Systematic examination of preprint platforms for use in the medical and biomedical sciences setting | BMJ Open

Abstract:  Objectives The objective of this review is to identify all preprint platforms with biomedical and medical scope and to compare and contrast the key characteristics and policies of these platforms.

Study design and setting Preprint platforms that were launched up to 25 June 2019 and have a biomedical and medical scope according to MEDLINE’s journal selection criteria were identified using existing lists, web-based searches and the expertise of both academic and non-academic publication scientists. A data extraction form was developed, pilot tested and used to collect data from each preprint platform’s webpage(s).

Results A total of 44 preprint platforms were identified as having biomedical and medical scope, 17 (39%) were hosted by the Open Science Framework preprint infrastructure, 6 (14%) were provided by F1000 Research (the Open Research Central infrastructure) and 21 (48%) were other independent preprint platforms. Preprint platforms were either owned by non-profit academic groups, scientific societies or funding organisations (n=28; 64%), owned/partly owned by for-profit publishers or companies (n=14; 32%) or owned by individuals/small communities (n=2; 5%). Twenty-four (55%) preprint platforms accepted content from all scientific fields although some of these had restrictions relating to funding source, geographical region or an affiliated journal’s remit. Thirty-three (75%) preprint platforms provided details about article screening (basic checks) and 14 (32%) of these actively involved researchers with context expertise in the screening process. Almost all preprint platforms allow submission to any peer-reviewed journal following publication, have a preservation plan for read access and most have a policy regarding reasons for retraction and the sustainability of the service.

Conclusion A large number of preprint platforms exist for use in biomedical and medical sciences, all of which offer researchers an opportunity to rapidly disseminate their research findings onto an open-access public server, subject to scope and eligibility.

#ASAPpdb: Structural biologists commit to releasing data with preprints – ASAPbio

“The Protein Data Bank (PDB) was established as the first open access repository for biological data, and the datasets it hosts have been invaluable to research in fundamental biology and the understanding of health and disease. Just this month, we witnessed the announcement of the AlphaFold2 results toward structure prediction, made possible thanks to the more than 170,000 freely accessible structures in the PDB which provided “training data” for the structure prediction software.

It was not always the case that such structural biology data were freely available, even upon journal publication. From the founding of the PDB in 1971 until the late 1980s, most journals did not require deposition of structures in a public database. A key moment was a petition, circulated in 1987 by a group of leading structural biologists, demanding that the data created be made openly available upon journal publication. This petition led to major journals adopting data deposition standards. In the early 1990s, the National Institute of General Medical Sciences (NIGMS) imposed similar requirements on all grantees. 

The revolution in publishing made possible by preprints calls for a re-evaluation of data disclosure practices in structural biology. While journal review processes take weeks, months, or even years, preprints allow researchers to rapidly communicate their findings to the community. However, withholding access to PDB files that accompany preprints inhibits the progress towards scientific discovery which preprints can enable. 

Commitment

We pledge to publicly release our PDB files (and associated structure factor, restraint, and map files) with deposition of our preprints.

We encourage all structural biologists to also deposit raw data in appropriate resources (e.g. EMPIAR, proteindiffraction.org, https://data.sbgrid.org/, etc). …”

Scientific Data recommended repositories

“Spreadsheet listing data repositories that are recommended by Scientific Data (Springer Nature) as being suitable for hosting data associated with peer-reviewed articles. Please see the repository list on Scientific Data’s website for the most up to date list….”

OceanDocs Home

“OceanDocs is supported by the Intergovernmental Oceanographic Commission (IOC) to collect, preserve and facilitate discovery and access to all research output from members of the ocean research and observation community and specifically their Ocean Data and Information Networks (ODINS). It is one of a number of complementary thematic digital marine and aquatic repositories including the Aquatic Commons, which is supported by the International Association of Aquatic and Marine Science Libraries and Information Centers (IAMSLIC).”

