Implementation of FAIR (findable, accessible, interoperable, and reusable) offers significant return on investment (ROI) but requires major changes in research culture, incentives, and substantial funding, and implementation is hindered by the need to coordinate across European Union’s member states.
FAIR is constituted by data objects and a wider technical and data ecosystem.
Publishers’ role is broad but prescribed in this report – although there may be business opportunities.
While the continued validity of non?open data is acknowledged, the report recognizes that ROI is maximized where data are both FAIR and open….”
Abstract: Compelling research has recently shown that cancer is so heterogeneous that single research centres cannot produce enough data to fit prognostic and predictive models of sufficient accuracy. Data sharing in precision oncology is therefore of utmost importance. The Findable, Accessible, Interoperable and Reusable (FAIR) Data Principles have been developed to define good practices in data sharing. Motivated by the ambition of applying the FAIR Data Principles to our own clinical precision oncology implementations and research, we have performed a systematic literature review of potentially relevant initiatives. For clinical data, we suggest using the Genomic Data Commons model as a reference as it provides a field-tested and well-documented solution. Regarding classification of diagnosis, morphology and topography and drugs, we chose to follow the World Health Organization standards, i.e. ICD10, ICD-O-3 and Anatomical Therapeutic Chemical classifications, respectively. For the bioinformatics pipeline, the Genome Analysis ToolKit Best Practices using Docker containers offer a coherent solution and have therefore been selected. Regarding the naming of variants, we follow the Human Genome Variation Society’s standard. For the IT infrastructure, we have built a centralized solution to participate in data sharing through federated solutions such as the Beacon Networks.
Abstract: Changes brought about by the Internet to Scholarly Communication and the spread of Open Access movement, have made it possible to increase the number of potential readers of published research dramatically. This two-phase study aims, at first, to assert the satisfaction of the potential for increased open access to articles published by authors at the University of Coimbra, in a context when there was no stimulus for the openness of published science other than an institutional mandate set by the University policy on Open Access (“Acesso Livre”). The satisfaction of the access openness was measured by observing the actual archiving behavior of researchers (either directly or through their agents). We started by selecting the top journal titles used to publish the STEM research of the University of Coimbra (2004-2013) by using Thomson Reuters’ Science Citation Index (SCI). These titles were available at the University libraries or through online subscriptions, some of them in open access (21%). By checking the journals’ policy at the time regarding self-archiving at the SHERPA/RoMEO service, we found that the percentage of articles in Open Access (OA) could rise to 80% if deposited at Estudo Geral, the Institutional Repository of the University of Coimbra, as prescribed by the Open Access Policy of the University. As we concluded by verifying the deposit status of every single paper of researchers of the University that published in those journals, this potential was far from being fulfilled, despite the existence of the institutional mandate and favorable editorial conditions. We concluded, therefore, that an institutional mandate was not sufficient by itself to fully implement an open access policy and to close the gap between publication and access. The second phase of the study, to follow, will rescan the status of published papers in a context where the Portuguese public funding agency, the Fundação para a Ciência e a Tecnologia, introduced in 2014 a new significant stimulus for open access in science. The FCT Open Access Policy stipulates that publicly funded published research must be available as soon as possible in a repository of the Portuguese network of scientific repositories, RCAAP, which integrates the Estudo Geral.
“Authors not responding to your emails to self-archive in your institutional repository, or just getting started? Our tried and tested templates are here to help get authors enthusiastic and educated about self-archiving. There’s one template for every situation, and each template is ready to use, backed up with performance data, and designed by experimentation and experience….”
“Plan S, the program to crack down on scientific journals’ paywalls led by European research funders, has fleshed out and relaxed some of its rules in revised implementation guidelinespublished today. The update addresses many concerns raised by researchers, librarians, and scientific publishers about Plan S’s rollout, allowing more time before full, immediate open access (OA) is required and dropping the proposed cap on publishing fees that funders will pay to journals.
