and the possibility of developments within the review's research topic can introduce unique challenges into the living review workflow. To investigate the potential of software tools to support living systematic or rapid reviews, we present a narrative review informed by an examination of tools contained on the Systematic Review Toolbox website. We identified 11 tools with relevant functionalities and discuss the important features of these tools with respect to different steps of the living review workflow. Four tools (NestedKnowledge, SWIFT-ActiveScreener, DistillerSR, EPPI-Reviewer) covered multiple, successive steps of the review process, and the remaining tools addressed specific components of the workflow, including scoping and protocol formulation, reference retrieval, automated data extraction, write-up and dissemination of data. We identify several ways in which living reviews can be made more efficient and practical. Most of these focus on general workflow management, or automation through artificial intelligence and machine-learning, in the screening process. More sophisticated uses of automation mostly target living rapid reviews to increase the speed of production or evidence maps to broaden the scope of the map. We use a case study to highlight some of the barriers and challenges to incorporating tools into the living review workflow and processes. These include increased workload, the need for organisation, ensuring timely dissemination and challenges related to the development of bespoke automation tools to facilitate the review process. We describe how current end-user tools address these challenges, and which knowledge gaps remain that could be addressed by future tool development. Dedicated web presences for automatic dissemination of in-progress evidence updates, rather than solely relying on peer-reviewed journal publications, help to make the effort of a living evidence synthesis worthwhile. Despite offering basic living review functionalities, existing end-user tools could be further developed to be interoperable with other tools to support multiple workflow steps seamlessly, to address broader automatic evidence retrieval from a larger variety of sources, and to improve dissemination of evidence between review updates.

Prevalence and predictors of data and code sharing in the medical and health sciences: systematic review with meta-analysis of individual participant data

OBJECTIVES

To synthesise research investigating data and code sharing in medicine and health to establish an accurate representation of the prevalence of sharing, how this frequency has changed over time, and what factors influence availability.

DESIGN

Systematic review with meta-analysis of individual participant data.

DATA SOURCES

Ovid Medline, Ovid Embase, and the preprint servers medRxiv, bioRxiv, and MetaArXiv were searched from inception to 1 July 2021. Forward citation searches were also performed on 30 August 2022.

REVIEW METHODS

Meta-research studies that investigated data or code sharing across a sample of scientific articles presenting original medical and health research were identified. Two authors screened records, assessed the risk of bias, and extracted summary data from study reports when individual participant data could not be retrieved. Key outcomes of interest were the prevalence of statements that declared that data or code were publicly or privately available (declared availability) and the success rates of retrieving these products (actual availability). The associations between data and code availability and several factors (eg, journal policy, type of data, trial design, and human participants) were also examined. A two stage approach to meta-analysis of individual participant data was performed, with proportions and risk ratios pooled with the Hartung-Knapp-Sidik-Jonkman method for random effects meta-analysis.

RESULTS

The review included 105 meta-research studies examining 2 121 580 articles across 31 specialties. Eligible studies examined a median of 195 primary articles (interquartile range 113-475), with a median publication year of 2015 (interquartile range 2012-2018). Only eight studies (8%) were classified as having a low risk of bias. Meta-analyses showed a prevalence of declared and actual public data availability of 8% (95% confidence interval 5% to 11%) and 2% (1% to 3%), respectively, between 2016 and 2021. For public code sharing, both the prevalence of declared and actual availability were estimated to be <0.5% since 2016. Meta-regressions indicated that only declared public data sharing prevalence estimates have increased over time. Compliance with mandatory data sharing policies ranged from 0% to 100% across journals and varied by type of data. In contrast, success in privately obtaining data and code from authors historically ranged between 0% and 37% and 0% and 23%, respectively.

CONCLUSIONS

The review found that public code sharing was persistently low across medical research. Declarations of data sharing were also low, increasing over time, but did not always correspond to actual sharing of data. The effectiveness of mandatory data sharing policies varied substantially by journal and type of data, a finding that might be informative for policy makers when designing policies and allocating resources to audit compliance.

SYSTEMATIC REVIEW REGISTRATION

Open Science Framework doi:10.17605/OSF.IO/7SX8U.

Quality Output Checklist and Content Assessment (QuOCCA): a new tool for assessing research quality and reproducibility

Research must be well designed, properly conducted and clearly and transparently reported. Our independent medical research institute wanted a simple, generic tool to assess the quality of the research conducted by its researchers, with the goal of identifying areas that could be improved through targeted educational activities. Unfortunately, none was available, thus we devised our own. Here, we report development of the Quality Output Checklist and Content Assessment (QuOCCA), and its application to publications from our institute's scientists. Following consensus meetings and external review by statistical and methodological experts, 11 items were selected for the final version of the QuOCCA: research transparency (items 1-3), research design and analysis (items 4-6) and research reporting practices (items 7-11). Five pairs of raters assessed all 231 articles published in 2017 and 221 in 2018 by researchers at our institute. Overall, the results were similar between years and revealed limited engagement with several recommended practices highlighted in the QuOCCA. These results will be useful to guide educational initiatives and their effectiveness. The QuOCCA is brief and focuses on broadly applicable and relevant concepts to open, high-quality, reproducible and well-reported science. Thus, the QuOCCA could be used by other biomedical institutions and individual researchers to evaluate research publications, assess changes in research practice over time and guide the discussion about high-quality, open science. Given its generic nature, the QuOCCA may also be useful in other research disciplines.

