Category: Open Science

"Data Management and Sharing in Neuroimaging: Practices and Perceptions of MRI Researchers"

John A. Borghi and Ana E. Van Gulick have published "Data Management and Sharing in Neuroimaging: Practices and Perceptions of MRI Researchers" in PLOS ONE.

Here's an excerpt:

Neuroimaging methods such as magnetic resonance imaging (MRI) involve complex data collection and analysis protocols, which necessitate the establishment of good research data management (RDM). Despite efforts within the field to address issues related to rigor and reproducibility, information about the RDM-related practices and perceptions of neuroimaging researchers remains largely anecdotal. To inform such efforts, we conducted an online survey of active MRI researchers that covered a range of RDM-related topics. Survey questions addressed the type(s) of data collected, tools used for data storage, organization, and analysis, and the degree to which practices are defined and standardized within a research group. Our results demonstrate that neuroimaging data is acquired in multifarious forms, transformed and analyzed using a wide variety of software tools, and that RDM practices and perceptions vary considerably both within and between research groups, with trainees reporting less consistency than faculty. Ratings of the maturity of RDM practices from ad-hoc to refined were relatively high during the data collection and analysis phases of a project and significantly lower during the data sharing phase. Perceptions of emerging practices including open access publishing and preregistration were largely positive, but demonstrated little adoption into current practice.

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"Supporting the Proliferation of Data-Sharing Scholars in the Research Ecosystem"

Ali Krzton has published "Supporting the Proliferation of Data-Sharing Scholars in the Research Ecosystem" in the Journal of eScience Librarianship.

Here's an excerpt:

Librarians champion the value of openness in scholarship and have been powerful advocates for the sharing of research data. College and university administrators have recently joined in the push for data sharing due to funding mandates. However, the researchers who create and control the data usually determine whether and how data is shared, so it is worthwhile to look at what they are incentivized to do. The current scholarly publishing landscape plus the promotion and tenure process create a "prisoner’s dilemma" for researchers as they decide whether or not to share data, consistent with the observation that researchers in general are eager for others to share data but reluctant to do so themselves. If librarians encourage researchers to share data and promote openness without simultaneously addressing the academic incentive structure, those who are intrinsically motivated to share data will be selected against via the promotion and tenure process. This will cause those who are hostile to sharing to be disproportionately recruited into the senior ranks of academia. To mitigate the risk of this unintended consequence, librarians must advocate for a change in incentives alongside the call for greater openness. Highly-cited datasets must be given similar weight to highly-cited articles in promotion and tenure decisions in order for researchers to reap the rewards of their sharing. Librarians can help by facilitating data citation to track the impact of datasets and working to persuade higher administration of the value of rewarding data sharing in tenure and promotion.

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Want to Support Open Access? Volunteer for the Open Access Tracking Project

The Open Access Tracking Project (OATP) provides a constant stream of up-to-date information about open access issues in a primary feed and in a number of secondary feeds that focus on specialized OA subtopics. It offers the primary feed in a variety of distribution options, including email, Google+, HTML, RSS, Twitter, and others. It is an invaluable source of information for open access advocates, research data specialists, and scholarly communication specialists, and it provides important support for the open access movement as a whole.

Based at the Harvard Open Access Project, the OATP was launched by Peter Suber. Suber's SPARC Open Access Newsletter and his Free Online Scholarship Newsletter played an important part in getting the open access movement off the ground. The OATP continues the mission of those groundbreaking publications using the open source TagTeam software, which was developed for the OATP.

Launched with the help of grant funding, the OATP will enter a new an all-volunteer phase at the end of August 2018. To continue this crowd-sourced project, new volunteers are needed. You can help move the OA agenda forward by being one of them. This wiki page explains how you can join the team and start tagging.

By volunteering just a bit of time to the OATP, you can make a significant difference.

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"A Funder-Imposed Data Publication Requirement Seldom Inspired Data Sharing"

Jessica L. Couture et al. have published "A Funder-Imposed Data Publication Requirement Seldom Inspired Data Sharing" in PLOS ONE.

