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

Posté le 11 juillet 2015 par Hans Dillaerts

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

Data journals: A survey

Posté le 15 juin 2015 par Hans Dillaerts

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

The Oligopoly of Academic Publishers in the Digital Era

Statut

“The consolidation of the scientific publishing industry has been the topic of much debate within and outside the scientific community, especially in relation to major publishers’ high profit margins. However, the share of scientific output published in the journals of these major publishers, as well as its evolution over time and across various disciplines, has not yet been analyzed. This paper provides such analysis, based on 45 million documents indexed in the Web of Science over the period 1973-2013. It shows that in both natural and medical sciences (NMS) and social sciences and humanities (SSH), Reed-Elsevier, Wiley-Blackwell, Springer, and Taylor & Francis increased their share of the published output, especially since the advent of the digital era (mid-1990s). Combined, the top five most prolific publishers account for more than 50% of all papers published in 2013. Disciplines of the social sciences have the highest level of concentration (70% of papers from the top five publishers), while the humanities have remained relatively independent (20% from top five publishers). NMS disciplines are in between, mainly because of the strength of their scientific societies, such as the ACS in chemistry or APS in physics. The paper also examines the migration of journals between small and big publishing houses and explores the effect of publisher change on citation impact. It concludes with a discussion on the economics of scholarly publishing.”

URL : The Oligopoly of Academic Publishers in the Digital Era

DOI :10.1371/journal.pone.0127502

Evolution or revolution? Publishers’ perceptions of future directions in research communications and the publisher role

Statut

“This report presents a snapshot of the views of a wide range of publishers, covering their perceptions of future directions in research communications, scholarly publishing and the role of publishers. It is important to emphasise that there is not a single “publishers’ view” on these matters: the publishers represented here are of differing scale, ownership, (dominant) business model, discipline, and tradition, and their views reflect that diversity of experience.

Nearly 20 publishers of different types and scale were interviewed: for-profit and not-for-profit; open access and subscription-based; commercial, society, university presses; and with representation from all scholarly fields. We aimed to synthesise the views thus gathered, while reflecting the diversity of opinion where salient.”

URL : Evolution or revolution? Publishers’ perceptions of future directions in research communications and the publisher role

Have the “mega-journals” reached the limits to growth?

Statut

“A “mega-journal” is a new type of scientific journal that publishes freely accessible articles, which have been peer reviewed for scientific trustworthiness, but leaves it to the readers to decide which articles are of interest and importance to them. In the wake of the phenomenal success of PLOS ONE, several other publishers have recently started mega-journals. This article presents the evolution of mega-journals since 2010 in terms of article publication rates. The fastest growth seems to have ebbed out at around 35,000 annual articles for the 14 journals combined. Acceptance rates are in the range of 50–70%, and speed of publication is around 3–5 months. Common features in mega-journals are alternative impact metrics, easy reusability of figures and data, post-publication discussions and portable reviews from other journals.”

URL : Have the “mega-journals” reached the limits to growth?

DOI : https://dx.doi.org/10.7717/peerj.981

Disrupting the subscription journals’ business model for the necessary large-scale transformation to open access

Statut

“This paper makes the strong, fact-based case for a large-scale transformation of the current corpus of scientific subscription journals to an open access business model. The existing journals, with their well-tested functionalities, should be retained and developed to meet the demands of 21st century research, while the underlying payment streams undergo a major restructuring. There is sufficient momentum for this decisive push towards open access publishing. The diverse existing initiatives must be coordinated so as to converge on this clear goal.

The international nature of research implies that this transformation will be achieved on a truly global scale only through a consensus of the world’s most eminent research organizations. All the indications are that the money already invested in the research publishing system is sufficient to enable a transformation that will be sustainable for the future. There needs to be a shared understanding that the money currently locked in the journal subscription system must be withdrawn and re-purposed for open access publishing services.

The current library acquisition budgets are the ultimate reservoir for enabling the transformation without financial or other risks. The goal is to preserve the established service levels provided by publishers that are still requested by researchers, while redefining and reorganizing the necessary payment streams. By disrupting the underlying business model, the viability of journal publishing can be preserved and put on a solid footing for the scholarly developments of the future.”

URL : MPDL_OA-Transition_White_Paper

Getting the Word Out Academic Libraries as Scholarly Publishers

Statut

“In the past decade there has been an intense growth in the number of library publishing services supporting faculty and students. Unified by a commitment to both access and service, library publishing programs have grown from an early focus on backlist digitization to encompass publication of student works, textbooks, research data, as well as books and journals. This growing engagement with publishing is a natural extension of the academic library’s commitment to support the creation of and access to scholarship. This volume includes chapters by some of the most talented thinkers in this area of librarianship, exploring topics such as the economics of publishing and the challenges of collaboration, and surveying the service landscape for publishing in support of a variety of formats and methods. Edited by library publishing experts Maria Bonn, University of Illinois Urbana-Champaign (UIUC) Graduate School of Library and Information Science, and Mike Furlough, HathiTrust Digital Library, “Getting the Word Out” deepens current discussions in the field, and provides both decision makers and current practitioners with an introduction to the current state of the field and an investigation of its future prospects.”

URL : http://www.ala.org/acrl/sites/ala.org.acrl/files/content/publications/booksanddigitalresources/digital/9780838986981_getting_OA.pdf