Sharing study materials in health and medical research

Making study materials available allows for a more comprehensive understanding of the scientific literature. Sharing can take many forms and include a wide variety of outputs including code and data. Biomedical research can benefit from increased transparency but faces unique challenges for sharing, for instance, confidentiality concerns around participants' medical data. Both general and specialised repositories exist to aid in sharing most study materials. Sharing may also require skills and resources to ensure that it is done safely and effectively. Educating researchers on how to best share their materials, and properly rewarding these practices, requires action from a variety of stakeholders including journals, funders and research institutions.

Neither carrots nor sticks? Challenges surrounding data sharing from the perspective of research funding agencies—A qualitative expert interview study

Background

Data Sharing is widely recognised as crucial for accelerating scientific research and improving its quality. However, data sharing is still not a common practice. Funding agencies tend to facilitate the sharing of research data by both providing incentives and requiring data sharing as part of their policies and conditions for awarding grants. The goal of our article is to answer the following question: What challenges do international funding agencies see when it comes to their own efforts to foster and implement data sharing through their policies?

Methods

We conducted a series of sixteen guideline-based expert interviews with representatives of leading international funding agencies. As contact persons for open science at their respective agencies, they offered their perspectives and experiences concerning their organisations’ data sharing policies. We performed a qualitative content analysis of the interviews and categorised the challenges perceived by funding agencies.

Results

We identify and illustrate six challenges surrounding data sharing policies as perceived by leading funding agencies: The design of clear policies, monitoring of compliance, sanctions for non-compliance, incentives, support, and limitations for funders’ own capabilities. However, our interviews also show how funders approach potential solutions to overcome these challenges, for example by coordinating with other agencies or adjusting grant evaluation metrics to incentivise data sharing.

Discussion and conclusion

Our interviews point to existing flaws in funders’ data sharing policies, such as a lack of clarity, a lack of monitoring of funded researchers’ data sharing behaviour, and a lack of incentives. A number of agencies could suggest potential solutions but often struggle with the overall complexity of data sharing and the implementation of these measures. Funders cannot solve each challenge by themselves, but they can play an active role and lead joint efforts towards a culture of data sharing.

Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals

Introduction

Preprints have been widely cited during the COVID-19 pandemics, even in the major medical journals. However, since subsequent publication of preprint is not always mentioned in preprint repositories, some may be inappropriately cited or quoted. Our objectives were to assess the reliability of preprint citations in articles on COVID-19, to the rate of publication of preprints cited in these articles and to compare, if relevant, the content of the preprints to their published version.

Methods

Articles published on COVID in 2020 in the BMJ, The Lancet, the JAMA and the NEJM were manually screened to identify all articles citing at least one preprint from medRxiv. We searched PubMed, Google and Google Scholar to assess if the preprint had been published in a peer-reviewed journal, and when. Published articles were screened to assess if the title, data or conclusions were identical to the preprint version.

Results

Among the 205 research articles on COVID published by the four major medical journals in 2020, 60 (29.3%) cited at least one medRxiv preprint. Among the 182 preprints cited, 124 were published in a peer-reviewed journal, with 51 (41.1%) before the citing article was published online and 73 (58.9%) later. There were differences in the title, the data or the conclusion between the preprint cited and the published version for nearly half of them. MedRxiv did not mentioned the publication for 53 (42.7%) of preprints.

Conclusions

More than a quarter of preprints citations were inappropriate since preprints were in fact already published at the time of publication of the citing article, often with a different content. Authors and editors should check the accuracy of the citations and of the quotations of preprints before publishing manuscripts that cite them.

Reproducibility of COVID-19 pre-prints

To examine the reproducibility of COVID-19 research, we create a dataset of pre-prints posted to arXiv, bioRxiv, and medRxiv between 28 January 2020 and 30 June 2021 that are related to COVID-19. We extract the text from these pre-prints and parse them looking for keyword markers signaling the availability of the data and code underpinning the pre-print. For the pre-prints that are in our sample, we are unable to find markers of either open data or open code for 75% of those on arXiv, 67% of those on bioRxiv, and 79% of those on medRxiv.

Data sharing practices across knowledge domains: A dynamic examination of data availability statements in PLOS ONE publications

As the importance of research data gradually grows in sciences, data sharing has come to be encouraged and even mandated by journals and funders in recent years. Following this trend, the data availability statement has been increasingly embraced by academic communities as a means of sharing research data as part of research articles. This article presents a quantitative study of which mechanisms and repositories are used to share research data in PLOS ONE articles. We offer a dynamic examination of this topic from the disciplinary and temporal perspectives based on all statements in English-language research articles published between 2014 and 2020 in the journal. We find a slow yet steady growth in the use of data repositories to share data over time, as opposed to sharing data in the article and/or supplementary materials; this indicates improved compliance with the journal’s data sharing policies. We also find that multidisciplinary data repositories have been increasingly used over time, whereas some disciplinary repositories show a decreasing trend. Our findings can help academic publishers and funders to improve their data sharing policies and serve as an important baseline dataset for future studies on data sharing activities.