Author Archives: peter.suber's bookmarks

Zenodo’s Open Repository Streamlines Sharing Science – SPARC

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“A decade ago, the scientific community recognized that to move from open access to open science, there was a need for free unrestricted access to scientific knowledge. This meant valuing, sharing and preserving data, software and other digital artifacts from research, but the on-ramp to participate had to be faster and simpler if the practice was going to gain traction.

The European Union decided to fund CERN (the European Organisation for Nuclear Research) through the OpenAIRE project to build a catch-all repository to ensure all researchers had a place to easily upload software, data, preprints and other digital outputs.

That was the beginning of Zenodo, which CERN and OpenAIRE launched in 2013. Since, the free global platform has expanded faster than imagined. It now has 25 million visits a year, hosts 3+ million uploads and over 1 petabyte of data. This year marks the platform’s 10th anniversary and today Zenodo is widely viewed as a trusted place to preserve research materials that could be of use to others in advancing science….”

An open-access laboratory medicine course for medical students – ScienceDirect

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Abstract:  The senior author created a 2-week online laboratory medicine course for fourth-year medical students to meet an unmet need at our institution for a brief survey course of clinical pathology in an online format. The course includes online videos, reading assignments, study questions, and a rubric for written assignments that apply the key principles to topics that are customized based on the specialty interests of each student. Anonymous course evaluation surveys were completed by 42 of 60 students (70%), and 92% of respondents stated that they strongly agree with the quality metrics statements in the survey. The complete course materials are shared in this article in the spirit of open access and may be used for medical students, pathology residents, and other learners.

 

Factors Associated With Open Access Publishing Costs in Oncology Journals: Cross-sectional Observational Study

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Abstract:  Background:

Open access (OA) publishing represents an exciting opportunity to facilitate the dissemination of scientific information to global audiences. However, OA publishing is often associated with significant article processing charges (APCs) for authors, which may thus serve as a barrier to publication.

Objective:In this observational cohort study, we aimed to characterize the landscape of OA publishing in oncology and, further, identify characteristics of oncology journals that are predictive of APCs.

Methods:We identified oncology journals using the SCImago Journal & Country Rank database. All journals with an OA publication option and APC data openly available were included. We searched journal websites and tabulated journal characteristics, including APC amount (in US dollars), OA model (hybrid vs full), 2-year impact factor (IF), H-index, number of citable documents, modality/treatment specific (if applicable), and continent of origin. All APCs were converted to US-dollar equivalents for final analyses. Selecting variables with significant associations in the univariable analysis, we generated a multiple regression model to identify journal characteristics independently associated with OA APC amount. An audit of a random 10% sample of the data was independently performed by 2 authors to ensure data accuracy, precision, and reproducibility.

Results:Of 367 oncology journals screened, 251 met the final inclusion criteria. The median APC was US $2957 (IQR 1958-3450). The majority of journals (n=156, 62%) adopted the hybrid OA publication model and were based in Europe (n=119, 47%) or North America (n=87, 35%). The median (IQR) APC for all journals was US $2957 (1958-3540). Twenty-five (10%) journals had APCs greater than US $4000. There were 10 (4%) journals that offered OA publication with no publication charge. Univariable testing showed that journals with a greater number of citable documents (P<.001), higher 2-year IF (P<.001), higher H-index (P<.001), and those using the hybrid OA model (P<.001), or originating in Europe or North America (P<.001) tended to have higher APCs. In our multivariable model, the number of citable documents (?=US $367, SD US $133; P=.006), 2-year IF (US $1144, SD US $177; P<.001), hybrid OA publishing model (US $991, SD US $189; P<.001), and North American origin (US $838, SD US $186; P<.001) persisted as significant predictors of processing charges.

Conclusions:OA publication costs are greater in oncology journals that publish more citable articles, use the hybrid OA model, have a higher IF, and are based in North America or Europe. These findings may inform targeted action to help the oncology community fully appreciate the benefits of open science.

Forum: How do we make accessible research papers a reality?

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“Hosted by arXiv, this half-day online forum will center the experiences of academic researchers with disabilities who face barriers to accessing and reading papers. The forum will be useful for people across the academic publishing pipeline who are committed to accessibility and want to collaborate on solutions. Together, we can chart a path towards fully accessible research papers, and leave with practical next steps for our own organizations….”

