Archives des mots-clés : open science

Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

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Authors : Joshua D. Wallach, Kevin W. Boyack, John P. A. Ioannidis

Currently, there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature. According to a previous evaluation of 441 biomedical journals articles published in 2000–2014, the biomedical literature largely lacked transparency in important dimensions.

Here, we surveyed a random sample of 149 biomedical articles published between 2015 and 2017 and determined the proportion reporting sources of public and/or private funding and conflicts of interests, sharing protocols and raw data, and undergoing rigorous independent replication and reproducibility checks.

We also investigated what can be learned about reproducibility and transparency indicators from open access data provided on PubMed. The majority of the 149 studies disclosed some information regarding funding (103, 69.1% [95% confidence interval, 61.0% to 76.3%]) or conflicts of interest (97, 65.1% [56.8% to 72.6%]).

Among the 104 articles with empirical data in which protocols or data sharing would be pertinent, 19 (18.3% [11.6% to 27.3%]) discussed publicly available data; only one (1.0% [0.1% to 6.0%]) included a link to a full study protocol. Among the 97 articles in which replication in studies with different data would be pertinent, there were five replication efforts (5.2% [1.9% to 12.2%]).

Although clinical trial identification numbers and funding details were often provided on PubMed, only two of the articles without a full text article in PubMed Central that discussed publicly available data at the full text level also contained information related to data sharing on PubMed; none had a conflicts of interest statement on PubMed.

Our evaluation suggests that although there have been improvements over the last few years in certain key indicators of reproducibility and transparency, opportunities exist to improve reproducible research practices across the biomedical literature and to make features related to reproducibility more readily visible in PubMed.

URL : Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

DOI : https://doi.org/10.1371/journal.pbio.2006930

Dimensions of open research: critical reflections on openness in the ROER4D project

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Authors : Thomas William King, Cheryl-Ann Hodgkinson-Williams, Michelle Willmers, Sukaina Walji

Open Research has the potential to advance the scientific process by improving the transparency, rigour, scope and reach of research, but choosing to experiment with Open Research carries with it a set of ideological, legal, technical and operational considerations.

Researchers, especially those in resource-constrained situations, may not be aware of the complex interrelations between these different domains of open practice, the additional resources required, or how Open Research can support traditional research practices.

Using the Research on Open Educational Resources for Development (ROER4D) project as an example, this paper attempts to demonstrate the interrelation between ideological, legal, technical and operational openness; the resources that conducting Open Research requires; and the benefits of an iterative, strategic approach to one’s own Open Research practice.

In this paper we discuss the value of a critical approach towards Open Research to ensure better coherence between ‘open’ ideology (embodied in strategic intention) and ‘open’ practice (the everyday operationalisation of open principles).

URL : Dimensions of open research: critical reflections on openness in the ROER4D project

Alternative location : https://www.openpraxis.org/index.php/OpenPraxis/article/view/285

Open Science by Design

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Contributors : National Academies of Sciences, Engineering, and Medicine; Policy and Global Affairs; Board on Research Data and Information; Committee on Toward an Open Science Enterprise

Openness and sharing of information are fundamental to the progress of science and to the effective functioning of the research enterprise. The advent of scientific journals in the 17th century helped power the Scientific Revolution by allowing researchers to communicate across time and space, using the technologies of that era to generate reliable knowledge more quickly and efficiently.

Harnessing today’s stunning, ongoing advances in information technologies, the global research enterprise and its stakeholders are moving toward a new open science ecosystem.

Open science aims to ensure the free availability and usability of scholarly publications, the data that result from scholarly research, and the methodologies, including code or algorithms, that were used to generate those data.

Open Science by Design is aimed at overcoming barriers and moving toward open science as the default approach across the research enterprise.

This report explores specific examples of open science and discusses a range of challenges, focusing on stakeholder perspectives. It is meant to provide guidance to the research enterprise and its stakeholders as they build strategies for achieving open science and take the next steps.

URL : https://www.nap.edu/catalog/25116/open-science-by-design-realizing-a-vision-for-21st-century

Leveraging Concepts in Open Access Publications

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Authors : Andrea Bertino, Luca Foppiano, Laurent Romary, Pierre Mounier

Aim

This paper addresses the integration of a Named Entity Recognition and Disambiguation (NERD) service within a group of open access (OA) publishing digital platforms and considers its potential impact on both research and scholarly publishing.

This application, called entity-fishing, was initially developed by Inria in the context of the EU FP7 project CENDARI (Lopez et al., 2014) and provides automatic entity recognition and disambiguation against Wikipedia and Wikidata. Distributed with an open-source licence, it was deployed as a web service in the DARIAH infrastructure hosted at the French HumaNum.

