PhilArchive: The Philosophy E-Print Archive

“PhilArchive is the largest open access e-print archive in philosophy. Formerly known as the PhilPapers Archive, it is built on and integrated with the PhilPapers database. Access to items on PhilArchive is free without a user account. PhilArchive is a non-profit project supported by the PhilPapers Foundation.

PhilArchive consists entirely of articles submitted by users. You can contribute by submitting your work….”

Open Access Uptake in Germany 2010-18: Adoption in a diverse research landscape

Abstract:  This study investigates the development of open access (OA) to journal articles from authors affiliated with German universities and non-university research institutions in the period 2010-2018. Beyond determining the overall share of openly available articles, a systematic classification of distinct categories of OA publishing allows to identify different patterns of adoption to OA. Taking into account the particularities of the German research landscape, variations in terms of productivity, OA uptake and approaches to OA are examined at the meso-level and possible explanations are discussed. The development of the OA uptake is analysed for the different research sectors in Germany (universities, non-university research institutes of the Helmholtz Association, Fraunhofer Society, Max Planck Society, Leibniz Association, and government research agencies). Combining several data sources (incl. Web of Science, Unpaywall, an authority file of standardised German affiliation information, the ISSN-Gold-OA 3.0 list, and OpenDOAR), the study confirms the growth of the OA share mirroring the international trend reported in related studies. We found that 45% of all considered articles in the observed period were openly available at the time of analysis. Our findings show that subject-specific repositories are the most prevalent OA type. However, the percentages for publication in fully OA journals and OA via institutional repositories show similarly steep increases. Enabling data-driven decision-making regarding OA implementation in Germany at the institutional level, the results of this study furthermore can serve as a baseline to assess the impact recent transformative agreements with major publishers will likely have on scholarly communication. 

PubMed Central archiving: a major milestone for a scholarly journal

“There are concerns that authors in developing countries and those lacking research funds are disadvantaged by Plan S and cut out of quality gold open-access journals.3 The latter, however, is largely compensated by the availability of platinum open-access journals, such as the MJR, where publishing and archiving charges are covered by professional societies, easing the authors’ and readers’ financial burden.4…”

Coronavirus Research Moves Faster than Medical Journals

“Many of the coronavirus-related papers being posted on MedRxiv are rushed and flawed, and some are terrible. But a lot report serious research findings, some of which will eventually find their way into prestigious journals, which have been softening their stance on previously released research. (“We encourage posting to preprint servers as a way to share information immediately,” emails Jennifer Zeis, director of communications at the New England Journal of Medicine.) In the meantime, the research is out there, being commented on and followed up on by other scientists, and reported on in the news media. The journals, which normally keep their content behind steep paywalls, are also offering coronavirus articles outside of it. New efforts to sort through the resulting bounty of available research are emerging, from a group of Johns Hopkins University scholars sifting manually through new Covid-19 papers to a 59,000-article machine-readable data set, requested by the White House Office of Science and Technology Policy and enabled by an assortment of tech corporations and academic and philanthropic organizations, that is meant to be mined for insights using artificial intelligence and other such means.

This is the future for scientific communication that has been predicted since the spread of the internet began to enable it in the early 1990s (and to some extent long before then), yet proved slow and fitful in its arrival. It involves more or less open access to scientific research and data, and a more-open review process with a much wider range of potential peers than the peer review offered by journals. For its most enthusiastic boosters, it is also an opportunity to break through disciplinary barriers, broaden and improve the standards for research success and generally just make science work better. To skeptics, it means abandoning high standards and a viable economic model for research publishing in favor of a chaotic, uncertain new approach.

I’m mostly on the side of the boosters here, but have learned during five years of writing on and off about academic publishing that the existing way of doing things is quite well entrenched, and that would-be innovators often misunderstand the challenges involved in displacing or replacing it….”

An XML Repository of All bioRxiv Articles is Now Available for Text and Data Mining

“bioRxiv and medRxiv provide free and unrestricted access to all articles posted on their servers. We believe this should apply not only to human readers but also to machine analysis of the content. A growing variety of resources have been created to facilitate this access.

bioRxiv and medRxiv metadata are made available via a number of dedicated RSS feeds and APIs. Simplified summary statistics covering the content and usage are also available. For bioRxiv, this information is available here’

Bulk access to the full text of bioRxiv articles for the purposes of text and data mining (TDM) is available via a dedicated Amazon S3 resource. Click here for details of this TDM resource and how to access it….”

Practices and policies of preprint platforms for life and biomedical sciences | Zenodo

“Given the increase in the use and profile of preprint servers – and alternative publishing hybrid platforms such as F1000 Research – in the life sciences, it is increasingly important to identify how many such servers and hybrids exist, to describe their scope in terms of the scientific disciplines they cover, and to compare and contrast their characteristics and policies.