Here's an excerpt:

Growth of the open science movement has drawn significant attention to data sharing and availability across the scientific community. In this study, we tested the ability to recover data collected under a particular funder-imposed requirement of public availability. We assessed overall data recovery success, tested whether characteristics of the data or data creator were indicators of recovery success, and identified hurdles to data recovery. Overall the majority of data were not recovered (26% recovery of 315 data projects), a similar result to journal-driven efforts to recover data. Field of research was the most important indicator of recovery success, but neither home agency sector nor age of data were determinants of recovery. While we did not find a relationship between recovery of data and age of data, age did predict whether we could find contact information for the grantee. The main hurdles to data recovery included those associated with communication with the researcher; loss of contact with the data creator accounted for half (50%) of unrecoverable datasets, and unavailability of contact information accounted for 35% of unrecoverable datasets. Overall, our results suggest that funding agencies and journals face similar challenges to enforcement of data requirements. We advocate that funding agencies could improve the availability of the data they fund by dedicating more resources to enforcing compliance with data requirements, providing data-sharing tools and technical support to awardees, and administering stricter consequences for those who ignore data sharing preconditions./p>

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University of California: "Re: Declaration of Rights and Principles to Transform Scholarly Communication"

The University of California's University Committee on Library and Scholarly Communication has released "Re: Declaration of Rights and Principles to Transform Scholarly Communication."

Here's an excerpt:

1. No copyright transfers. Our authors shall be allowed to retain copyright in their work and grant a Creative Commons Attribution license of their choosing.

2. No restrictions on preprints. Our authors shall have the right to submit for publication work they have previously made available as preprints.

3. No waivers of OA Policy. Publishers shall not require our authors to provide waivers of our Institutional OA Policy as a condition for publishing our work.

4. No delays to sharing. Publishers shall make work by our authors immediately available for harvest or via automatic deposit into our Institutional OA repository or another public archive.

5. No limitations on author reuse. Our authors shall have the right to reuse figures, tables, data, and text from their published work without permission or payment.

6. No impediments to rights reversion. Publishers shall provide a simple process for our authors to regain copyright in their previously published work.

7. No curtailment of copyright exceptions. Licenses shall not restrict, and should instead expressly protect, the rights of authors, institutions, and the public to reuse excerpts of published work consistent with legal exceptions and limitations on copyright such as fair use.

8. No barriers to data availability. Our authors shall have the right to make all of their data, figures, and other supporting materials from their published work publicly available.

9. No constraints on content mining. Publishers shall make licensed materials open, accessible, and machine-readable for text and data mining by our researchers, at no additional cost and under terms that allow retention and reuse of results.

10. No closed metadata. Publishers shall make bibliographic records, usage metrics, and citation data for our authors freely available, easy to parse, and machine-readable.

11. No free labor. Publishers shall provide our Institution with data on peer review and editorial contributions by our authors in support of journals, and such contributions shall be taken into account when determining the cost of our subscriptions or OA fees for our authors.

12. No long-term subscriptions. Publishers shall provide our Institution with plans and timelines for transitioning their subscription journals to OA.

13. No permanent paywalls. Our Institution shall receive perpetual access for previously licensed content and back files shall be made freely available once a journal transitions to OA.

14. No double payments. Publishers shall provide our Institution with data on hybrid OA payments from our authors and such payments shall reduce the cost of our subscriptions.

15. No hidden profits. Publishers shall use transparent pricing for the services they provide our authors when levying article processing charges and other fees associated with publishing.

16. No deals without OA offsets. Our Institution shall only enter into publishing agreements that include offsets for OA publishing by our authors.

17. No new paywalls for our work. Work by our authors shall be made OA on the publisher’s website as part of subscription terms for new journals.

18. No non-disclosure agreements. Publisher agreements with our Institution shall be transparent and shall not contain terms that prevent the sharing of their contents.

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"Open Science Support as a Portfolio of Services and Projects: From Awareness to Engagement"

Birgit Schmidt et al. have published "Open Science Support as a Portfolio of Services and Projects: From Awareness to Engagement" in Publications.

Here's an excerpt:

Together with many other universities worldwide, the University of Göttingen has aimed to unlock the full potential of networked digital scientific communication by strengthening open access as early as the late 1990s. Open science policies at the institutional level consequently followed and have been with us for over a decade. However, for several reasons, their adoption often is still far from complete when it comes to the practices of researchers or research groups. To improve this situation at our university, there is dedicated support at the infrastructural level: the university library collaborates with several campus units in developing and running services, activities and projects in support of open access and open science. This article outlines our main activity areas and aligns them with the overall rationale to reach higher uptake and acceptance of open science practice at the university. The mentioned examples of our activities highlight how we seek to advance open science along the needs and perspectives of diverse audiences and by running it as a multi-stakeholder endeavor. Therefore, our activities involve library colleagues with diverse backgrounds, faculty and early career researchers, research managers, as well as project and infrastructure staff. We conclude with a summary of achievements and challenges to be faced.