Welcome to Aquatic Commons – Aquatic Commons

“The Aquatic Commons is a thematic digital repository covering the natural marine, estuarine /brackish and fresh water environments . It includes all aspects of the science, technology, management and conservation of these environments, their organisms and resources, and the economic, sociological and legal aspects. It is complementary to OceanDocs, which is supported by the Intergovernmental Oceanographic Commission (IOC)/ International Oceanographic Data and Information Exchange (IODE) specifically to collect, preserve and facilitate access to all research output from members of their Ocean Data and Information Networks (ODINS). Click to read more information about this repository….”

Archive-It – South Asian Gender and Sexuality Web Archive

“Amplifying the voices of those fighting against long histories of patriarchal dominance, the South Asian Gender and Sexuality Web Archive documents and preserves the work of activists, grassroots organizations, and social justice movements committed to promoting the visibility and experiences of LGBTQAI+ people and women in South Asia and its diasporas. With an emphasis on the websites of non-governmental organizations, and on the resources generated by social justice activist groups and individuals, the Archive demonstrates how organizations approach goals of advocacy, education, and capacity building related to issues of gender and sexuality across South Asian regions. An additional focus on resources that showcase the voices of LGBTQAI+ people and women — as revealed in expressions such as oral narratives, writings, performance, and the arts — provides insight into the struggles and resilience of the marginalized, offering content that is largely unavailable or preserved elsewhere and which is likely to disappear. Under the auspices of the Ivy Plus Libraries Confederation, and curated by Laura Ring (University of Chicago), Jef Pierce (University of Pennsylvania), Aruna Magier (New York University), and Richard Lesage (Harvard University), the Archive foregrounds the lives of South Asian LGBTQAI+ peoples and South Asian women around the world, and chronicles their movements against gender and sexuality based violence and discrimination.”

Not One but Many Models of Open-Access Publishing – Association for Psychological Science – APS

“The OA movement has proliferated in numerous directions over the last two decades, and a color-naming system has evolved in an attempt to simplify this diversity. PsyArXiv is classified in this system as “green” OA because it is a repository for authors who seek to freely share their scholarly output with both consumers (readers) and producers of research (Samberg et al., 2018). The niches that Kitayama has described—serving “cutting-edge” and “nontraditional” research projects—are both examples of “gold” OA. These outlets are peer-reviewed journals that publish open articles and make use of article processing charges (APCs). This approach differs substantially from traditional publishing models where peer-reviewed articles are published without expense for the authors, but at substantial expense to libraries; further, articles are locked away behind a “paywall.” Many readers of the APS Observer are likely familiar with hybrid approaches as well (sometimes called “paid open access”). This model gives authorship teams the choice, after peer review, to pay APCs to add OA publishing to their accepted paper, or they can choose to publish without expense by effectively signing away the licensing rights to their article. Many additional variations exist, each with its own color-name (see Barnes, 2020, and Samberg et al., 2018)….

At the most fundamental level, PsyArXiv complements all forms of publishing by equitably providing psychological researchers with a free, simple, and immediate outlet that can be accessed by anyone with reliable Internet service. This gives early access to timely research findings, provides an alternative access option for works that are not published openly, increases discoverability (Norris et al., 2008; Lewis, 2018), and reduces the file-drawer problem (Franco et al., 2014). Beyond this, the PsyArXiv infrastructure allows for further innovation in psychology publishing that can build on the benefits of OA. These might include overlay journals, which have gained considerable attention in other scientific disciplines recently and provide peer-review and/or editorial curation of content posted on arXiv (for examples, see Discrete Analysis and The Open Journal of Astrophysics). Models like these offer the potential for niche journals to flourish in a manner that would not be viable within the traditional publishing ecosystem. In short, we hope that researchers, including submitters to APS journals, will take advantage of APS’s generous article-posting policies and make copies of their pre- and post-publication work available for the community at PsyArXiv, thereby helping the community capitalize on these many benefits.”

Submissions and Downloads of Preprints in the First Year of medRxiv | Medical Journals and Publishing | JAMA | JAMA Network

“Preprint servers offer a means to disseminate research reports before they undergo peer review and are relatively new to clinical research.1-4 medRxiv is an independent, not-for-profit preprint server for clinical and health science researchers that was introduced in June 2019.4 A central question was whether there would be adoption of a new approach to dissemination of pre–peer-review science. Now, a year after its establishment, we report medRxiv’s submissions, posts, and downloads.”