“COAlition S and the Global Young Academy are joining forces to develop a Plan S Monitor Task Force. Plan S is a radical and controversial initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funders. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms.
The aim of the Plan S Monitor Task Force is to provide robust indicators by which the impact of Plan S on the research and publication ecosystem can be continuously evaluated. The impact of major policy changes such as Plan S is hard to predict, so it is essential to closely follow their effect from the start. For this, the Task Force will develop key indicators that will allow it to monitor the current situation and every phase of the implementation of Plan S. This will enable lessons to be learned, shared and implemented in a timely fashion to enhance the positive effects and reduce any negative effects of Plan S.”
“We face multiple challenges as we develop and implement institution-wide policies to help support an open and information-rich future within our universities. Our ability to work across multiple complex units within the university, to align our priorities and interests, and to understand how decisions are made within our institutions is critical to the success and sustainability of policies and the infrastructure needed to support them.
This course offers an opportunity to engage deeply in how policies and supporting implementing structures are developed, agreed upon, and sustained. Participants will share practice and experiences to broaden the discussion and help find commonalities. Throughout the course, we will be using a range of teaching and workshop tools that in themselves can be repurposed by participants for sessions they might wish to run subsequent to the course….”
“The biggest change is the one-year postponement of when the full open-access mandate of Plan S will take effect; it will now apply to 2021 research proposals, which will start to affect publications over the following years. In addition, Plan S organizers have scrapped the proposed limit to the amount of money funders will provide for journals’ OA article-processing charges (APCs). The new guidelines also discuss ways in which researchers can comply with Plan S and clarify the initiative’s stance on publishing practices such as hybrid journals that charge both subscription fees for readers and APCs for researchers who choose to publish OA articles….”
Abstract: There is an increasing focus on the part of academic institutions, funding agencies, and publishers, if not researchers themselves, on preservation and sharing of research data. Motivations for sharing include research integrity, replicability, and reuse. One of the barriers to publishing data is the extra work involved in preparing data for publication once a journal article and its supporting information have been completed. In this work, a method is described to generate both human and machine-readable supporting information directly from the primary instrumental data files and to generate the metadata to ensure it is published in accordance with findable, accessible, interoperable, and reusable (FAIR) guidelines. Using this approach, both the human readable supporting information and the primary (raw) data can be submitted simultaneously with little extra effort. Although traditionally the data package would be sent to a journal publisher for publication alongside the article, the data package could also be published independently in an institutional FAIR data repository. Workflows are described that store the data packages and generate metadata appropriate for such a repository. The methods both to generate and to publish the data packages have been implemented for NMR data, but the concept is extensible to other types of spectroscopic data as well.
Abstract: Shared scientific resources, also known as core facilities, support a significant portion of the research conducted at biomolecular research institutions. The Association of Biomolecular Resource Facilities (ABRF) established the Committee on Core Rigor and Reproducibility (CCoRRe) to further its mission of integrating advanced technologies, education, and communication in the operations of shared scientific resources in support of reproducible research. In order to first assess the needs of the scientific shared resource community, the CCoRRe solicited feedback from ABRF members via a survey. The purpose of the survey was to gain information on how U.S. National Institutes of Health (NIH) initiatives on advancing scientific rigor and reproducibility influenced current services and new technology development. In addition, the survey aimed to identify the challenges and opportunities related to implementation of new reporting requirements and to identify new practices and resources needed to ensure rigorous research. The results revealed a surprising unfamiliarity with the NIH guidelines. Many of the perceived challenges to the effective implementation of best practices (i.e., those designed to ensure rigor and reproducibility) were similarly noted as a challenge to effective provision of support services in a core setting. Further, most cores routinely use best practices and offer services that support rigor and reproducibility. These services include access to well-maintained instrumentation and training on experimental design and data analysis as well as data management. Feedback from this survey will enable the ABRF to build better educational resources and share critical best-practice guidelines. These resources will become important tools to the core community and the researchers they serve to impact rigor and transparency across the range of science and technology.
“This special one day workshop for data and information professionals, information technologists, and for disciplinary scientists interested in effective data sharing is focused on the wave of activities related to making data “FAIR” (Findable, Accessible, Interoperable, and Reusable).
We will focus on the implementations and ultimate impacts and implications, especially as data is made FAIR for people and machines….”
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….”