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"An Expertise Recommender System Based on Data from an Institutional Repository (DiVA)"

Milena Angelova et al. have self-archived "An Expertise Recommender System Based on Data from an Institutional Repository (DiVA)."

Here's an excerpt:

Finding experts in academics is an important practical problem, e.g. recruiting reviewers for reviewing conference, journal or project submissions, partner matching for research proposals, finding relevant M. Sc. or Ph. D. supervisors etc. In this work, we discuss an expertise recommender system that is built on data extracted from the Blekinge Institute of Technology (BTH) instance of the institutional repository system DiVA. The developed prototype system is evaluated and validated on information extracted from the BTH DiVA installation, concerning thesis supervision of researchers affiliated with BTH. The extracted DiVA classification terms are used to build an ontology that conceptualizes the thesis domain supported by the university. The supervisor profiles of the tutors affiliated with the BTH are constructed based on the extracted DiVA data. These profiles can further be used to identify and recommend relevant subject thesis supervisors.

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Open Science Training Handbook

Fourteen authors have released Open Science Training Handbook.

Here's an excerpt:

Bringing together methods, techniques, and practices, the handbook aims at supporting educators of Open Science. The result is intended as a helpful guide on how to forward knowledge on Open Science principles to our networks, institutions, colleagues, and students. It will instruct and inspire trainers how to create high quality and engaging trainings. Addressing challenges and giving solutions, it will strengthen the community of Open Science trainers who are educating, informing, and inspiring themselves.

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Funder Perspectives on Open Infrastructure

The Open Research Funders Group has released Funder Perspectives on Open Infrastructure.

Here's an excerpt from the announcement:

The Open Research Funders Group (ORFG) recently conducted a survey to better understand funder perspectives with respect to supporting open infrastructure. Sixteen organizations completed the questionnaire, evenly split between ORFG members and other funding bodies. The results suggest an underlying support for open initiatives and the infrastructure buttressing these activities. This is tempered by reservations about how best to discern and smartly invest in open infrastructure projects.

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Open Science: Altmetrics and Rewards

The Mutual Learning Exercise on Open Science has released Open Science: Altmetrics and Rewards.

Here's an excerpt from the announcement:

Its focus is on three topics: 1) The potential of altmetrics—alternative (i.e. non-traditional) metrics that go beyond citations of articles—to foster Open Science; 2) Incentives and rewards for researchers to engage in Open Science activities; 3) Guidelines for developing and implementing national policies for Open Science. It identifies good practices, lists priorities and outlines potential courses of action for the best possible transition to Open Science.

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Version 9 of the Research Data Curation Bibliography Released

Digital Scholarship has released Version 9 of the Research Data Curation Bibliography. This selective bibliography includes over 750 English-language articles, books, and technical reports that are useful in understanding the curation of digital research data in academic and other research institutions. Printed from the HTML page, it is over 130 pages long.

The Research Data Curation Bibliography covers topics such as research data creation, acquisition, metadata, provenance, repositories, management, policies, support services, funding agency requirements, open access, peer review, publication, citation, sharing, reuse, and preservation.

Most sources have been published from January 2009 through December 2017; however, a limited number of earlier key sources are also included. The bibliography includes links to included works.

Abstracts are included in this bibliography if a work is under a Creative Commons Attribution License (BY and national/international variations), a Creative Commons public domain dedication (CC0), or a Creative Commons Public Domain Mark and this is clearly indicated in the work.

The Research Data Curation Bibliography is under a Creative Commons Attribution 4.0 International License.

Journal Access Problem Note

The International Journal of Digital Curation server is having access problems today resulting in the following error message: "DB Error: Can't create/write to file '/var/tmp/#sql_565_1.MAI' (Errcode: 28)."

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"Are the FAIR Data Principles Fair?"

Alastair Dunning, Madeleine de Smaele, and Jasmin Bõhmer have published "Are the FAIR Data Principles Fair?" in the International Journal of Digital Curation.

Here's an excerpt:

This practice paper describes an ongoing research project to test the effectiveness and relevance of the FAIR Data Principles. Simultaneously, it will analyse how easy it is for data archives to adhere to the principles. The research took place from November 2016 to January 2017, and will be underpinned with feedback from the repositories.

