Lost Green OA articles from Semantic Scholar

“Over the last two weeks, one of the largest repositories we index, Semantic Scholar, removed most of the articles it had been hosting. The end result for Unpaywall is that about 1 million formerly Green OA articles are now Closed. This is about 12% of all Green OA. We’re working on finding new locations for as many articles as we can.

The total number of articles removed from Semantic Scholar was about 8 million, but most of them are still OA because we had other locations….”

COVID-19 and the research scholarship ecosystem: help! – Journal of Clinical Epidemiology

Highlights

Data sharing is not common as part of biomedical publications
To increase data sharing biomedical journals, funders and academic institutions should introduce policies that will enhance data sharing and other open science practices
As part of research assessments incentives and rewards need to be introduced

Abstract

Objectives

Data sharing practices remain elusive in biomedicine. The COVID-19 pandemic has highlighted the problems associated with the lack of data sharing. The objective of this article is to draw attention to the problem and possible ways to address it.

Study Design and Setting

This article examines some of the current open access and data sharing practices at biomedical journals and funders. In the context of COVID-19 the consequences of these practices is also examined.

Results

Despite the best of intentions on the part of funders and journals, COVID-19 biomedical research is not open. Academic institutions need to incentivize and reward data sharing practices as part of researcher assessment. Journals and funders need to implement strong polices to ensure that data sharing becomes a reality. Patients support sharing of their data.

Conclusion

Biomedical journals, funders and academic institutions should act to require stronger adherence to data sharing policies.

Bill Gates, Vaccine Monster | The New Republic

“Battle-scarred veterans of the medicines-access and open-science movements hoped the immensity of the pandemic would override a global drug system based on proprietary science and market monopolies. By March, strange but welcome melodies could be heard from unexpected quarters. Anxious governments spoke of shared interests and global public goods; drug companies pledged “precompetitive” and “no-profit” approaches to development and pricing. The early days featured tantalizing glimpses of an open-science, cooperative pandemic response. In January and February 2020, a consortium led by the National Institutes of Health and the National Institute of Allergy and Infectious Diseases collaborated to produce atomic-level maps of the key viral proteins in record time. “Work that would normally have taken months—or possibly even years—has been completed in weeks,” noted the editors of Nature. …

By then, however, the optimism and sense of possibility that defined the early days were long gone. Advocates for pooling and open science, who seemed ascendant and even unstoppable that winter, confronted the possibility they’d been outmatched and outmaneuvered by the most powerful man in global public health.

In April, Bill Gates launched a bold bid to manage the world’s scientific response to the pandemic. Gates’s Covid-19 ACT-Accelerator expressed a status quo vision for organizing the research, development, manufacture, and distribution of treatments and vaccines. Like other Gates-funded institutions in the public health arena, the Accelerator was a public-private partnership based on charity and industry enticements. Crucially, and in contrast to the C-TAP, the Accelerator enshrined Gates’s long-standing commitment to respecting exclusive intellectual property claims. Its implicit arguments—that intellectual property rights won’t present problems for meeting global demand or ensuring equitable access, and that they must be protected, even during a pandemic—carried the enormous weight of Gates’s reputation as a wise, beneficent, and prophetic leader. …

“Early on, there was space for Gates to have a major impact in favor of open models,” says Manuel Martin, a policy adviser to the Médecins Sans Frontières Access Campaign. “But senior people in the Gates organization very clearly sent out the message: Pooling was unnecessary and counterproductive. They dampened early enthusiasm by saying that I.P. is not an access barrier in vaccines. That’s just demonstratively false.”…

“Things could have gone either way,” says Love, “but Gates wanted exclusive rights maintained. He acted fast to stop the push for sharing the knowledge needed to make the products—the know-how, the data, the cell lines, the tech transfer, the transparency that is critically important in a dozen ways. The pooling approach represented by C-TAP included all of that. Instead of backing those early discussions, he raced ahead and signaled support for business-as-usual on intellectual property by announcing the ACT-Accelerator in March.” …”

 

Bill Gates, Vaccine Monster | The New Republic

“Battle-scarred veterans of the medicines-access and open-science movements hoped the immensity of the pandemic would override a global drug system based on proprietary science and market monopolies. By March, strange but welcome melodies could be heard from unexpected quarters. Anxious governments spoke of shared interests and global public goods; drug companies pledged “precompetitive” and “no-profit” approaches to development and pricing. The early days featured tantalizing glimpses of an open-science, cooperative pandemic response. In January and February 2020, a consortium led by the National Institutes of Health and the National Institute of Allergy and Infectious Diseases collaborated to produce atomic-level maps of the key viral proteins in record time. “Work that would normally have taken months—or possibly even years—has been completed in weeks,” noted the editors of Nature. …

By then, however, the optimism and sense of possibility that defined the early days were long gone. Advocates for pooling and open science, who seemed ascendant and even unstoppable that winter, confronted the possibility they’d been outmatched and outmaneuvered by the most powerful man in global public health.

