Open Science – Page 21

"Wide-Open: Accelerating Public Data Release by Automating Detection of Overdue Datasets"

Maxim Grechkin, Hoifung Poon, and Bill Howe have published "Wide-Open: Accelerating Public Data Release by Automating Detection of Overdue Datasets" in PLOS Biology.

Here's an excerpt:

Open data is a vital pillar of open science and a key enabler for reproducibility, data reuse, and novel discoveries. Enforcement of open-data policies, however, largely relies on manual efforts, which invariably lag behind the increasingly automated generation of biological data. To address this problem, we developed a general approach to automatically identify datasets overdue for public release by applying text mining to identify dataset references in published articles and parse query results from repositories to determine if the datasets remain private. We demonstrate the effectiveness of this approach on 2 popular National Center for Biotechnology Information (NCBI) repositories: Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA). Our Wide-Open system identified a large number of overdue datasets, which spurred administrators to respond directly by releasing 400 datasets in one week.

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"Four Decades Of Open Science"

Bernard L. Hecker has published "Four Decades Of Open Science" in Nature Physics.

Here's an excerpt:

INSPIRE, the central information resource of the high-energy physics community, pioneered the open dissemination of scientific literature. I

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An Analysis of Open Data and Open Science Policies in Europe, May 2017

SPARC Europe has released An Analysis of Open Data and Open Science Policies in Europe, May 2017 .

Here's an excerpt from the announcement:

Among the report’s most striking findings: 11 of the 28 European Union member states, as well as Norway and Switzerland, have national, research data-related policies in place. Of these, all were implemented in the past eight years, with most having taken effect recently. In about half of the countries, research data is covered under the same policy that applies to Open Access or Open Science.

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"Making Progress Toward Open Data: Reflections on Data Sharing at PLOS ONE"

Meg Byrne has published "Making Progress Toward Open Data: Reflections on Data Sharing at PLOS ONE" in the EveryONE Blog

Here's an excerpt:

PLOS ONE has published over 65,000 papers with a DAS in the three years since the open data policy was put in place. We were initially concerned we would not be able to consider a significant number of submissions because authors could not share data, but this did not turn out to be the case. Since the implementation of the updated policy, we estimate staff have rejected less than 0.1% of submissions due to authors’ unwillingness or inability to share data. What we have seen is a growing acceptance of data sharing and evolution of data sharing practices. For instance, there has been a steady growth in datasets available directly via public data repositories such as the NCBI databases, Figshare or Dryad. While the proportion of articles with a data availability statement linking to one of these repositories is still relatively low, at around 20% in 2016, the growth is encouraging.

Another 60% of articles include data in the main text and supplementary information. While we strongly recommend discipline-specific open repositories where they exist, we also deposit the supporting information files, figures, and tables included with every article to Figshare and give each of these its own DOI. Thus, in addition to being available via the PLOS ONE article, this content is also available through an external data repository. The remaining 20% of papers have data available upon request due to restrictions acceptable under our policy, including restrictions related to sensitive data or because the data are owned by and available from a third party.

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"The Influence of Journal Submission Guidelines on Author’s Reporting of Statistics and Use of Open Research Practices"

David Giofrè et al. have published "The Influence of Journal Submission Guidelines on Author's Reporting of Statistics and Use of Open Research Practices" in PLOS ONE.

Here's an excerpt:

From January 2014, Psychological Science introduced new submission guidelines that encouraged the use of effect sizes, estimation, and meta-analysis (the "new statistics"), required extra detail of methods, and offered badges for use of open science practices. We investigated the use of these practices in empirical articles published by Psychological Science and, for comparison, by the Journal of Experimental Psychology: General, during the period of January 2013 to December 2015. The use of null hypothesis significance testing (NHST) was extremely high at all times and in both journals. In Psychological Science, the use of confidence intervals increased markedly overall, from 28% of articles in 2013 to 70% in 2015, as did the availability of open data (3 to 39%) and open materials (7 to 31%). The other journal showed smaller or much smaller changes. Our findings suggest that journal-specific submission guidelines may encourage desirable changes in authors’ practices.

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"The World’s Approach towards Publishing in Springer and Elsevier’s APC-Funded Open Access Journals "

College & Research Libraries has released an e-print of "The World's Approach towards Publishing in Springer and Elsevier's APC-Funded Open Access Journals.

Here's an excerpt:

The Netherlands, Norway and Poland ranked highest in terms of their OA shares. This can be attributed to the financial resources allocated to publication in general, and publishing in OA journals, in particular, by the countries. All developed countries and a large number of scientifically lagging and developing nations were found to publish OA articles in the APC journals. The OA papers have been exponentially growing across all the country scientific groups annually. Although the advanced nations published the lion share of the OA-APC papers and exhibited the highest growth, the under-development groups have been displaying high OA growth rates.