The FAIR Data Principles feature 15 facets corresponding to the four letters of FAIR—Findable, Accessible, Interoperable, Reusable. These principles have already gained traction within the research world. The European Commission has recently expanded its demand for research to produce open data. The relevant guidelines1are explicitly written in the context of the FAIR Data Principles. Given an increasing number of researchers will have exposure to the guidelines, understanding their viability and suggesting where there may be room for modification and adjustment is of vital importance.

This practice paper is connected to a dataset(Dunning et al.,2017) containing the original overview of the sample group statistics and graphs, in an Excel spreadsheet. Over the course of two months, the web-interfaces, help-pages and metadata-records of over 40 data repositories have been examined, to score the individual data repository against the FAIR principles and facets. The traffic-light rating system enables colour-coding according to compliance and vagueness. The statistical analysis provides overall, categorised, on the principles focussing, and on the facet focussing results.

The analysis includes the statistical and descriptive evaluation, followed by elaborations on Elements of the FAIR Data Principles, the subject specific or repository specific differences, and subsequently what repositories can do to improve their information architecture.

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Implementation Roadmap for the European Open Science Cloud

The European Commission has released Implementation Roadmap for the European Open Science Cloud.

Here's an excerpt from the announcement:

Overall, the document presents the results and available evidence from an extensive and conclusive consultation process that started with the publication of the Communication: European Cloud initiative (COM(2016)178) in April 2016.

The consultation upheld the intervention logic presented in the Communication, to create a fit for purpose pan-European federation of research data infrastructures, with a view to moving from the current fragmentation to a situation where data is easy to store, find, share and re-use.

On the basis of the consultation, the implementation Roadmap gives and overview of six actions lines for the implementation of the EOSC:

a) architecture, b) data, c) services, d) access & interfaces, e) rules and f) governance.

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"Converting the Literature of a Scientific Field to Open Access through Global Collaboration: The Experience of SCOAP3 in Particle Physics"

Alexander Kohls and Orcid and Salvatore MeleOrcid have published "Converting the Literature of a Scientific Field to Open Access through Global Collaboration: The Experience of SCOAP3 in Particle Physics" in Publications.

Here's an excerpt:

Gigantic particle accelerators, incredibly complex detectors, an antimatter factory and the discovery of the Higgs boson—this is part of what makes CERN famous. Only a few know that CERN also hosts the world largest Open Access initiative: SCOAP3. The Sponsoring Consortium for Open Access Publishing in Particle Physics started operation in 2014 and has since supported the publication of 20,000 Open Access articles in the field of particle physics, at no direct cost, nor burden, for individual authors worldwide. SCOAP3 is made possible by a 3000-institute strong partnership, where libraries re-direct funds previously used for subscriptions to 'flip' articles to 'Gold Open Access'. With its recent expansion, the initiative now covers about 90% of the journal literature of the field. This article describes the economic principles of SCOAP3, the collaborative approach of the partnership, and finally summarizes financial results after four years of successful operation.

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Global Access to Research Software: The Forgotten Pillar of Open Science Implementation

The Global Young Academy has released Global Access to Research Software: The Forgotten Pillar of Open Science Implementation .

Here's an excerpt:

The Global Young Academy (GYA), in collaboration with the Oxford-based organisation INASP, carried out a pilot survey to assess the quantity and quality of access to proprietary and open source software among researchers from all disciplines. . . .Emphasis was placed on gathering data from researchers based in Bangladesh, Ghana and Nigeria, whose access to and use of research software had not yet been extensively documented.

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"Predator in the Pool? A Quantitative Evaluation of Non-indexed Open Access Journals in Aquaculture Research"

Jeff C. Clements et al. have published "Predator in the Pool? A Quantitative Evaluation of Non-indexed Open Access Journals in Aquaculture Research" in Frontiers in Marine Science.