We surveyed forty-four (44) platforms that host preprints relevant to life and biomedical sciences and that were active online and accepting submissions on 25 June 2019. Information on preprint platform policies, features and practices was collected through online research by the authors and by surveying preprint platform representatives directly. 

Full data sheets include an additional 5 platforms hosted on OSF Preprints (rows 49-53) to fulfil the wider scope for the ASAPbio project, not in disciplinary scope (biology and medical sciences) for the manuscript with Jamie Kirkham….”

arXiv Annual Update, January 2020 | arXiv e-print repository

“Our next-generation arXiv (arXiv-NG) initiative to improve the service’s core infrastructure by incremental and modular renewal of the existing arXiv system continues to progress. This includes significant effort towards laying the foundations for the NG submission system, which the team hopes to alpha test in Q12020. Existing search, browse, accounts, documentation NG components received incremental improvements. The team also took the initial and essential steps to improve the overall accessibility of arXiv’s user interfaces, both through behind-the-scenes structural improvements and user-facing changes (e.g. support for a mobile-friendly abstract page)….

Key Accomplishments in 2019 and Plans for 2020 Since we started the arXiv sustainability initiative in 2010, an integral part of our work has been assessing the services, technologies, standards, and policies that constitute arXiv. Here are some of our key accomplishments from 2019 to illustrate the range of issues we have been trying to tackle. Please see the 2019 Roadmap for a full account of our work.

We continue to improve facilities for administrators and moderators in order to streamline their workflows, and to improve clarity and transparency of arXiv communications. During 2019, the arXiv team expanded quality control flags.
Our development team continued to improve and extend various search, browse, documentation, and other features as we reimplement, test, refine and continue to improve the arXiv platform. The team made significant progress reimplementing the submission user interface towards an alpha release, new and legacy APIs, as well as backend services. Wherever possible, new software components are developed in public repositories and released under permissive open source licenses. With a reduction of effort in Q42019 due to staff departures, the team shifted most of its remaining resources towards improving and maintaining the operational stability of the arXiv services.
Our Scientific Advisory Board (SAB), under the leadership of Licia Verde, has clarified roles and responsibilities for the arXiv Subject Advisory Committees and the Committee Chairs. The effort for outreach and recruitment of new moderators has increased in 2019 with an aim to increase diversity among moderators. We have also modified the SAB membership to include greater representation and engagement with the newer fields that have joined arXiv.
Two major policies were adopted in 2019 including the arXiv Code of Conduct and a Privacy Policy. We thank the staff, moderators, advisory boards, and arXiv users who have contributed to the development of the Code of Conduct.
The arXiv team wished farewells to Janelle Morano (Community Engagement and Membership Coordinator), Jaimie Murdock (arXiv NG Developer), Erick Peirson (Lead System Architect), Liz Woods (User Experience Specialist) and Matt Bierbaum (arXiv Labs). We were pleased to welcome Shamsi Brinn as our new User Experience Specialist in October 2019 and Alison Fromme as new Community Engagement and Membership Coordinator in January 2020. We also initiated a search for a new Backend Python Developer in the last quarter of 2019.
We moved information about our governance, business model, and reports to arXiv.org, to improve overall accessibility to pertinent information about arXiv’s operations. This information was previously available on the arXiv Public Wiki. We continue to regularly update our community at the arXiv.org blog.
As part of the organizational change to Cornell CIS we moved offices in 2019. The arXiv team now has its own dedicated space in historic Uris Library.

The 2020 Roadmap includes our goals as we strive to improve the technical infrastructure, moderation system, user support, and the sustainability framework….”

Blog – Europe PMC: The new Europe PMC is here

“It’s time to embrace change. Today Europe PMC proudly unveils a new website, packed with useful features. The improved Europe PMC offers a better search and reading experience, as well as better access to data….”

bioRxiv: the preprint server for biology | bioRxiv

Abstract:  The traditional publication process delays dissemination of new research, often by months, sometimes by years. Preprint servers decouple dissemination of research papers from their evaluation and certification by journals, allowing researchers to share work immediately, receive feedback from a much larger audience, and provide evidence of productivity long before formal publication. Launched in 2013 as a non-profit community service, the bioRxiv server has brought preprint practice to the life sciences and recently posted its 64,000th manuscript. The server now receives more than four million views per month and hosts papers spanning all areas of biology. Initially dominated by evolutionary biology, genetics/genomics and computational biology, bioRxiv has been increasingly populated by papers in neuroscience, cell and developmental biology, and many other fields. Changes in journal and funder policies that encourage preprint posting have helped drive adoption, as has the development of bioRxiv technologies that allow authors to transfer papers easily between the server and journals. A bioRxiv user survey found that 42% of authors post their preprints prior to journal submission whereas 37% post concurrently with journal submission. Authors are motivated by a desire to share work early; they value the feedback they receive, and very rarely experience any negative consequences of preprint posting. Rapid dissemination via bioRxiv is also encouraging new initiatives that experiment with the peer review process and the development of novel approaches to literature filtering and assessment.