EN

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

Posted on by 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

Non classé

Fair Shares and Sharing Fairly: A Survey of Public Views on Open Science, Informed Consent and Participatory Research in Biobanking

Posted on by Hans Dillaerts

« Context

Biobanks are important resources which enable large-scale genomic research with human samples and data, raising significant ethical concerns about how participants’ information is managed and shared. Three previous studies of the Canadian public’s opinion about these topics have been conducted. Building on those results, an online survey representing the first study of public perceptions about biobanking spanning all Canadian provinces was conducted. Specifically, this study examined qualitative views about biobank objectives, governance structure, control and ownership of samples and data, benefit sharing, consent practices and data sharing norms, as well as additional questions and ethical concerns expressed by the public.

Results

Over half the respondents preferred to give a one-time general consent for the future sharing of their samples among researchers. Most expressed willingness for their data to be shared with the international scientific community rather than used by one or more Canadian institutions. Whereas more respondents indicated a preference for one-time general consent than any other model of consent, they constituted less than half of the total responses, revealing a lack of consensus among survey respondents regarding this question. Respondents identified biobank objectives, governance structure and accountability as the most important information to provide participants.

Respondents’ concerns about biobanking generally centred around the control and ownership of biological samples and data, especially with respect to potential misuse by insurers, the government and other third parties. Although almost half the respondents suggested that these should be managed by the researchers’ institutions, results indicate that the public is interested in being well-informed about these projects and suggest the importance of increased involvement from participants. In conclusion, the study discusses the viability of several proposed models for informed consent, including e-governance, independent trustees and the use of exclusion clauses, in the context of these new findings about the views of the Canadian public. »

URL : Fair Shares and Sharing Fairly: A Survey of Public Views on Open Science, Informed Consent and Participatory Research in Biobanking

DOI : 10.1371/journal.pone.0129893

Non classé

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

Posted on by Hans Dillaerts

« 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/

Non classé

The One Repo: background, implementation and call for funding

Posted on by Hans Dillaerts
« 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

Non classé

From Concerned to Cautiously Optimistic: Assessing Faculty Perceptions and Knowledge of Open Access in a Campus-Wide Study

Posted on by Hans Dillaerts

« INTRODUCTION : Though open access publishing has many advantages for scholars, very few are interested in learning about and pursuing open access publishing. This article discusses the results of a survey administered to faculty across disciplines at a single university to assess their perceptions, knowledge, and perceived knowledge of open access publishing and related topics.

METHODS : Anonymous electronic survey of 240 faculty members with a response rate of 23%.

RESULTS : Although many respondents considered themselves familiar with open access, very few had practical knowledge of open access publishing. Faculty were uncertain about the value and reliability of open access publishing and were particularly concerned about its applicability in the promotion and tenure process.

CONCLUSION:  Misinformation, lack of motivation, and fear appear to be the main causes of negative perceptions of open access among faculty surveyed. Though science faculty had the highest overall perceived knowledge of open access, they were also most likely to view open access negatively and to believe that the current publishing model works well. Education faculty were more likely to think highly of open access publishing, in part due to a lack of funding for that discipline. Librarians and information professionals should take a tailored approach to discussing open access with faculty by working within the knowledge of the discipline if possible. »

URL : From Concerned to Cautiously Optimistic: Assessing Faculty Perceptions and Knowledge of Open Access in a Campus-Wide Study

DOI : http://dx.doi.org/10.7710/2162-3309.1212

Non classé

Scholarly Communication as a Core Competency: Prevalence, Activities, and Concepts of Scholarly Communication Librarianship as Shown Through Job Advertisements

Posted on by Hans Dillaerts

« INTRODUCTION : The dynamic nature of the scholarly communication landscape has produced a need for the creation of positions specifically focused on these issues. Yet, no clear title or job description for scholarly communication librarianship has emerged. The lack of standardization in this area is problematic for educators, professionals, and prospective professionals.

METHODS : Analyzing 13,869 job advertisements published between 2006 and 2014, this study attempts to examine the prevalence of scholarly communication terms and activities and the types of positions in which these terms and activities appear.

RESULTS : This study finds an increase in the use of the term “scholarly communication” in the title or text of job advertisements over the last nine years, with more than 7% of positions in the most recent year containing the term.

CONCLUSIONS : An analysis of the levels of engagement with scholarly communication demonstrates that jobs with substantial levels of engagement are increasing; whereas those requiring passive knowledge or awareness of scholarly communication issues are decreasing. Jobs with scholarly communication as a primary job responsibility are differentiated by a focus on repositories, open access, copyright, authors’ rights, and intellectual property differentiate core scholarly communication positions. »

URL : Scholarly Communication as a Core Competency: Prevalence, Activities, and Concepts of Scholarly Communication Librarianship as Shown Through Job Advertisements

DOI : http://dx.doi.org/10.7710/2162-3309.1236

Non classé

A Triangulation Method to Dismantling a Disciplinary « Big Deal »

Posted on by Hans Dillaerts

« In late 2012, it appeared that the University Library, University of Saskatchewan would likely no longer be able to afford to subscribe to the entire American Chemical Society « Big Deal » of 36 journals. Difficult choices would need to be made regarding which titles to retain as individual subscriptions. In an effort to arrive at the most conscientious and evidence-based decisions possible, three discrete sources of data were collected and compared: full-text downloads, citation analysis of faculty publications, and user feedback.

This case study will describe the triangulation method developed — including the unconventional approach of applying a citation analysis technique to usage data and survey responses. Such a thorough, labor-intensive, method is likely not practical for analyzing larger, multidisciplinary journal bundles. When it becomes necessary to break up a smaller collection important to researchers in a particular discipline, this technique may provide strong evidence to support librarian decisions as well as involve faculty in the process. »

URL : http://www.istl.org/15-spring/refereed3.html