The Transformation of the Green Road to Open Access[v1] | Preprints

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Abstract:  (1) Background: The 2002 Budapest Open Access Initiative recommended on self-archiving of scientific articles in open repositories as the “green road” to open access. Twenty years later, only one part of the researchers deposits their publications in open repositories; moreover, one part of the repositories’ content is not based on self-archived deposits but on mediated nonfaculty contributions. The purpose of the paper is to provide more empirical evidence on this situation and to assess the impact on the future of the green road. (2) Methods: We analyzed the contributions on the French national HAL repository from more than 1,000 laboratories affiliated to the ten most important French research universities, with a focus on 2020, representing 14,023 contributor accounts and 166,939 deposits. (3) Results: We identified seven different types of contributor accounts, including deposits from nonfaculty staff and import flows from other platforms. Mediated nonfaculty contribution accounts for at least 48% of the deposits. We also identified difference between institutions and disciplines. (4) Conclusions: Our empirical results reveal a transformation of open repositories from self-archiving and direct scientific communication towards research information management. Repositories like HAL are somewhere in the middle of the process. The paper describes data quality as the main issue and major challenge of this transformation.

 

UK Institutional Rights Retention Policies

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“This page contains information about UK universities that have institutional rights retention policies. The raw data underlying these visualisations is available on github along with the code that generates this page….”

Strife at eLife: inside a journal’s quest to upend science publishing

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“Last October, the pioneering life-sciences journal eLife introduced bold changes to its editorial practice — which some researchers applauded as reimagining the purpose of a scientific journal. From 31 January this year, eLife said, it would publish every paper it sent out for peer review: authors would never again receive a rejection after a negative review. Instead, reviewers’ reports would be published alongside the paper, together with a short editorial assessment of the work’s significance and rigour. Authors could then decide whether to revise their paper to address any comments.

The change followed an earlier decision by eLife to require that all submissions be posted as preprints online. The cumulative effect was to turn eLife into a producer of public reviews and assessments about online research. It was “relinquishing the traditional journal role of gatekeeper”, editor-in-chief Michael Eisen explained in a press release, and “promoting the evaluation of scientists based on what, rather than where, they publish”….”

JAMA’s new editor brings open access and other changes – STAT

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“[Kirsten Bibbins-Domingo] recently spoke at the annual conference of the Association of Health Care Journalists, in St. Louis, where STAT’s Usha Lee McFarling sat down with her to learn more about the changes she’s implemented at the journal, including a new open access policy. Under this policy, most JAMA articles remain accessible only to subscribers, but authors can publicly post their research manuscripts the day they are published, and they are not charged open access fees as many journals do….

So what we decided as a journal was that authors, on the day we publish their work, can make their work available to any public repository and post it. So if you want to find the results of an article and you’re in a country or at an institution that doesn’t subscribe to our journals, you can still find that science because it’s available in a public repository. This decision is rooted in the principles of what’s good for science and it’s rooted in equity, frankly, because not all institutions, and not all people, have a subscription to JAMA.

This public access approach is also rooted in the principles of equity of who can publish. Open access has focused on mostly making sure there’s equity in what’s accessible to read, but that’s on the backs of sometimes very high fees that authors pay to publish in open access journals. What we’re saying is we believe in open access — and also believe in the value of what we do. We still think people will pay to subscribe to JAMA because there is value in the final version of record, the graphics editors making the figures, the podcasts, the corrections that get posted because things do change over time, that is what that subscription is buying you, all of those pieces.

But we can’t have open access fees put publishing out of reach for authors that might be early-career, or in disciplines or at institutions that aren’t as well-funded. We’re really pleased that the National Institutes of Health just announced and posted for public comment that this is the approach they are considering for all funded researchers in the NIH….”

Well-maintained digital repositories can bolster research

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“Universities in Africa should establish digital research data repositories to archive important information gathered over time for posterity purposes, an important tool that can serve as an alternative to and complement open-access publishing.

Digital repositories would store critical data gathered by different researchers who are doing different research work over time, enriching archives already maintained by universities but, even more importantly, boosting the visibility of academics and their institutions….”