In April, Bill Gates launched a bold bid to manage the world’s scientific response to the pandemic. Gates’s Covid-19 ACT-Accelerator expressed a status quo vision for organizing the research, development, manufacture, and distribution of treatments and vaccines. Like other Gates-funded institutions in the public health arena, the Accelerator was a public-private partnership based on charity and industry enticements. Crucially, and in contrast to the C-TAP, the Accelerator enshrined Gates’s long-standing commitment to respecting exclusive intellectual property claims. Its implicit arguments—that intellectual property rights won’t present problems for meeting global demand or ensuring equitable access, and that they must be protected, even during a pandemic—carried the enormous weight of Gates’s reputation as a wise, beneficent, and prophetic leader. …

“Early on, there was space for Gates to have a major impact in favor of open models,” says Manuel Martin, a policy adviser to the Médecins Sans Frontières Access Campaign. “But senior people in the Gates organization very clearly sent out the message: Pooling was unnecessary and counterproductive. They dampened early enthusiasm by saying that I.P. is not an access barrier in vaccines. That’s just demonstratively false.”…

“Things could have gone either way,” says Love, “but Gates wanted exclusive rights maintained. He acted fast to stop the push for sharing the knowledge needed to make the products—the know-how, the data, the cell lines, the tech transfer, the transparency that is critically important in a dozen ways. The pooling approach represented by C-TAP included all of that. Instead of backing those early discussions, he raced ahead and signaled support for business-as-usual on intellectual property by announcing the ACT-Accelerator in March.” …”

 

Opinion | Joe Biden Made a Promise to Scientists. He Can Still Keep It. – The New York Times

“Researchers who receive federal help consistently fail to report their results to the public. The government should hold them accountable….

Researchers using federal funds to conduct cancer trials — experiments involving drugs or medical devices that rely on volunteer subjects — were sometimes taking more than a year to report their results to the N.I.H., as required. “If you don’t report, the law says you shouldn’t get any funding,” he said, citing an investigation I had published in Stat with my colleague Talia Bronshtein. “Doc, I’m going to find out if it’s true, and if it’s true, I’m going to cut funding. That’s a promise.”

It was true then. It’s true now. More than 150 trials completed since 2017 by the N.I.H’s National Cancer Institute, which leads the $1.8 billion Moonshot effort, should have reported results by now. About two-thirds reported after their deadlines or not at all, according to a University of Oxford website that tracks clinical trials regulated by the Food and Drug Administration and National Institutes of Health. Some trial results are nearly two years overdue. Over all, government-sponsored scientists have complied less than half the time for trial results due since 2018. (A spokeswoman for the N.I.H. said, “We are willing to do all measures to ensure compliance with ClinicalTrials.gov results reporting.”)…

In 2016, Dr. Francis Collins, the director of the National Institutes of Health, announced that the agency would begin penalizing researchers for failing to comply with its reporting requirements. “We are serious about this,” he said at the time. Yet in the years since, neither the F.D.A. nor N.I.H. has enforced the law. …”

The American Sociological Association is collapsing and its organization is a perpetual stagnation machine – Family Inequality

“One virtually inevitable outcome is the association further committing to its reliance on paywalled journal publishing and the profit-maximizing contract with Sage, and opposing efforts to open access to research for the public….

I can’t say that the things I tried to do on the publications committee would have had a positive effect on ASA membership, journal rankings, majors, or any other metric of impact for the association. However, I do believe what I proposed would have helped the association take a few small steps in the direction of keeping up with the social science community on issues of research transparency and openness. In November I reported how, more than two years ago now, I proposed that the association adopt the Transparency and Openness Promotion Guidelines from the Center for Open Science, and to start using their Open Science Badges, which recognize authors who provide open data, open materials, or use preregistration for their studies. (In the November post I discussed the challenge of cultural and institutional change on this issue, and why it’s important, so I won’t repeat that here.)…

While I’m at it, I should update you on the petition many of you signed in December 2019, in opposition to the ASA leadership sending a letter to President Trump against a potential federal policy that would make the results of taxpayer-funded research immediately available to the public for free — presumably at some cost to ASA’s paywall revenues. At the January 2020 meeting the publications committee passed two motions:

For the Committee on Publications to express opposition to the decision by the ASA to sign the December 18, 2019 letter.
To encourage Council to discuss implications of the existing embargo and possible changes to the policy and to urge decisionmakers to consult with the scientific community before making executive orders.