Here's an excerpt:

Predatory open access (OA) journals can be defined as non-indexed journals that exploit the gold OA model for profit, often spamming academics with questionable e-mails promising rapid OA publication for a fee. In aquaculture—a rapidly growing and highly scrutinized field—the issue of such journals remains undocumented. We employed a quantitative approach to determine whether attributes of scientific quality and rigor differed between OA aquaculture journals not indexed in reputable databases and well-established, indexed journals. Using a Google search, we identified several non-indexed OA journals, gathered data on attributes of these journals and articles therein, and compared these data to well-established aquaculture journals indexed in quality-controlled bibliometric databases. We then used these data to determine if non-indexed journals were likely predatory OA journals and if they pose a potential threat to aquaculture research. On average, non-indexed OA journals published significantly fewer papers per year, had cheaper fees, and were more recently established than indexed journals. Articles in non-indexed journals were, on average, shorter, had fewer authors and references, and spent significantly less time in peer review than their indexed counterparts; the proportion of articles employing rigorous statistical analyses was also lower for non-indexed journals. Additionally, articles in non-indexed journals were more likely to be published by scientists from developing nations. Worryingly, non-indexed journals were more likely to be found using a Google search, and their articles superficially resembled those in indexed journals. These results suggest that the non-indexed aquaculture journals identified herein are likely predatory OA journals and pose a threat to aquaculture research and the public education and perception of aquaculture. Several points of reference from this study, in combination, may help scientists and the public more easily identify these possibly predatory journals, as these journals were typically established after 2010, publishing <20 papers per year, had fees <$1,000, and published articles <80 days after submission. Subsequently checking reputable and quality-controlled databases such as the Directory of Open Access Journals, Web of Science, Scopus, and Thompson Reuters can aid in confirming the legitimacy of non-indexed OA journals and can facilitate avoidance of predatory OA aquaculture journals.

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"Data Availability, Reusability, and Analytic Reproducibility: Evaluating the Impact of a Mandatory Open Data Policy at the Journal Cognition"

Tom Hardwicke et al. have self-archived "Data Availability, Reusability, and Analytic Reproducibility: Evaluating the Impact of a Mandatory Open Data Policy at the Journal Cognition."

Here's an excerpt:

Access to research data is a critical feature of an efficient, progressive, and ultimately self-correcting scientific ecosystem. But the extent to which in-principle benefits of data sharing are realized in practice is unclear. Crucially, it is largely unknown whether published findings can be reproduced by repeating reported analyses upon shared data ("analytic reproducibility"). To investigate, we conducted an observational evaluation of a mandatory open data policy introduced at the journal Cognition. Interrupted time-series analyses indicated a substantial post-policy increase in data available statements (104/417, 25% pre-policy to 136/174, 78% post-policy), and data that were in-principle reusable (23/104, 22% pre-policy to 85/136, 62%, post-policy). However, for 35 articles with in-principle reusable data, the analytic reproducibility of target outcomes related to key findings was poor: 11 (31%) cases were reproducible without author assistance, 11 (31%) cases were reproducible only with author assistance, and 13 (37%) cases were not fully reproducible despite author assistance. Importantly, original conclusions did not appear to be seriously impacted. Mandatory open data policies can increase the frequency and quality of data sharing. However, suboptimal data curation, unclear analysis specification, and reporting errors can impede analytic reproducibility, undermining the utility of data sharing and the credibility of scientific findings.

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Practical Challenges For Researchers in Data Sharing

Springer Nature has released Practical Challenges For Researchers in Data Sharing.

Here's an excerpt:

This survey aims to understand researcher activity around sharing data at a particular point in the research lifecycle—when they are preparing their work for publication. In this it builds on previously published studies that explore data sharing more generally during the research process. It explores attitudes briefly, but focuses on actions and challenges in sharing data. Responses from over 7,700 researchers enabled us to draw new insights across subject felds and, to a lesser extent, across geographies.

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"Releasing 1.8 Million Open Access Publications from Publisher Systems for Text and Data Mining"

Petr Knoth, Nancy Pontika and Lucas Anastasiou have published "Releasing 1.8 Million Open Access Publications from Publisher Systems for Text and Data Mining" in LSE Impact of Social Sciences.

Here's an excerpt:

Text and data mining offers an opportunity to improve the way we access and analyse the outputs of academic research. But the technical infrastructure of the current scholarly communication system is not yet ready to support TDM to its full potential, even for open access outputs. To address this problem, Petr Knoth, Nancy Pontika and Lucas Anastasiou have developed the CORE Publisher Connector, a toolkit service designed to assist text miners in accessing content though a single machine interface. The Connector aims to solve the heterogeneity among publisher APIs and assist text miners with data collection, provide a centralised point of access to all openly available scientific publications, and provide a high-performance, constantly updated access interface.

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