Scientific Openness and Integrity: Two Decades of Interactive Open Access Publishing and Open Peer Review

“For more than 20 years, the scientific journal Atmospheric Chemistry and Physics (ACP) has been a pioneer in open access publishing and public peer review with interactive discussion. All articles published in it are accessible free of charge via the internet. By recording and opening up the peer review process, the interactive open access journals lead to an internet of knowledge or epistemic web that does not only reflect what we know but also how we know it, i.e., how well it has been validated.

The achievements of ACP and further interactive open access sister journals of the European Geosciences Union (EGU) will be celebrated, reflected, and further developed at a special meeting of the ACP editorial board and the EGU publications committee on 19 September 2022 at the Max Planck Institute for Chemistry (MPIC) in Mainz. The meeting is supported by the open access publisher Copernicus, which operates the journal on behalf of EGU in a not-for-profit manner.

Ensure free speech, critical discussion, and transparency in scientific communication and quality assurance

Since the journal launch in 2001, ACP has grown to become one of the major international journals in atmospheric science, now handling around a thousand submissions per year. ACP’s success was not assured when it launched. Open peer review, in which the reviewer comments, author replies, and additional public comments from the scientific community are published immediately, was radical in 2001. “Our guiding principle was to achieve highest levels of scientific integrity through free speech and transparency in scientific exchange and quality assurance”, says Max Planck Director Ulrich Pöschl, who had initiated ACP.

The interactive open access publishing concept was developed more than 20 years ago by researchers connected through the MPI for Chemistry. “It has been a lot of joy and work to initiate, design, and establish interactive open-access publishing with an equally pleasant and strong team of friends and colleagues, including Paul Crutzen and Arne Richter, who are unfortunately not with us anymore but deserve special thanks for the swift initial gain of momentum”, says Uli Pöschl, who led ACP until recently, chaired the EGU publications committee for many years, and continues to promote open access also through the global initiative OA2020 and related activities.”

Preprints in Chemistry: a Research Team’s Journey** – Ciriminna – ChemistryOpen – Wiley Online Library

Abstract:  The benefits of publishing research papers first in preprint form are substantial and long-lasting also in chemistry. Recounting the outcomes of our team’s nearly six-year journey through preprint publishing, we show evidence that preprinting research substantially benefits both early career and senior researchers in today’s highly interdisciplinary chemical research. These findings are of general value, as shown by analyzing the case of four more research teams based in economically developed and developing countries.

 

Five Years of ChemRxiv: Where We Are and Where We Go From Here | Chemical Education | ChemRxiv | Cambridge Open Engage

“ChemRxiv was launched on August 15, 2017 to provide researchers in chemistry and related fields a home for the immediate sharing of their latest research. In the past five years, ChemRxiv has grown into the premier preprint server for the chemical sciences, with a global audience and a wide array of scholarly content that helps advance science more rapidly. On the service’s fifth anniversary, we would like to reflect on the past five years and take a look at what is next for ChemRxiv.”

Best-selling chemistry textbook is now free | News | Chemistry World

“The author of a popular organic chemistry textbook is making it freely available to students after learning about a loophole in his copyright agreement with the publisher.

John McMurry’s Organic Chemistry has been one of the best selling chemistry textbooks since it was first printed in 1984. Under his agreement with Cengage Learning, the book’s publisher, McMurry realised he could ask for the book’s copyright to be returned to him 30 years after it was first printed. Without copyright of the first edition, the publisher is unable to produce any more new editions, McMurry notes.

McMurry, an emeritus professor of chemistry and chemical biology at Cornell University, US, says the move was a tribute to his son who passed away from cystic fibrosis three years ago….”

‘The entire protein universe’: AI predicts shape of nearly every known protein

“From today, determining the 3D shape of almost any protein known to science will be as simple as typing in a Google search.

Researchers have used AlphaFold — the revolutionary artificial-intelligence (AI) network — to predict the structures of some 200 million proteins from 1 million species, covering nearly every known protein on the planet.