The architects of Plan S “have engaged in a good quality dialogue” with the people and institutions that are going to deal with the plan’s consequences, says Lidia Borrell-Damián, director for reseach and innovation at the European University Association in Brussels. As a result, the revised guidelines seem “much more nuanced and more realistic” than the initial set, says astrophysicist Luke Drury, former president of the Royal Irish Academy in Dublin.
Still unclear is whether the changes will convince other funders to join the movement. And the plan’s fiercest detractors are unmoved….”
“With effect from 2021, all scholarly publications on the results from research funded by public or private grants provided by national, regional and international research councils and funding bodies, must be published in Open Access Journals, on Open Access Platforms, or made immediately available through Open Access Repositories without embargo….”
“Following a large consultation, we have updated our open access (OA) policy so it now aligns with Plan S. The changes will apply from 1 January 2021. …
These are the key changes to our OA policy.
All Wellcome-funded research articles must be made freely available through PubMed Central (PMC) and Europe PMC at the time of publication. We previously allowed a six-month embargo period. This change will make sure that the peer-reviewed version is freely available to everyone at the time of publication.
All articles must be published under a Creative Commons attribution licence (CC-BY), unless we have agreed, as an exception, to allow publication under a CC-BY-ND licence. We previously only required a CC-BY licence when an article processing charge (APC) was paid. This change will make sure that others – including commercial entities and AI/text-data mining services – can reuse our funded research to discover new knowledge.
Authors or their institutions must retain copyright for their research articles and hold the rights necessary to make a version of the article immediately available under a compliant open licence.
We will no longer cover the cost of OA publishing in subscription journals (‘hybrid OA’), outside of a transformative arrangement. We previously supported this model, but no longer believe that it supports a transition to full OA.
Where there is a significant public health benefit to preprints being shared widely and rapidly, such as a disease outbreak, these preprints must be published:
before peer review
on an approved platform that supports immediate publication of the complete manuscript
under a CC-BY licence.
This is a new requirement which will make sure that important research findings are shared as soon possible and before peer review.
Wellcome-funded organisations must sign or publicly commit to the San Francisco Declaration on Research Assessment(opens in a new tab) (DORA), or an equivalent. We may ask organisations to show that they’re complying with this as part of our organisation audits. This is a new requirement to encourage organisations to consider the intrinsic merit of the work when making promotion and tenure decisions, not just the title of the journal or publisher….”
“The revised Plan S maintains the fundamental principles
No scholarly publication should be locked behind a paywall;
Open Access should be immediate i.e., without embargoes;
Full Open Access is implemented by the default use of a Creative Commons Attribution CC BY licence as per the Berlin Declaration;
Funders commit to support Open Access publication fees at a reasonable level;
Funders will not support publication in hybrid (or mirror/sister) journals unless they are part of a transformative arrangement with a clearly defined endpoint.
But a number of important changes are proposed in the implementation guidance
In order to provide more time for researchers and publishers to adapt to the changes under Plan S, the timeline has been extended by one year to 2021;
Transformative agreements will be supported until 2024;
More options for transitional arrangements (transformative agreements, transformative model agreements, ‘transformative journals’) are supported;
Greater clarity is provided about the various compliance routes: Plan S is NOT just about a publication fee model of Open Access publishing. cOAlition S supports a diversity of sustainability models for Open Access journals and platforms;
More emphasis is put on changing the research reward and incentive system: cOAlition S funders explicitly commit to adapt the criteria by which they value researchers and scholarly output;
The importance of transparency in Open Access publication fees is emphasised in order to inform the market and funders’ potential standardisation and capping of payments of such fees;
The technical requirements for Open Access repositories have been revised….”
“A major push by some science agencies to make the research they fund open-access on publication — Plan S — has been delayed by a year. Funders now don’t have to start implementing the initiative until 2021, the agencies announced today, to give researchers and publishers more time to adapt to the changes the bold plan requires….”
In view of the forthcoming publication of the Plan S’ revised Implementation Guidance, The Guild has published a position paper presenting its proposals for a successful transition towards Open Access. With these recommendations, The Guild builds on its submission to the Plan S consultation, contributing to a wider debate about how Plan S can help realise the ambitions of Open Science.