Weekly digest: open access protein structures, article retractions and Plan S

Mark Elms

This week, we read that the contents of the AlphaFold database have been made freely available to all. We also hear about the current landscape in relation to research retraction and about how the majority of European physicists have never heard of Plan S. We highlight a study discussing EU legislation regarding data sharing, as well as articles about Springer Nature’s AI-driven editing services and the increasing participation of publishers in the OA Switchboard. Finally, we read about the updated NIH policy on data sharing and a yearly round-up of the progress made by IOI.

To read:

AI predicts the structures of nearly every known protein via Nature | 6-minute read

Understanding protein structures is key to understanding biological processes within the body and for the design of new therapeutics. Therefore, the news that the artificial intelligence (AI) system AlphaFold has been able to predict the structure of nearly every known protein (more than 200 million!) from almost 1 million species is revolutionary. A database of these AlphaFold protein structures is now freely available and is mediated by DeepMind and the European Molecular Biology Laboratory’s Bioinformatics Institute (EMBL-EBI). You can read more about what’s next for AlphaFold and what this means for the future of structural biology by selecting these links.

Retractions grow, but we must do more via Nature | 5-minute read

An increase in article retractions is a double-edged sword. On the positive side, it shows that scientific scrutiny and rigour are increasing, but, on the other side, it’s never a good thing when scientific data are being retracted because of fraud, plagiarism or major errors. In this article, written by one of the founders of Retraction Watch and The Retraction Watch Database, the author argues that more must be done to root out problematic papers that should be retracted. The author also highlights that a huge number of researchers do not know that they are citing retracted research in their own papers, which was discussed in a study published in July 2022.

Majority of European physicists are unaware of Plan S via STM Publishing News | 2-minute read

Plan S is an open science initiative that aims to promote and enhance open access in the academic research world. However, a study published in August 2022 by AIP Publishing, the American Physical Society, IOP Publishing and the Optica Publishing Group found that 82% of over 3000 European physics researchers surveyed were unaware of the existence of Plan S.  

The effects of EU copyright legislation on open access and data sharing via Publications Office of the European Union | 2-hour read

To maintain legal compliance with data sharing practices in Europe, the barriers and challenges that arise from European Union (EU) copyright legislation must be identified and addressed. This study discusses the interplay between EU copyright laws and data access and sharing, as well as suggesting measures that could be employed to improve the current EU regulations. 

Free access to AI-driven digital editing services for certain authors and editors via STM Publishing News | 2-minute read

Springer Nature has announced a pilot scheme alongside American Journal Experts to make Springer Nature’s AI-driven editing services available to authors and editors in selected disciples for free. The AI digital editing service enables authors to have their grammar, phrasing and word choices checked and improved, and aims to ensure that researchers spend less of their time writing and more of their time doing important research. You can read more about Springer Nature’s editing services here.

Lighting up the switchboard via OASPA | 3-minute read

In 2020, the Open Access Scholarly Publishing Association (OASPA) founded the OA Switchboard – an initiative to provide essential open access infrastructure and standards. Now, several open access publishers have integrated their own open access policies with the OA Switchboard. This includes Hindawi, Journal of Medical Internet Research (JMIR), eLife, PLOS, AboutScience, Beilstein Institut, and Copernicus. Publishers can learn more about the benefits of joining the OA Switchboard in this ‘How-to’ webinar and also on the OA Switchboard website.

Data sharing: we’re all in this together via Harvard Data Science Review | 40-minute read

The National Institutes of Health (NIH) published their policy on sharing research data in 2003. However, the world has changed substantially since then, with dramatic increases in the quantity of data and the services that exist to store and share data. In response to these changes, the NIH announced a new policy on data sharing, which will take effect in January 2023 and will build upon FAIR principles. This article discusses what the new policy will mean for the future of data sharing and why effective data sharing must be practised by multiple stakeholders within the research world, rather than relying solely on principal investigators.

Invest in Open Infrastructure: a year in review via Invest in Open Infrastructure | 15-minute read

This article looks at the progress that Invest in Open Infrastructure (IOI) has achieved over 2021–2022 in its endeavour to improve funding and resourcing of open access infrastructure. The review looks back at IOI research projects discussing the costs of open infrastructure and the future of open scholarship, as well as new open infrastructure resources and committees such as the Catalog of Open Infrastructure Services, the Open Infrastructure Tracking Project, and the Community Oversight Council. You can find out how to support IOI here.

Have you heard about the Open Pharma Satellite Symposium at the 2022 Association of Learned and Professional Society Publishers Annual Conference and Awards? Check the programme and register here to secure a place.