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"Open Data, [Open] Access: Linking Data Sharing and Article Sharing in the Earth Sciences"

Samantha Teplitzky has published "Open Data, [Open] Access: Linking Data Sharing and Article Sharing in the Earth Science" in the Journal of Librarianship and Scholarly Communication.

Here's an excerpt:

INTRODUCTION The norms of a research community influence practice, and norms of openness and sharing can be shaped to encourage researchers who share in one aspect of their research cycle to share in another. Different sets of mandates have evolved to require that research data be made public, but not necessarily articles resulting from that collected data. In this paper, I ask to what extent publications in the Earth Sciences are more likely to be open access (in all of its definitions) when researchers open their data through the Pangaea repository. METHODS Citations from Pangaea data sets were studied to determine the level of open access for each article. RESULTS This study finds that the proportion of gold open access articles linked to the repository increased 25% from 2010 to 2015 and 75% of articles were available from multiple open sources.

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Open Data: The Researcher Perspective

Elsevier and the Centre for Science and Technology Studies have released Open Data: The Researcher Perspective .

Here's an excerpt:

Combining information from a bibliometric analysis, a survey and case studies, this report examines how researchers share data, the attitudes of researchers toward sharing data, and why researchers might be reticent to share data.

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"Openness as Social Praxis"

Matthew Longshore Smith and Ruhiya Seward have published "Openness as Social Praxis" in First Monday.

Here's an excerpt:

The paper "Fifty shades of open" by Pomerantz and Peek (2016) highlighted the increasing ambiguity and even confusion surrounding this term. This article builds on Pomerantz and Peek’s attempt to disambiguate the term by offering an alternative understanding to openness —that of social praxis. More specifically, our framing can be broken down into three social processes: open production, open distribution, and open consumption. Each process shares two traits that make them open: you don’t have to pay (free price), and anyone can participate (non-discrimination) in these processes.

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"European Commission Considering Leap into Open-Access Publishing"

Martin Enserink has published "European Commission Considering Leap into Open-Access Publishing" in Science.

Here's an excerpt:

The European Commission, which spends more than £10 billion annually on research, may follow two other big league funders, the Wellcome Trust and the Bill & Melinda Gates Foundation, and set up a “publishing platform” for the scientists it funds, in an attempt to accelerate the transition to open-access publishing in Europe.

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"On the Reuse of Scientific Data"

Irene V. Pasquetto, Bernadette M. Randles, and Christine L. Borgman have published "On the Reuse of Scientific Data" in Data Science Journal.

Here's an excerpt:

Data sharing practices, especially motivations and incentives, have received far more study than has data reuse, perhaps because of the array of contested concepts on which reuse rests and the disparate contexts in which it occurs. Here we explicate concepts of data, sharing, and open data as a means to examine data reuse. We explore distinctions between use and reuse of data. Lastly we propose six research questions on data reuse worthy of pursuit by the community: How can uses of data be distinguished from reuses? When is reproducibility an essential goal? When is data integration an essential goal? What are the tradeoffs between collecting new data and reusing existing data? How do motivations for data collection influence the ability to reuse data? How do standards and formats for data release influence reuse opportunities? We conclude by summarizing the implications of these questions for science policy and for investments in data reuse.

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Towards a Competitive and Sustainable Open Access Publishing Market in Europe

OpenAIRE has released Towards a Competitive and Sustainable Open Access Publishing Market in Europe.

Here's an excerpt:

Without intervention, immediate OA to just half of Europe's scientific publications will not be achieved until 2025 or later. Readers in academia have greater access, to more content, than ever before. Despite this, the majority of publications arising from public investments in research remain in accessible to the public, and the growth of OA appears to be slowing.

This study considers the economic factors contributing to the current state of the open access publishing market, and evaluates the potential for European policymakers to enhance market competition and sustainability in parallel to increasing access.

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PubMed Launches LinkOut to Institutional Repository Full-Text Publications and Other Resources

PubMed has launched LinkOut.

Here's an excerpt from the announcement:

PubMed users can now see the icon that links to the full text deposited at an institutional repository (IR) using LinkOut. The LinkOut service allows you to link to full text, library holdings, and other relevant external resources from PubMed and other NCBI databases.

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A Snapshot of Open Data and Open Science Policies in Europe

SPARC Europe and the DCC have released A Snapshot of Open Data and Open Science Policies in Europe.

Here's an excerpt from the announcement:

This report is the first in a series that will seek to shed light on similarities and differences in Open Data and Open Science policies between European nations, and to assess their effectiveness in opening research data.

