Catégorie : EN

Publié le

Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives

Authors : Charles Vesteghem, Rasmus Froberg Brøndum, Mads Sønderkær, Mia Sommer, Alexander Schmitz, Julie Støve Bødker, Karen Dybkær, Tarec Christoffer El-Galaly, Martin Bøgsted

Compelling research has recently shown that cancer is so heterogeneous that single research centres cannot produce enough data to fit prognostic and predictive models of sufficient accuracy. Data sharing in precision oncology is therefore of utmost importance.

The Findable, Accessible, Interoperable and Reusable (FAIR) Data Principles have been developed to define good practices in data sharing. Motivated by the ambition of applying the FAIR Data Principles to our own clinical precision oncology implementations and research, we have performed a systematic literature review of potentially relevant initiatives.

For clinical data, we suggest using the Genomic Data Commons model as a reference as it provides a field-tested and well-documented solution. Regarding classification of diagnosis, morphology and topography and drugs, we chose to follow the World Health Organization standards, i.e. ICD10, ICD-O-3 and Anatomical Therapeutic Chemical classifications, respectively.

For the bioinformatics pipeline, the Genome Analysis ToolKit Best Practices using Docker containers offer a coherent solution and have therefore been selected. Regarding the naming of variants, we follow the Human Genome Variation Society’s standard.

For the IT infrastructure, we have built a centralized solution to participate in data sharing through federated solutions such as the Beacon Networks.

URL : Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives

DOI : https://doi.org/10.1093/bib/bbz044

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The complex nature of research dissemination practices among public health faculty researchers

Authors : Rosie Hanneke, Jeanne M. Link

Objective

This study explores the variety of information formats used and audiences targeted by public health faculty in the process of disseminating research.

Methods

The authors conducted semi-structured interviews with twelve faculty members in the School of Public Health at the University of Illinois at Chicago, asking them about their research practices, habits, and preferences.

Results

Faculty scholars disseminate their research findings in a variety of formats intended for multiple audiences, including not only their peers in academia, but also public health practitioners, policymakers, government and other agencies, and community partners.

Conclusion

Librarians who serve public health faculty should bear in mind the diversity of faculty’s information needs when designing and improving library services and resources, particularly those related to research dissemination and knowledge translation.

Promising areas for growth in health sciences libraries include supporting data visualization, measuring the impact of non-scholarly publications, and promoting institutional repositories for dissemination of research.

URL : The complex nature of research dissemination practices among public health faculty researchers

Alternative location : http://jmla.pitt.edu/ojs/jmla/article/view/524

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The impact of digital copyright law and policy on access to knowledge and learning

Authors : Tana Pistorius, Odirachukwu S. Mwim

Background

The evolution in digital technologies has had an enormous impact on traditional copyright notions. Works in digital form have uniform characteristics and these works can be copied, distributed and stored with ease.

Objectives

The focus of this article was how to attain a balance between the need to promote access to works and therefore knowledge and learning, on the one hand, and the protection of the interests of copyright holders, on the other.

Method

Technological protection measures (TPMs) are applied to copyright works in digital form to curb infringement. The authors explore the extent to which TPMs impact on access the knowledge and learning.

Results

The findings of this article suggest a need for possible countermeasures in promoting knowledge and literacy through legislative reform that address the needs of creators and users in developing communities.

Conclusion

The authors conclude that TPMs may hinder data literacy, access to works, teaching and learning, particularly in developing communities. For example, recent attempts to revise South African copyright law have not attained a balanced approach.

URL : The impact of digital copyright law and policy on access to knowledge and learning

DOI : https://doi.org/10.4102/rw.v10i1.196

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The citation advantage of linking publications to research data

Authors : Giovanni Colavizza, Iain Hrynaszkiewicz, Isla Staden, Kirstie Whitaker, Barbara McGillivray

Efforts to make research results open and reproducible are increasingly reflected by journal policies encouraging or mandating authors to provide data availability statements.

As a consequence of this, there has been a strong uptake of data availability statements in recent literature. Nevertheless, it is still unclear what proportion of these statements actually contain well-formed links to data, for example via a URL or permanent identifier, and if there is an added value in providing them.

We consider 531,889 journal articles published by PLOS and BMC which are part of the PubMed Open Access collection, categorize their data availability statements according to their content and analyze the citation advantage of different statement categories via regression.

We find that, following mandated publisher policies, data availability statements have become common by now, yet statements containing a link to a repository are still just a fraction of the total.

