Tag Archives: scientific data

Issues in the development of open access to research data

« This paper explores key issues in the development of open access to research data. The use of digital means for developing, storing and manipulating data is creating a focus on ‘data-driven science’. One aspect of this focus is the development of ‘open access’ to research data. Open access to research data refers to the way in which various types of data are openly available to public and private stakeholders, user communities and citizens. Open access to research data, however, involves more than simply providing easier and wider access to data for potential user groups. The development of open access requires attention to the ways data are considered in different areas of research. We identify how open access is being unevenly developed across the research environment and the consequences this has in terms of generating data gaps. Data gaps refer to the way data becomes detached from published conclusions. To address these issues, we examine four main areas in developing open access to research data: stakeholder roles and values; technological requirements for managing and sharing data; legal and ethical regulations and procedures; institutional roles and policy frameworks. We conclude that problems of variability and consistency across the open access ecosystem need to be addressed within and between these areas to ensure that risks surrounding a data gap are managed in open access. »

URL : http://dx.doi.org/10.1080/08109028.2014.956505

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19 novembre 2014 · 21 h 46 min

Publishing without Publishers: a Decentralized Approach to Dissemination, Retrieval, and Archiving of Data

« Making available and archiving scientific results is for the most part still considered the task of classical publishing companies, despite the fact that classical forms of publishing centered around printed narrative articles no longer seem well-suited in the digital age. In particular, there exist currently no efficient, reliable, and agreed-upon methods for publishing scientific datasets, which have become increasingly important for science. Here we propose to design scientific data publishing as a Web-based bottom-up process, without top-down control of central authorities such as publishing companies. We present a protocol and a server network to decentrally store and archive data in the form of nanopublications, an RDF-based format to represent scientific data with formal semantics. We show how this approach allows researchers to produce, publish, retrieve, address, verify, and recombine datasets and their individual nanopublications in a reliable and trustworthy manner, and we argue that this architecture could be used for the Semantic Web in general. Our evaluation of the current small network shows that this system is efficient and reliable, and we discuss how it could grow to handle the large amounts of structured data that modern science is producing and consuming. »

URL : http://arxiv-web3.library.cornell.edu/abs/1411.2749

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14 novembre 2014 · 8 h 00 min

The Dawn of Open Access to Phylogenetic Data

« The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation – extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Importantly, our survey spans recent policy initiatives and infrastructural changes; our analyses indicate that the positive impact of these community initiatives has been both dramatic and immediate. Although the results of our study indicate that the situation is dire, our findings also reveal tremendous recent progress in the sharing and preservation of phylogenetic data. »

URL : The Dawn of Open Access to Phylogenetic Data

DOI: 10.1371/journal.pone.0110268

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27 octobre 2014 · 22 h 34 min

Open exchange of scientific knowledge and European copyright: The case of biodiversity information

« Background. The 7th Framework Programme for Research and Technological Development is helping the European to prepare for an integrative system for intelligent management of biodiversity knowledge. The infrastructure that is envisaged and that will be further developed within the Programme “Horizon 2020” aims to provide open and free access to taxonomic information to anyone with a requirement for biodiversity data, without the need for individual consent of other persons or institutions. Open and free access to information will foster the re-use and improve the quality of data, will accelerate research, and will promote new types of research. Progress towards the goal of free and open access to content is hampered by numerous technical, economic, sociological, legal, and other factors. The present article addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights.

We present a legal point of view as to what will be needed to bring distributed information together and facilitate its re-use by data mining, integration into semantic knowledge systems, and similar techniques. We address exceptions and limitations of copyright or database protection within Europe, and we point to the importance of data use agreements. We illustrate how exceptions and limitations have been transformed into national legislations within some European states to create inconsistencies that impede access to biodiversity information.

Conclusions. The legal situation within the EU is unsatisfactory because there are inconsistencies among states that hamper the deployment of an open biodiversity knowledge management system. Scientists within the EU who work with copyright protected works or with protected databases have to be aware of regulations that vary from country to country. This is a major stumbling block to international collaboration and is an impediment to the open exchange of biodiversity knowledge. Such differences should be removed by unifying exceptions and limitations for research purposes in a binding, Europe-wide regulation. »

URL : Open exchange of scientific knowledge and European copyright

Alternative URL : http://www.pensoft.net/journals/zookeys/article/7717/abstract/open-exchange-of-scientific-knowledge-and-european-copyright-the-case-of-biodiversity-information

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7 juin 2014 · 11 h 18 min

Ten Simple Rules for the Care and Feeding of Scientific Data

« This article offers a short guide to the steps scientists can take to ensure that their data and associated analyses continue to be of value and to be recognized. In just the past few years, hundreds of scholarly papers and reports have been written on questions of data sharing, data provenance, research reproducibility, licensing, attribution, privacy, and more—but our goal here is not to review that literature. Instead, we present a short guide intended for researchers who want to know why it is important to “care for and feed” data, with some practical advice on how to do that. The final section at the close of this work offers links to the types of services referred to throughout the text. »

URL : Ten Simple Rules for the Care and Feeding of Scientific Data

Alternative URL : http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003542

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1 juin 2014 · 17 h 00 min