Hospitals Reportedly Hiding Mandatory Pricing Data From Search Engines

“Starting this year, hospitals across the country were mandated to disclose their rates for certain medical procedures as part of a new federal rule meant to bring a bit more transparency to the public health sector. But according to a new Wall Street Journal investigation, hundreds of hospitals nationwide have found a relatively sneaky way to keep the public from prying into their proprietary pricing data….”

Critics decry access, transparency issues with key trove of coronavirus sequences | Science | AAAS

“In December 2020, software developer Angie Hinrichs at the University of California, Santa Cruz (UCSC), applied for access to a labor-saving data feed from GISAID, a nonprofit database of viral sequences including those of the pandemic coronavirus, SARS-CoV-2. She wanted GISAID’s data so she could display mutations on UCSC’s coronavirus Genome Browser. That tool ties any position in the virus’ nearly 30,000-letter genome to other scientific information, much as Google Maps shows gas stations and restaurants near addresses.

With more than 700,000 genomes from more than 160 countries, GISAID is by far the world’s largest database of SARS-CoV-2 sequences. Access to the free, nonprofit repository has become vital to Hinrichs and thousands of other scientists and public health agencies tracking the virus’ alarmingly rapid evolution.

But instead of getting a direct data feed, Hinrichs lost her existing access to two conveniently packaged GISAID files that are the next best thing. She emailed GISAID repeatedly pleading for restored access, but hasn’t gotten it. Since December, she has had to download GISAID’s sequences 10,000 at a time, with no access to most of the metadata unless she looks at each of the 10,000 sequences individually. …

But critics complain about GISAID’s constraints on access, chief among them its prohibition on resharing of its data. Its agreement for access to the direct data feed also requires applicants to use only GISAID data in their websites and tools, as well as only GISAID-approved strain names. (GISAID says allowing users to mix data on their websites “would duplicate data already in GISAID, resulting in bias and distorted results.”)….”

Critics decry access, transparency issues with key trove of coronavirus sequences | Science | AAAS

“In December 2020, software developer Angie Hinrichs at the University of California, Santa Cruz (UCSC), applied for access to a labor-saving data feed from GISAID, a nonprofit database of viral sequences including those of the pandemic coronavirus, SARS-CoV-2. She wanted GISAID’s data so she could display mutations on UCSC’s coronavirus Genome Browser. That tool ties any position in the virus’ nearly 30,000-letter genome to other scientific information, much as Google Maps shows gas stations and restaurants near addresses.

With more than 700,000 genomes from more than 160 countries, GISAID is by far the world’s largest database of SARS-CoV-2 sequences. Access to the free, nonprofit repository has become vital to Hinrichs and thousands of other scientists and public health agencies tracking the virus’ alarmingly rapid evolution.

But instead of getting a direct data feed, Hinrichs lost her existing access to two conveniently packaged GISAID files that are the next best thing. She emailed GISAID repeatedly pleading for restored access, but hasn’t gotten it. Since December, she has had to download GISAID’s sequences 10,000 at a time, with no access to most of the metadata unless she looks at each of the 10,000 sequences individually. …

But critics complain about GISAID’s constraints on access, chief among them its prohibition on resharing of its data. Its agreement for access to the direct data feed also requires applicants to use only GISAID data in their websites and tools, as well as only GISAID-approved strain names. (GISAID says allowing users to mix data on their websites “would duplicate data already in GISAID, resulting in bias and distorted results.”)….”

Amazon’s monopoly is squeezing your public library, too – The Washington Post

“Turns out, the tech giant [Amazon] has also become a publishing powerhouse — and it won’t sell downloadable versions of its more than 10,000 e-books or tens of thousands of audiobooks to libraries. That’s right, for a decade, the company that killed bookstores has been starving the reading institution that cares for kids, the needy and the curious. And that’s turned into a mission-critical problem during a pandemic that cut off physical access to libraries and left a lot of people unable to afford books on their own….

Amazon is the only big publisher that flat-out blocks library digital collections. …

In testimony to Congress, the American Library Association called digital sales bans like Amazon’s “the worst obstacle for libraries” moving into the 21st century….

“All books in all formats should be available through libraries. Authors want their books available through libraries,” Mary Rasenberger, executive director of the Authors Guild, told me….”

 

Amazon’s monopoly is squeezing your public library, too – The Washington Post

“Turns out, the tech giant [Amazon] has also become a publishing powerhouse — and it won’t sell downloadable versions of its more than 10,000 e-books or tens of thousands of audiobooks to libraries. That’s right, for a decade, the company that killed bookstores has been starving the reading institution that cares for kids, the needy and the curious. And that’s turned into a mission-critical problem during a pandemic that cut off physical access to libraries and left a lot of people unable to afford books on their own….

Amazon is the only big publisher that flat-out blocks library digital collections. …

In testimony to Congress, the American Library Association called digital sales bans like Amazon’s “the worst obstacle for libraries” moving into the 21st century….

