Assessment of transparency indicators across the biomedical literature: how open is open?

Serghiou, Stylianos; Contopoulos‐Ioannidis, Despina G.; Boyack, Kevin W.; Riedel, Nico; Wallach, John R.; Ioannidis, John P. A.

doi:10.1101/2020.10.30.361618

Cited by 6 publications

(5 citation statements)

References 35 publications

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“…Furthermore, we charted differences in transparency practices between 59 distinct clinical medicine disciplines over time. The sensitivity and specificity of the rtransparent tool (17) were used to generate 95% confidence intervals (CIs) for the estimates of the transparency practices. We used visual presentation and Pearson's product-moment correlation to analyze the yearly trend in transparency practices.…”

Section: Discussionmentioning

confidence: 99%

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Research Transparency in 59 Disciplines of Clinical Medicine: A Meta-Research Study

Sofi-Mahmudi,

Raittio,

Uribe

et al. 2024

Preprint

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Background: Transparency in research is crucial as it allows for the scrutiny and replication of findings, fosters confidence in scientific outcomes, and ultimately contributes to the advancement of knowledge and the betterment of society. Aim: We aimed to assess adherence to five practices promoting transparency in scientific publications (data availability, code availability, protocol registration, conflicts of interest (COI) and funding disclosures) from open-access articles published in medical journals. Methods: We searched and exported all open-access articles from Science Citation Index Expanded (SCIE)-indexed journals through the Europe PubMed Central database published until March 16, 2024. Basic journal- and article-related information was retrieved from the database. We used R to produce descriptive statistics. Results: The analysis included 2,189,542 open-access articles from SCIE-indexed medical journals. Of these, 87.5% (95% CI: 87.4%-87.5%) disclosed COI and 80.1% (95% CI: 80.0%-80.1%) disclosed funding. Protocol registration was present in 6.6% (95% CI: 6.6%-6.6%), data sharing in 7.6% (95% CI: 7.6%-7.6%), and code sharing in 1.4% (95% CI: 1.4%-1.4%) of the articles. More than 76.0% adhered to at least two transparency practices, while full adherence to all five practices was less than 0.02%. The data showed an increasing trend in adherence to transparency practices since the late 2000s. COI and funding were disclosed more often in lower impact factor journals whereas protocol registration and data and code sharing were more prevalent in higher impact factor journals (all had P-values<0.001). Also, articles that did not disclose their COI had higher median citations. Among all fields, Rheumatology (97.2%), Neuroimaging (94.6%), Anesthesiology (32.4%), Genetics & Heredity (36.7%), and Neuroimaging (12.5%) showed the highest level of transparency in COI and funding disclosure, protocol registration, and data and code sharing, respectively. Whereas Medicine, Legal (61.5%), Andrology (59.0%), Materials Science, Biomaterials (0.3%), Surgery (1.5%), and Nursing (<0.01%) showed the lowest adherence. Conclusion: While most articles and fields had a COI disclosure, adherence to other transparent practices was far from acceptable. To increase protocol registration, data, and code sharing, much stronger commitment is needed from all stakeholders.

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Section: Discussionmentioning

confidence: 99%

“…We used the rtransparent package (17), a validated and automated programmatic tool (13), to identify five transparent practices from the full texts we were able to download from EPMC:…”

Section: Data Extraction and Synthesismentioning

confidence: 99%

Research Transparency in 59 Disciplines of Clinical Medicine: A Meta-Research Study

Sofi-Mahmudi,

Raittio,

Uribe

et al. 2024

Preprint

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“…The searches and data export from the EPMC were conducted with the europepmc package [16]. Indicators of transparency practices from the available full texts were extracted with the rtransparent package [17]. Trends over time in transparency practices were reported using descriptive tabulations and visualizations using the ggplot2 package [18].…”

Section: Discussionmentioning

confidence: 99%

Transparency of COVID-19-related research: A meta-research study

Sofi‐Mahmudi¹,

Raittio²,

Uribe³

2023

PLoS ONE

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Background We aimed to assess the adherence to five transparency practices (data availability, code availability, protocol registration and conflicts of interest (COI), and funding disclosures) from open access Coronavirus disease 2019 (COVID-19) related articles. Methods We searched and exported all open access COVID-19-related articles from PubMed-indexed journals in the Europe PubMed Central database published from January 2020 to June 9, 2022. With a validated and automated tool, we detected transparent practices of three paper types: research articles, randomized controlled trials (RCTs), and reviews. Basic journal- and article-related information were retrieved from the database. We used R for the descriptive analyses. Results The total number of articles was 258,678, of which we were able to retrieve full texts of 186,157 (72%) articles from the database Over half of the papers (55.7%, n = 103,732) were research articles, 10.9% (n = 20,229) were review articles, and less than one percent (n = 1,202) were RCTs. Approximately nine-tenths of articles (in all three paper types) had a statement to disclose COI. Funding disclosure (83.9%, confidence interval (CI): 81.7–85.8 95%) and protocol registration (53.5%, 95% CI: 50.7–56.3) were more frequent in RCTs than in reviews or research articles. Reviews shared data (2.5%, 95% CI: 2.3–2.8) and code (0.4%, 95% CI: 0.4–0.5) less frequently than RCTs or research articles. Articles published in 2022 had the highest adherence to all five transparency practices. Most of the reviews (62%) and research articles (58%) adhered to two transparency practices, whereas almost half of the RCTs (47%) adhered to three practices. There were journal- and publisher-related differences in all five practices, and articles that did not adhere to transparency practices were more likely published in lowest impact journals and were less likely cited. Conclusion While most articles were freely available and had a COI disclosure, adherence to other transparent practices was far from acceptable. A much stronger commitment to open science practices, particularly to protocol registration, data and code sharing, is needed from all stakeholders.

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“…18 Our previous analysis of journals' endorsements, however, showed that only 13% of journals across disciplines recommended the use of reporting guidelines, and only 2% required it. 15 Data sharing practices across sciences have not been systematically explored, but recent estimates indicated that data sharing was mentioned in 15% of biomedical, 19 and in only 2% of psychological articles. 20 A 2020 systematic review indicated that most researchers have positive attitudes toward data sharing.…”

Section: Discussionmentioning

confidence: 99%

Transparency in conducting and reporting research: a survey of authors, reviewers, and editors across scholarly disciplines

Malički

Aalbersberg

Bouter

et al. 2022

Preprint

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Calls have been made for improving transparency in conducting and reporting research, improving work climates, and preventing detrimental research practices. To assess attitudes and practices regarding these topics, we sent a survey to authors, reviewers, and editors. We received 3,659 (4.9%) responses out of 74,749 delivered emails. We found no significant differences between authors’, reviewers’, and editors’ attitudes towards transparency in conducting and reporting research, or towards their perceptions of work climates. Undeserved authorship was perceived by all groups as the most prevalent detrimental research practice, while fabrication, falsification, plagiarism, and not citing prior relevant research, were seen as more prevalent by editors than authors or reviewers. Overall, 20% of respondents admitted sacrificing the quality of their publications for quantity, and 14% reported that funders interfered in their study design or reporting. Our results indicate that greater involvement of all stakeholders is needed to align actual practices with current recommendations.

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Assessment of transparency indicators across the biomedical literature: how open is open?

Cited by 6 publications

References 35 publications

Research Transparency in 59 Disciplines of Clinical Medicine: A Meta-Research Study

Research Transparency in 59 Disciplines of Clinical Medicine: A Meta-Research Study

Transparency of COVID-19-related research: A meta-research study

Transparency in conducting and reporting research: a survey of authors, reviewers, and editors across scholarly disciplines

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