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"No Scholar Is an Island: The Impact of Sharing in the Work Life of Scholars"

Carol Tenopir et al. have published "No Scholar Is an Island: The Impact of Sharing in the Work Life of Scholars" in .

Here's an excerpt:

In an international survey of 1,000 published scholars, the Beyond Downloads project examined their sharing behaviours in order to gain a more contextualized and accurate picture of their usage beyond download patterns and citation counts. Scholars share published articles with others as a mode of content discovery and dissemination, particularly if they work in groups, and most expect to increase their sharing in the future.

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PLOS: Response to NIH RFI—Strategies for NIH Data Management, Sharing, and Citation

PLOS has released Response to NIH RFI—Strategies for NIH Data Management, Sharing, and Citation.

Here's an excerpt:

We write to express the views of the Public Library of Science, a fully Open Access Publisher of seven Research Journals, in response to your RFI on Data Sharing, Management, and Citation. Open access to Research Articles is just the first step in what we consider should be the end state for all publicly funded research, and we support broader efforts towards open science. We are developing our own policies to help establish a new norm in which upon publication of a journal article, if not before, all of the underlying data (where ethically appropriate) is openly available to access and reuse without restriction according to the FAIR principles for data management to make data Findable, Accessible, Interoperable and Re-usable.

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"Does Online Access Promote Research in Developing Countries? Empirical Evidence from Article-Level Data"

Frank Mueller-Langer et al. have self-archived "Does Online Access Promote Research in Developing Countries? Empirical Evidence from Article-Level Data."

Here's an excerpt:

Universities in developing countries have rarely been able to subscribe to academic journals in the past. The "Online Access to Research in the Environment" initiative (OARE) provides institutions in developing countries with free online access to more than 5,700 environmental science journals. Here we analyze the effect of OARE registration on scientific output by research institutions in five developing countries. We apply a difference-in-difference estimation method using panel data for 18,955 journal articles from 798 research institutions. We find that online access via OARE increases publication output by at least 43% while lower-ranked institutions located in remote areas benefit less.

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"The Durability and Fragility of Knowledge Infrastructures: Lessons Learned from Astronomy"

Christine L. Borgman, Peter T. Darch, Ashley E. Sands, and Milena S. Golshan have self-archived "The Durability and Fragility of Knowledge Infrastructures: Lessons Learned from Astronomy."

Here's an excerpt:

Infrastructures are not inherently durable or fragile, yet all are fragile over the long term. Durability requires care and maintenance of individual components and the links between them. Astronomy is an ideal domain in which to study knowledge infrastructures, due to its long history, transparency, and accumulation of observational data over a period of centuries. Research reported here draws upon a long-term study of scientific data practices to ask questions about the durability and fragility of infrastructures for data in astronomy. Methods include interviews, ethnography, and document analysis. As astronomy has become a digital science, the community has invested in shared instruments, data standards, digital archives, metadata and discovery services, and other relatively durable infrastructure components. Several features of data practices in astronomy contribute to the fragility of that infrastructure. These include different archiving practices between ground- and space-based missions, between sky surveys and investigator-led projects, and between observational and simulated data. Infrastructure components are tightly coupled, based on international agreements. However, the durability of these infrastructures relies on much invisible work—cataloging, metadata, and other labor conducted by information professionals. Continual investments in care and maintenance of the human and technical components of these infrastructures are necessary for sustainability.

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"On the Cost of Knowledge: Evaluating the Boycott against Elsevier"

Tom Heyman Pieter Moors, and Gert Storms have published "On the Cost of Knowledge: Evaluating the Boycott against Elsevier" in Frontiers in Research Metrics and Analytics.

Here's an excerpt:

To get an idea about the success rate of the "won't publish" resolution, we checked signatories' publication history after they signed the petition. Using ResearchGate, Google Scholar, Academia.edu, LinkedIn, ScienceDirect, and lab or personal websites, we were able to compile a bibliography for a large sample of "won't publish" signatories. Due to the time-consuming nature of this research, we limited ourselves to two subject areas, Chemistry and Psychology, each with approximately 500 signatories.

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"SCOAP³ Journals Double Downloads"

SCOAP³ has released "SCOAP3 Journals Double Downloads."

Here's an excerpt from the announcement:

The four largest journals participating in SCOAP3, two published by Elsevier and two by SpringerNature in partnership with the Italian Physical Society (SIF), and the Italian Institute for Advanced Studies (SISSA) have now analysed their logs to understand the impact of SCOAP3.