The data dump will be freely available on a database set up by DeepMind, Google’s London-based AI company that developed AlphaFold, and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI), an intergovernmental organization near Cambridge, UK….”

AlphaFold reveals the structure of the protein universe

“It’s been one year since we released and open sourced AlphaFold and created the AlphaFold Protein Structure Database (AlphaFold DB) to freely share this scientific knowledge with the world. Proteins are the building blocks of life, they underpin every biological process in every living thing. And, because a protein’s shape is closely linked with its function, knowing a protein’s structure unlocks a greater understanding of what it does and how it works. We hoped this groundbreaking resource would help accelerate scientific research and discovery globally, and that other teams could learn from and build on the advances we made with AlphaFold to create further breakthroughs. That hope has become a reality far quicker than we had dared to dream. Just twelve months later, AlphaFold has been accessed by more than half a million researchers and used to accelerate progress on important real-world problems ranging from plastic pollution to antibiotic resistance.

Today, I’m incredibly excited to share the next stage of this journey. In partnership with EMBL’s European Bioinformatics Institute (EMBL-EBI), we’re now releasing predicted structures for nearly all catalogued proteins known to science, which will expand the AlphaFold DB by over 200x – from nearly 1 million structures to over 200 million structures – with the potential to dramatically increase our understanding of biology….

All 200+ million structures will also be available for bulk download via Google Cloud Public Datasets, making AlphaFold even more accessible to scientists around the world….”

 

ResearchGate Newsroom | Thieme and ResearchGate launch content syndication partnership

“Thieme and ResearchGate have begun a collaboration to increase the visibility of scientific content. With over 20 million members, ResearchGate provides a platform for researchers to share and discover research, build their networks, and advance their careers. The collaboration will enable direct access on ResearchGate to all scientific articles in the 50 open access journals published by Thieme, whose mission is to improve health and healthcare by providing the key information at the right time and in the right place….”

Early firm engagement, government research funding, and the privatization of public knowledge | SpringerLink

Abstract:  Early firm engagement in the scientific discovery process in public institutions is an important form of science-based innovation. However, early firm engagement may negatively affect the academic value of public papers due to firms’ impulse to privatize public knowledge. In this paper, we crawl all patent and paper text data of the Distinguished Young Scholars of the National Science Foundation of China (NSFC) in the chemical and pharmaceutical field. We use semantic recognition techniques to establish the link between scientific discovery papers and patented technologies to explore the relationship between the quality of public knowledge production, government research funding, and early firm engagement in the science-based innovation process. The empirical results show that, first, there is a relatively smooth inverted U-shaped relationship between government research funding for scholars and the quality of their publications. An initial increase in government research funding positively drives the quality of public knowledge production, but the effect turns negative when research funding is excessive. Second, government research funding for scholars can act as a value signal, triggering the firm’s impulse to privatize high-value scientific discoveries. Hence, early firm engagement moderates the inverted U-shaped relationship such that at low levels of research funding, early firm engagement can improve the quality of public knowledge production, and at high levels of research funding, early firm engagement can further reduce the quality of public knowledge production.

 

Towards an open access future | Research Information

“Open Access keeps me up at night. Not the why…or the what, but the how.  With the advantages of Open Access to research so clear now – especially in the midst of a global pandemic – I lay awake thinking how we, as researchers, as publishers, as societies, as institutions can get there. How can we co-create the new open research environment we need while preserving integral aspects of the current ecosystem?