“All books in all formats should be available through libraries. Authors want their books available through libraries,” Mary Rasenberger, executive director of the Authors Guild, told me….”

 

Access Denied: Federal Website Governance Under the Trump Administration

“The Trump administration pushed the boundaries of rules, guidelines, and norms in most areas of governance. Manipulating public information was a key tactic, which included dramatic and damaging changes to federal agency websites relating to environmental regulations. These changes led the Environmental Data and Governance Initiative (EDGI) to identify acute gaps in federal website governance and develop recommendations for reforms under the Biden administration and beyond. Websites are the primary means by which federal environmental agencies communicate with the public and serve as resources paid for by American tax dollars to benefit the public. Changes to language, content, or access to federal websites can directly affect public knowledge of and participation in environmental decision-making. While considerable guidance exists for the delivery of federal digital services, there is scant policy focused on the web content provided by federal agencies, and born-digital resources are by and large excluded from record-keeping laws. There are no repercussions, for example, for agencies stripping websites that contain inconvenient factual information for a given political agenda….”

New Report Shows Pattern Under Trump of Federal Agencies Removing Public Information Prior to Environmental Proceedings – Environmental Data and Governance Initiative

“Today, the Environmental Data & Governance Initiative (EDGI) releases Access Denied: Federal Web Governance Under the Trump Administration. The report examines the Trump administration’s management of federal websites related to environmental regulation and makes recommendations for the Biden administration moving forward. Currently, there are few policies governing website content.

Access Denied highlights the need to address these policy gaps. It’s the most comprehensive report yet from EDGI’s website monitoring program, which has monitored federal environmental websites ever since Trump took office in January 2017, documenting more than 1,000 changes.

Websites are how federal agencies communicate with the public, and changes to them can impact public participation in environmental regulatory processes. The information that’s available—or unavailable—on federal websites matters for the health of democracy and the environment….”

OSF Preprints | A survey of researchers’ needs and priorities for data sharing

Abstract:  PLOS has long supported Open Science. One of the ways in which we do so is via our stringent data availability policy established in 2014. Despite this policy, and more data sharing policies being introduced by other organizations, best practices for data sharing are adopted by a minority of researchers in their publications. Problems with effective research data sharing persist and these problems have been quantified by previous research as a lack of time, resources, incentives, and/or skills to share data.

  In this study we built on this research by investigating the importance of tasks associated with data sharing, and researchers’ satisfaction with their ability to complete these tasks. By investigating these factors we aimed to better understand opportunities for new or improved solutions for sharing data. In May-June 2020 we surveyed researchers from Europe and North America to rate tasks associated with data sharing on (i) their importance and (ii) their satisfaction with their ability to complete them. We received 728 completed and 667 partial responses. We calculated mean importance and satisfaction scores to highlight potential opportunities for new solutions to and compare different cohorts. Tasks relating to research impact, funder compliance, and credit had the highest importance scores. 52% of respondents reuse research data but the average satisfaction score for obtaining data for reuse was relatively low. Tasks associated with sharing data were rated somewhat important and respondents were reasonably well satisfied in their ability to accomplish them. Notably, this included tasks associated with best data sharing practice, such as use of data repositories. However, the most common method for sharing data was in fact via supplemental files with articles, which is not considered to be best practice. We presume that researchers are unlikely to seek new solutions to a problem or task that they are satisfied in their ability to accomplish, even if many do not attempt this task. This implies there are few opportunities for new solutions or tools to meet these researcher needs. Publishers can likely meet these needs for data sharing by working to seamlessly integrate existing solutions that reduce the effort or behaviour change involved in some tasks, and focusing on advocacy and education around the benefits of sharing data. There may however be opportunities – unmet researcher needs – in relation to better supporting data reuse, which could be met in part by strengthening data sharing policies of journals and publishers, and improving the discoverability of data associated with published articles.

Evaluation of Data Sharing After Implementation of the International Committee of Medical Journal Editors Data Sharing Statement Requirement | Medical Journals and Publishing | JAMA Network Open | JAMA Network

“Question  What are the rates of declared and actual sharing of clinical trial data after the medical journals’ implementation of the International Committee of Medical Journal Editors data sharing statement requirement?

Findings  In this cross-sectional study of 487 clinical trials published in JAMA, Lancet, and New England Journal of Medicine, 334 articles (68.6%) declared data sharing. Only 2 (0.6%) individual-participant data sets were actually deidentified and publicly available on a journal website, and among the 89 articles declaring that individual-participant data would be stored in secure repositories, data from only 17 articles were found in the respective repositories as of April 10, 2020.

Meaning  These findings suggest that there is a wide gap between declared and actual sharing of clinical trial data.”