Elsevier announced that downloads to their two journals, Physics Letters B and Nuclear Physics B have doubled since they became Open Access at the start of SCOAP3 in January 2014. This increase is remarkable as SCOAP3 covers the most recent 3,500 articles in the journals, while most of the historic content of over 77,000 articles, is available to subscribers.

SpringerNature announced that since January 2014 they have observed a doubling of downloads across their two learned-society journals participating in SCOAP3: European Physical Journal C and the Journal of High Energy Physics.

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"How Do Scientists Define Openness? Exploring the Relationship between Open Science Policies and Research Practice"

Nadine Levin et al. have published "How Do Scientists Define Openness? Exploring the Relationship between Open Science Policies and Research Practice " in the Bulletin of Science, Technology & Society

Here's an excerpt:

This article documents how biomedical researchers in the United Kingdom understand and enact the idea of "openness." . . . This study is based on 22 in-depth interviews with U.K. researchers in systems biology, synthetic biology, and bioinformatics, which were conducted between September 2013 and February 2014. Through an analysis of the interview transcripts, we identify seven core themes that characterize researchers' understanding of openness in science and nine factors that shape the practice of openness in research.

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"Truth in Science Publishing: A Personal Perspective"

Thomas C. Südhof has published "Truth in Science Publishing: A Personal Perspective" in PLoS Biology.

Here's an excerpt:

Scientists, public servants, and patient advocates alike increasingly question the validity of published scientific results, endangering the public's acceptance of science. Here, I argue that emerging flaws in the integrity of the peer review system are largely responsible. Distortions in peer review are driven by economic forces and enabled by a lack of accountability of journals, editors, and authors. One approach to restoring trust in the validity of published results may be to establish basic rules that render peer review more transparent, such as publishing the reviews (a practice already embraced by some journals) and monitoring not only the track records of authors but also of editors and journals.

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"The Journal Article as a Means to Share Data: A Content Analysis of Supplementary Materials from Two Disciplines"

Jeremy Kenyon, Nancy Sprague, and Edward Flathers have published "The Journal Article as a Means to Share Data: a Content Analysis of Supplementary Materials from Two Disciplines" in the Journal of Librarianship and Scholarly Communication.

Here's an excerpt:

INTRODUCTION The practice of publishing supplementary materials with journal articles is becoming increasingly prevalent across the sciences. We sought to understand better the content of these materials by investigating the differences between the supplementary materials published by authors in the geosciences and plant sciences. METHODS We conducted a random stratified sampling of four articles from each of 30 journals published in 2013. In total, we examined 297 supplementary data files for a range of different factors. RESULTS We identified many similarities between the practices of authors in the two fields, including the formats used (Word documents, Excel spreadsheets, PDFs) and the small size of the files. There were differences identified in the content of the supplementary materials: the geology materials contained more maps and machine-readable data; the plant science materials included much more tabular data and multimedia content. DISCUSSION Our results suggest that the data shared through supplementary files in these fields may not lend itself to reuse. Code and related scripts are not often shared, nor is much 'raw' data. Instead, the files often contain summary data, modified for human reading and use. CONCLUSION Given these and other differences, our results suggest implications for publishers, librarians, and authors, and may require shifts in behavior if effective data sharing is to be realized.

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Open Access: The Beast That No-One Could—or Should—Control?

Stephen Curry has self-archived "Open Access: The Beast That No-One Could—or Should—Control?"

Here's an excerpt:

To set the scene, I will begin with a brief description of the open access movement and recent policy initiatives before discussing their impact on the attitudes of scientists towards the broader open science agenda and public engagement. I will then consider the effects of open access (and allied moves) on the authority and independence of science—concepts that are perturbed by the increasingly blurred boundary between the academy and the public. Lastly, I will focus attention on the various publics that are actively seeking to engage with science and scientists, mainly through advocacy groups or the growing ranks of citizen scientists; here, while the impact of open access appears relatively modest, it has the capacity to spring surprises that point to future growth.

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"A Vision for Open Cyber-Scholarly Infrastructures"

Costantino Thanos has published "A Vision for Open Cyber-Scholarly Infrastructures" in Publications.

Here's an excerpt:

The characteristics of modern science, i.e., data-intensive, multidisciplinary, open, and heavily dependent on Internet technologies, entail the creation of a linked scholarly record that is online and open. Instrumental in making this vision happen is the development of the next generation of Open Cyber-Scholarly Infrastructures (OCIs), i.e., enablers of an open, evolvable, and extensible scholarly ecosystem. The paper delineates the evolving scenario of the modern scholarly record and describes the functionality of future OCIs as well as the radical changes in scholarly practices including new reading, learning, and information-seeking practices enabled by OCIs.

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