Transparency in infectious disease research: meta-research survey of specialty journals | The Journal of Infectious Diseases | Oxford Academic

Abstract:  Background

Infectious diseases carry large global burdens and have implications for society at large. Therefore, reproducible, transparent research is extremely important.


We evaluated transparency indicators (code and data sharing, registration, conflict and funding disclosures) in the 5340 PubMed Central Open Access articles published in 2019 or 2021 in the 9 most-cited specialty journals in infectious disease using the text-mining R package, rtransparent.


5340 articles were evaluated (1860 published in 2019 and 3480 in 2021 (of which 1828 on COVID-19)). Text-mining identified code sharing in 98 (2%) articles, data sharing in 498 (9%), registration in 446 (8%), conflict of interest disclosures in 4209 (79%) and funding disclosures in 4866 (91%). There were substantial differences across the 9 journals: 1-9% for code sharing, 5-25% for data sharing, 1-31% for registration, 7-100% for conflicts of interest, and 65-100% for funding disclosures. Validation-corrected imputed estimates were 3%, 11%, 8%, 79% and 92%, respectively. There were no major differences between articles published in 2019 and non-COVID-19 articles in 2021. In 2021, non-COVID-19 articles had more data sharing (12%) than COVID-19 articles (4%).


Data sharing, code sharing, and registration are very uncommon in infectious disease specialty journals. Increased transparency is required.

The New England Journal of Medicine, open access, Plan S, and undeclared conflicts of interest   | Richard Smith’s non-medical blogs

The New England Journal of Medicine disapproves of open access publishing and Plan S.  There’s nothing surprising in that. (The opposite would have been surprising.) What is surprising is that the journal does not declare its substantial conflicts of interest, when the International Committee of Medical Journal Editors, of which it is a founding and prominent member, has made clear for 30 years that all conflicts of interest should be declared.

The New England Journal of Medicine is immensely profitable (although we don’t know exactly how profitable), and those profits—and the compensation and livelihood of its employees—are potentially disrupted by open access and particularly Plan S, the European plan to extend open access publishing….”