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From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

Motivation

Reproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed.

The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler.

Results

Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP, and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings.

The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata. »

URL : From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

DOI : 10.1371/journal.pone.0127612

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EN

Amplifying the Impact of Open Access: Wikipedia and the Diffusion of Science

Authors : Misha Teplitskiy, Grace Lu, Eamon Duede

With the rise of Wikipedia as a first-stop source for scientific knowledge, it is important to compare its representation of that knowledge to that of the academic literature. This article approaches such a comparison through academic references made within the worlds 50 largest Wikipedias.

Previous studies have raised concerns that Wikipedia editors may simply use the most easily accessible academic sources rather than sources of the highest academic status. We test this claim by identifying the 250 most heavily used journals in each of 26 research fields (4,721 journals, 19.4M articles in total) indexed by the Scopus database, and modeling whether topic, academic status, and accessibility make articles from these journals more or less likely to be referenced on Wikipedia.

We find that, controlling for field and impact factor, the odds that an open access journal is referenced on the English Wikipedia are 47% higher compared to closed access journals. Moreover, in most of the worlds Wikipedias a journals high status (impact factor) and accessibility (open access policy) both greatly increase the probability of referencing.

Among the implications of this study is that the chief effect of open access policies may be to significantly amplify the diffusion of science, through an intermediary like Wikipedia, to a broad public audience.

URL : Amplifying the Impact of Open Access: Wikipedia and the Diffusion of Science

Alternative location : http://onlinelibrary.wiley.com/doi/10.1002/asi.23687/full

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EN

Data journals: A survey

Data occupy a key role in our information society. However, although the amount of published data continues to grow and terms such as data deluge and big data today characterize numerous (research) initiatives, much work is still needed in the direction of publishing data in order to make them effectively discoverable, available, and reusable by others.

Several barriers hinder data publishing, from lack of attribution and rewards, vague citation practices, and quality issues to a rather general lack of a data-sharing culture.

Lately, data journals have overcome some of these barriers. In this study of more than 100 currently existing data journals, we describe the approaches they promote for data set description, availability, citation, quality, and open access. We close by identifying ways to expand and strengthen the data journals approach as a means to promote data set access and exploitation. »

URL : http://www.niso.org/apps/group_public/download.php/14938/DataJournalsSurvey%20%281%29.pdf

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New Consortial Model for E-Books Acquisitions

Author : Luke Swindler

E-books constitute major challenges for library collections generally and present fundamental problems for consortial collection development specifically. The Triangle Research Libraries Network (TRLN) and Oxford University Press (OUP) have created a mutually equitable and financially sustainable model for the consortial acquisition of e-books coupled with print titles needed to support instruction and research across the disciplinary spectrum within a transitional framework that is acceptable to users while moving both libraries and publishers to a decidedly electronic environment for monographs.

Working with YBP Library Services, TRLN and OUP developed a flexible vending model for systematically increasing e-books acquisitions in tandem with reducing print intake over time and keeping net costs constant that other consortia and publishers would find useful.

This article focuses on creating an acceptable and sustainable model that allows libraries to shift to e-books and the implications for traditional cooperative collection development.

The research reports on the principles undergirding the pilot, how it developed, challenges encountered and lessons learned, librarian and user reactions to this format shift, and resulting philosophical and practical evolutions in consortial approaches to monographic acquisitions and understandings of what constitutes cooperative collections success in a digital environment.

URL : New Consortial Model for E-Books Acquisitions

Alternative location : http://crl.acrl.org/content/77/3/269.abstract

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EN

Study of Open Access Publishing in Social Sciences and its Implications for Libraries

The Open Access Movement (OAM), which started as a gradual realisation by authors mainly in biomedical sciences to make available results of public-funded research projects to the public without much barrier pertaining to cost, permission, copyright obligations, etc., gradually gained momentum across the world and India was no exception to it.

Though the movement was confined mainly to science, technology and medical fields in India, since last few years, a number of open access repositories and open access journals in Social Science subjects have started appearing.

The present study which is confined to the open access Social Science journals published from India as mentioned in the Directory of Open Access Journals, identified 60 open access Social Sciences journals in India.

The study also analysed the journals on the basis of certain parameters as to trend of open access journals in Social Sciences, and was found that most of open access journals in Social Sciences appeared between 2009 and 2014 and about half of the journals charge authors for publishing their papers in the journals and only a few are published under Creative Commons Attribution.

Lastly, the paper discusses about implications of open access publishing on Social Science research libraries made few suggestions towards encouraging open access publishing in Social Science subjects in India.

URL : Study of Open Access Publishing in Social Sciences and its Implications for Libraries

Related URL : http://publications.drdo.gov.in/ojs/index.php/djlit/article/view/8720

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EN

Bibliogifts in LibGen? A study of a text-sharing platform driven by biblioleaks and crowdsourcing

Author : Guillaume Cabanac

Research articles disseminate the knowledge produced by the scientific community. Access to this literature is crucial for researchers and the general public. Apparently, “bibliogifts” are available online for free from text-sharing platforms.

However, little is known about such platforms. What is the size of the underlying digital libraries? What are the topics covered? Where do these documents originally come from? This article reports on a study of the Library Genesis platform (LibGen).

The 25 million documents (42 terabytes) it hosts and distributes for free are mostly research articles, textbooks, and books in English. The article collection stems from isolated, but massive, article uploads (71%) in line with a “biblioleaks” scenario, as well as from daily crowdsourcing (29%) by worldwide users of platforms such as Reddit Scholar and Sci-Hub.

By relating the DOIs registered at CrossRef and those cached at LibGen, this study reveals that 36% of all DOI articles are available for free at LibGen. This figure is even higher (68%) for three major publishers: Elsevier, Springer, and Wiley. More research is needed to understand to what extent researchers and the general public have recourse to such text-sharing platforms and why.

URL : http://www.irit.fr/publis/SIG/2015_JASIST_C.pdf

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EN

Research Data Explored II: the Anatomy and Reception of figshare

This is the second paper in a series of bibliometric studies of research data. In this paper, we present an analysis of figshare, one of the largest multidisciplinary repositories for research materials to date.

We analysed the structure of items archived in figshare, their usage, and their reception in two altmetrics sources (PlumX and ImpactStory). We found that figshare acts as a platform for newly published research materials, and as an archive for PLOS.

Depending on the function, we found different bibliometric characteristics. Items archived from PLOS tend to be coming from the natural sciences and are often unviewed and non-downloaded. Self-archived items, however, come from a variety of disciplines and exhibit some patterns of higher usage.

In the altmetrics analysis, we found that Twitter was the social media service where research data gained most attention; generally, research data published in 2014 were most popular across social media services.

PlumX detects considerably more items in social media and also finds higher altmetric scores than ImpactStory.

URL : http://arxiv.org/abs/1503.01298