Archives des mots-clés : scientific communication

Accelerating Scientific Publication in Biology

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“Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences over the past thirty years. Considerably more experimental data is now required for publication, and the average time required for graduate students to publish their first paper has increased and is approaching the desirable duration of Ph.D. training.

Since publication is generally a requirement for career progression, schemes to reduce the time of graduate student and postdoctoral training may be difficult to implement without also considering new mechanisms for accelerating communication of their work. The increasing time to publication also delays potential catalytic effects that ensue when many scientists have access to new information. The time has come for the life scientists, funding agencies, and publishers to discuss how to communicate new findings in a way that best serves the interests of the public and scientific community.”

URL : http://biorxiv.org/content/early/2015/07/11/022368

Mining and Analyzing the Future Works in Scientific Articles

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“Future works in scientific articles are valuable for researchers and they can guide researchers to new research directions or ideas. In this paper, we mine the future works in scientific articles in order to 1) provide an insight for future work analysis and 2) facilitate researchers to search and browse future works in a research area.

First, we study the problem of future work extraction and propose a regular expression based method to address the problem. Second, we define four different categories for the future works by observing the data and investigate the multi-class future work classification problem. Third, we apply the extraction method and the classification model to a paper dataset in the computer science field and conduct a further analysis of the future works.

Finally, we design a prototype system to search and demonstrate the future works mined from the scientific papers. Our evaluation results show that our extraction method can get high precision and recall values and our classification model can also get good results and it outperforms several baseline models. Further analysis of the future work sentences also indicates interesting results.”

URL : http://arxiv.org/abs/1507.02140

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

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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

Much Obliged: Analyzing the Importance and Impact of Acknowledgements in Scholarly Communication

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“Author rights, peer review, open access, and the role of institutional repositories have all come under scrutiny by scholars, librarians, and legal experts in the last decade. Much of the conversation is centered on liberating information from the confinements of legal, financial, and hierarchical restraints. The relevancy of traditional citation analysis too, understood within the framework of an h-Index and Eigen factor, is under scrutiny with the rise of altmetrics. Collectively, these issues form the core of the scholarly communication process, from creation to dissemination to impact.

However, an overlooked facet of the scholarly communication process is the acknowledgement. As an expression of scholarly debt, the acknowledgment is an important facet of intellectual networks. Not only does the acknowledgement demonstrate the intellectual contributions of colleagues, advisors, funding agencies, and mentors but also the significance of librarians in the scholarly communication process.”

URL : http://eprints.rclis.org/25428/

The One Repo: background, implementation and call for funding

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“As scholarly communication undergoes seismic changes, endless opportunities are opening up. In an open-access world, there is potential for Internet-enabled research on huge corpuses, discovering new correlations and making new connections. To facilitate these processes, we need platform that provides uniform access to the metadata and full text of all open-access articles, whether in repositories or open-access journals. The platform must provide data that is complete, up to date, high quality and open for every kind of re-use.

The One Repo ( http://onerepo.net/) is is that platform. It aims to make the entire open-access scholarly record available via a Web UI, embeddable widgets and various web-services, as well providing all of the metadata for direct download. It is built from battle-tested components that are in use in high-volume commercial systems.

Numerous harvesting methods are used. The existing demonstrator presents a UI that integrates results from a small number of repositories and other sources. We seek funding to rapidly increase coverage. The One Repo has dramatic implications forscholarship, research and engineering across every field of human endeavour.”


URL : http://onerepo.net/onerepo-whitepaper.pdf

The public impact of Latin America’s approach to open access

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“This study explores the extent to which research published in Latin America—where the vast majority of which is made freely available to the public—has an impact and reach beyond the academic community. It addresses the ways in which the study of research impact is moving beyond the counting citations, which has dominated bibliometrics for well over the last 50 years. As more of the world’s research is made freely available to the public, there is an increasing probability that the impact and reach of research extends beyond the confines of academia.

To establish the current extent of public access, this study explores who the users of Latin American research are, as well as their motivations for accessing the work by using a series of simple pop-up surveys, which were displayed to users of the two largest scholarly journal portals in Latin America.

The results, after thousands of responses, indicate that traditional scholarly use makes up only a quarter of the total use in Latin America. The majority of use is from non-scholar communities, namely students (around 50% of the total use) and from individuals interested for professional or personal reasons (collectively around 20% of the total use). By linking the survey responses to the articles being read, it was also possible to identify points of convergence and divergence in student, faculty, and public interest groups.

Finally, this study employed methods from a new field of inquiry, altmetrics, in an attempt to capture engagement with research on the social Web. The success of such methods for the Latin American case were limited due to low coverage levels, but the research nevertheless contributes to the understanding of nascent field of altmetrics more broadly. The study concludes with a discussion of the conceptual, political, curricular, and methodological implications of this new approach to scientific communication.”

URL : https://microblogging.infodocs.eu/wp-content/uploads/2015/06/AlperinDissertationFinalPublicImpact-augmented.pdf

Related URL : http://purl.stanford.edu/jr256tk1194

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

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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