Wiley Manipal Academy Of Higher Education Inks Open Access Agreement – BW Education

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“Today, Wiley, global publisher has signed an open access agreement with Manipal Academy of Higher Education (MAHE). Beginning in 2023, this agreement will be in effect with MAHE, an institute of eminence.

The agreement, which represents Wiley’s first in India, provides authors affiliated with the Manipal Academy of Higher Education with access to Wiley’s journal portfolio and enables participating researchers to publish articles open access in nearly 2,000 hybrid and gold open access journals, including those published by Hindawi….”

Open Science Festival 2023

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“On July 4th and 5th, 2023, the second German Open Science Festival will take place in Cologne. A festival with a mix of current topics and formats related to Open Science

     • Organized by ZB MED – Information Centre for Life Sciences, the University of Cologne and the University Library Cologne

     • For students, (young) scientists and anyone who wants to know more about Open Science….”

OA monograph costs | Open Research

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“The majority of University and scholarly society presses that publish on open access monographs do not charge authors or readers, except for those ordering print copies.The OAPEN-UK HSS Researcher Survey (between Feb-May 2012) examined the source of funding for research underpinning authors’ last HSS monograph and found that only 22% came from research council grants, whereas 62% came from core university funds or self-funding.

The Open Book Publishers membership scheme (OBP) is a new agreement from Jisc Collections that supports the publication of Open Access research monographs. By joining this scheme, member institutions will support the publication of at least twelve new Open Access research monographs every year. For an annual fee of £270 member institutions can also offer all staff, students and alumni with a discount on any print copies of OBP titles. Any print sales to member institutions are offset against membership fees in the following year.

How much do commercial publishers charge for OA monographs?

As with open access journals there is a need for a new business model. The Wellcome Trust extended their open access policy to include monographs in 2013. They estimate: “the fee for existing open access options – ensuring all published material is converted to XML, and then made available in html and PDF – for books currently averages around £9,500, and we anticipate the average cost to make a book chapter open access will be £1,800″.

This book price seems to be halfway between what is charged by traditional publishers offering and OA option, and OA only publishers. Prices seem to vary considerably (note prices from September 2018)…”

Open Science course available on new knowledge platform | NWO

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“NWO teamed up with the Research Council Norway (RCN) and the Centre for Science and Technology Studies (CWTS) to create an open science course. This course was offered last year to employees of NWO and RCN. Its content is now available to anyone through an open knowledge platform set up by CWTS….”

Librarians should stand with the Internet Archive (opinion)

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“The Internet Archive, a nonprofit library in San Francisco, has grown into one of the most important cultural institutions of the modern age. What began in 1996 as an audacious attempt to archive and preserve the World Wide Web has grown into a vast library of books, musical recordings and television shows, all digitized and available online, with a mission to provide “universal access to all knowledge.”

Right now, we are at a pivotal stage in a copyright infringement lawsuit against the Internet Archive, still pending, brought by four of the biggest for-profit publishers in the world, who have been trying to shut down core programs of the archive since the start of the pandemic. For the sake of libraries and library users everywhere, let’s hope they don’t succeed….”

Work at PeerJ – Publishing Editor (new role)

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“PeerJ is an award-winning, open access, peer-reviewed, scholarly journal publisher covering many academic disciplines (including biology, life science, medicine, environmental science, computer science and chemistry). We have a staff vacancy for an experienced Publishing Editor to support and grow our journal program. This senior position will operate at a high level in the company and participate in initiatives to grow and develop the editorial program (i.e. it is focused on editorial strategies and content development). In addition, the role will help maintain an effective quality control and peer review process and will involve frequent interactions with academics worldwide. This role works closely with internal teams and the external Academic Editors and peer-reviewers of our peer-reviewed journal publications. It is initially focused on ‘field biology’ areas such as ecology, plant sciences, and zoology but will expand to cover other areas as needed. Starting immediately, this is a full-time position working from home with flexible working hours. Note: We are also hiring for a more junior role (of ‘Staff Editor’) at https://peerj.com/expertrxiv/823 -This Staff Editor position will work alongside the Publishing Editor.”