As the new Head of Open Access Journals at the Royal Society of Chemistry, it makes sense this keeps me up at night since these questions form the very core of my role and responsibilities. I’m tasked – in collaboration with my colleagues – to figure out how we can sustainably transition our successful publishing business that, for decades, has relied on subscriptions, to a model that will support Open Access (OA) to the over 37,000 articles we publish annually. …”

Comparative Analyses of Medicinal Chemistry and Cheminformatics Filters with Accessible Implementation in Konstanz Information Miner (KNIME)

Abstract:  High-throughput virtual screening (HTVS) is, in conjunction with rapid advances in computer hardware, becoming a staple in drug design research campaigns and cheminformatics. In this context, virtual compound library design becomes crucial as it generally constitutes the first step where quality filtered databases are essential for the efficient downstream research. Therefore, multiple filters for compound library design were devised and reported in the scientific literature. We collected the most common filters in medicinal chemistry (PAINS, REOS, Aggregators, van de Waterbeemd, Oprea, Fichert, Ghose, Mozzicconacci, Muegge, Egan, Murcko, Veber, Ro3, Ro4, and Ro5) to facilitate their open access use and compared them. Then, we implemented these filters in the open platform Konstanz Information Miner (KNIME) as a freely accessible and simple workflow compatible with small or large compound databases for the benefit of the readers and for the help in the early drug design steps. View Full-Text

 

American Chemical Society Transformative Open Access Agreement – Office of Scholarly Communication

“As of May 17, 2022, the University of California, together with the California State University (CSU) and members of the Statewide California Electronic Library Consortium (SCELC), entered into a transformative open access agreement with the American Chemical Society (ACS), the first such California-wide agreement. 

The three-year agreement provides readers and researchers at nearly 60 California research institutions – including all 10 UC campuses and the Lawrence Berkeley National Laboratory – with access to subscription content while allowing authors at the participating institutions to publish open access in ACS’ portfolio of over 75 chemistry journals at a reduced cost.

The goal of the agreement is to enable authors from UC, CSU, and SCELC institutions to transition from the traditional ”read-only” subscription model to a transformative model that makes it easier and more affordable for authors to publish open access. As with UC’s other transformative agreements, the agreement supports UC’s mission as a public university and advances the global shift toward sustainable open access publishing by making more UC-authored research articles open to the world, while containing the university’s journal-related expenditures….”

MACE – An Open Access Data Repository of Mass Spectra for Chemical Ecology | SpringerLink

Abstract:  MACE is an open access collection of electron impact (EI) mass spectra for coupled gas chromatography-mass spectrometry (GC/MS) that serves as an add-on database, comprising curated spectra not present in widely available commercial mass spectral libraries, such as the NIST or WILEY databases. The spectra are stored as text files that allow easy integration into individual GC/MS systems. The article describes the concept of MACE, the data structure, how to contribute, and its usage. MACE is designed as a community effort and will require contributions from the community to be successful.

ACS Publications commits its entire hybrid journal portfolio to become Plan S-aligned Transformative Journals | Plan S

“cOAlition S is pleased to announce that the American Chemical Society (ACS) has committed its full portfolio of more than 60 hybrid journals to become Plan S-aligned Transformative Journals.

ACS publishes 12 completely open access journals, which are already compliant with Plan S requirements. The commitment for the rest of its portfolio to become Transformative Journals will allow authors even greater flexibility in their choice of publication outlet….”

Agreement will allow UC articles to be published open access

An agreement with the UC system and the American Chemical Society, or ACS, will allow every UC-authored article in the ACS to be published open access.

Open access means that these researchers’ works will be available to more people and have a greater impact, particularly in lower-income countries, according to Jeff MacKie-Mason, UC Berkeley librarian.

MacKie-Mason noted that this has been a long-term goal of the UC Academic Senate and UC libraries. He added this will also include a lower cost of publication for the researchers.

Institutions partner with ACS to advance first California-wide transformative open access agreement – Office of Scholarly Communication

“Three California consortia, representing nearly 60 academic and research institutions, and the Publications Division of the American Chemical Society (ACS) today announced the first-ever California-wide transformative open access agreement. It is also ACS’ first “read and publish” agreement in the U.S. composed of multiple consortia. Through a partnership with the 10-campus University of California (UC) system, the 23-campus California State University (CSU) system, and 25 subscribing institutions represented by the Statewide California Electronic Library Consortium (SCELC), readers and researchers at dozens of California research institutions will be able to benefit from full access to subscription content while receiving support for open access publication in ACS’ portfolio of more than 75 premier chemistry journals….”