We also find that articles with these statements, in particular, can have up to 25.36% higher citation impact on average: an encouraging result for all publishers and authors who make the effort of sharing their data. All our data and code are made available in order to reproduce and extend our results.

URL : https://arxiv.org/abs/1907.02565

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Open Access Routes Dichotomy and Opportunities: Consolidation, Analysis and Trends at the Spanish National Research Council

Authors : Mercedes Baquero-Arribas, Luis Dorado, Isabel Bernal

This article gives a comprehensive overview of recent Spanish National Research Council (CSIC) publications available in Open Access. With a focus on research articles from the last decade (2008–2018), this work aims to fill the gap in previous studies about publishing trends and impact monitoring of publications by researchers from the Spanish National Research Council.

Evolution and main trends of Green and Gold Open Access routes at CSIC are addressed through a close insight into DIGITAL.CSIC repository and institutional Open Access Publishing Support Programme.

The article draws on major conclusions at a time when an institutional Open Access mandate has just entered into force. The article also relates findings about performance of institutional Open Access Publishing Initiative and total volume of CSIC articles published in Open Access with an estimation of overall costs on article processing charges during these years.

Furthermore, the data serve as a basis to make preliminary considerations as to opportunities to move from a subscription-based model to one fully aligned with Gold Open Access publishing.

The data analyzed come from a variety of sources, including public information and internal records maintained by the CSIC E-resources Subscription programme, DIGITAL.CSIC and data retrieved from GesBIB, an internal, in-house development tool that integrates bibliographic information about CSIC publications as well as data from several external APIs, including Unpaywall, DOAJ and Sherpa Romeo.

URL : Open Access Routes Dichotomy and Opportunities: Consolidation, Analysis and Trends at the Spanish National Research Council

DOI : https://doi.org/10.3390/publications7030049

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A model for initiating research data management services at academic libraries

Authors : Kevin B. Read, Jessica Koos, Rebekah S. Miller, Cathryn F. Miller, Gesina A. Phillips, Laurel Scheinfeld, Alisa Surkis

Background

Librarians developed a pilot program to provide training, resources, strategies, and support for medical libraries seeking to establish research data management (RDM) services. Participants were required to complete eight educational modules to provide the necessary background in RDM.

Each participating institution was then required to use two of the following three elements: (1) a template and strategies for data interviews, (2) a teaching tool kit to teach an introductory RDM class, or (3) strategies for hosting a data class series.

Case Presentation

Six libraries participated in the pilot, with between two and eight librarians participating from each institution. Librarians from each institution completed the online training modules.

Each institution conducted between six and fifteen data interviews, which helped build connections with researchers, and taught between one and five introductory RDM classes.

All classes received very positive evaluations from attendees. Two libraries conducted a data series, with one bringing in instructors from outside the library.

Conclusion

The pilot program proved successful in helping participating librarians learn about and engage with their research communities, jump-start their teaching of RDM, and develop institutional partnerships around RDM services.

The practical, hands-on approach of this pilot proved to be successful in helping libraries with different environments establish RDM services.

The success of this pilot provides a proven path forward for libraries that are developing data services at their own institutions.

URL : A model for initiating research data management services at academic libraries

Alternative location : http://jmla.pitt.edu/ojs/jmla/article/view/545

Publié le

Reading practices in scholarly work: from articles and books to blogs

Authors : Elina Late, Carol Tenopir, Sanna Talja, Lisa Christian

Purpose

The purpose of this paper is to examine the role of reading in scholarly work among academics in Finland. This study analyzes readings from a variety of publication types including books, conference proceedings, research reports, magazines, newspapers, blogs, non-fiction and fiction.

Design/methodology/approach

An online survey was developed and distributed in Finland in 2016–2017 (n=528). Participants were asked their finding and use of scholarly information resources of all types.

Findings

Scholars read from a variety of publications. Different types of publications are read and used differently. Reading also varies between disciplines, ranks, work responsibilities and type of research performed.

Research limitations/implications

The study was a nationwide study of researchers in Finland; therefore, all findings are within the context of researchers in a single country. All results are self-reported; therefore, the authors assume but cannot be sure that respondents accurately recollect the specifics of their use of scholarly information.

Practical implications

The results of this study are relevant to publishers, research librarians, editors and others who serve consumers of scholarly information resources, design information products and services for those scholars, and seek to better understand the information needs and use of a variety of types of scholarly publications.

Originality/value

This study replicates previous studies in a variety of countries and provides a more up-to-date and single-country contextualized overview of how researchers find and use scholarly information in their work.

URL : http://urn.fi/URN:NBN:fi:tuni-201906172055