Methods

In this paper, we focus on the specific issues related to its integration on five OA platforms specialized in the publication of scholarly monographs in social sciences and humanities as part of the work carried out within the EU H2020 project HIRMEOS (High Integration of Research Monographs in the European Open Science infrastructure).

Results and Discussion

In the following sections, we give a brief overview of the current status and evolution of OA publications and how HIRMEOS aims to contribute to this.

We then give a comprehensive description of the entity-fishing service, focusing on its concrete applications in real use cases together with some further possible ideas on how to exploit the generated annotations.

Conclusions

We show that entity-fishing annotations can improve both research and publishing process. Entity-fishing annotations can be used to achieve a better and quicker understanding of the specific and disciplinary language of certain monographs and so encourage non-specialists to use them.

In addition, a systematic implementation of the entity-fishing service can be used by publishers to generate thematic indexes within book collections to allow better cross-linking and query functions.

URL : https://hal.inria.fr/hal-01900303/

Identifying the challenges in implementing open science

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Authors : Sarah E. Ali-Khan, Antoine Jean, E. Richard Gold

Areas of open science (OS) policy and practice are already relatively well-advanced in several countries and sectors through the initiatives of some governments, funders, philanthropy, researchers and the community. Nevertheless, the current research and innovation system, including in the focus of this report, the life sciences, remains weighted against OS.

In October 2017, thought-leaders from across the world gathered at an Open Science Leadership Forum in the Washington DC office of the Bill and Melinda Gates Foundation to share their views on what successful OS looks like.

We focused on OS partnerships as this is an emerging model that aims to accelerate science and innovation. These outcomes are captured in a first meeting report: Defining Success in Open Science.

On several occasions, these conversations turned to the challenges that must be addressed and new policies required to effectively and sustainably advance OS practice.

Thereupon, in this report, we describe the concerns raised and what is needed to address them supplemented by our review of the literature, and suggest the stakeholder groups that may be best placed to begin to take action.

It emerges that to be successful, OS will require the active engagement of all stakeholders: while the research community must develop research questions, identify partners and networks, policy communities need to create an environment that is supportive of experimentation by removing barriers.

This report aims to contribute to ongoing discussions about OS and its implementation. It is also part of a step-wise process to develop and mobilize a toolkit of quantitative and qualitative indicators to assist global stakeholders in implementing high value OS collaborations.

Currently in co-development through an open and international process, this set of measures will allow the generation of needed evidence on the influence of OS partnerships on research, innovation, and critical social and economic goals.

URL : Identifying the challenges in implementing open science

DOI : http://dx.doi.org/10.12688/mniopenres.12805.1

Citizen Science: Innovation in Open Science, Society and Policy

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Edited by Susanne Hecker, Muki Haklay, Anne Bowser, Zen Makuch, Johannes Vogel and Aletta Bonn

Citizen science, the active participation of the public in scientific research projects, is a rapidly expanding field in open science and open innovation. It provides an integrated model of public knowledge production and engagement with science.

As a growing worldwide phenomenon, it is invigorated by evolving new technologies that connect people easily and effectively with the scientific community.

Catalysed by citizens’ wishes to be actively involved in scientific processes, as a result of recent societal trends, it also offers contributions to the rise in tertiary education. In addition, citizen science provides a valuable tool for citizens to play a more active role in sustainable development.

Citizen Science: Innovation in Open Science, Society and Policy identifies and explains the role of citizen science within innovation in science and society, and as a vibrant and productive science-policy interface.

The scope of this volume is global, geared towards identifying solutions and lessons to be applied across science, practice and policy.

The chapters consider the role of citizen science in the context of the wider agenda of open science and open innovation, and discusses progress towards responsible research and innovation, two of the most critical aspects of science today.

URL : Citizen Science: Innovation in Open Science, Society and Policy

Alternative location : https://www.ucl.ac.uk/ucl-press/browse-books/citizen-science

Opening Science with Institutional Repository: A Case Study of Vilnius University Library

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Authors : Jūratė Kuprienė, Žibutė Petrauskien

The future strategies for opening science have become important to libraries which serve scientific institutions by providing institutional repository infrastructures and services.

Vilnius University Library provides such an infrastructure for Vilnius University, which is the biggest higher education institution in Lithuania (with more than 20,200 students, 1,330 academic staff members, and 450 researchers ), and manages services and infrastructure of the national open access repository eLABa and the national open access data archive MIDAS.

As the new platforms of these repositories began operating in the beginning of 2015, new policies and routines for organizing work with scientific publications and data had to be implemented.

This meant new roles for the Library and librarians, too. The University Senate approved the new Regulations of the Library on 13 June 2017 with the task to develop the scholarly communication tools dedicated to sustaining open access to information and open science.

Thus, Vilnius University Library performs the leading role in opening science by providing strategic insights and solutions for development of services dedicated to researchers, students and the public in Lithuania.

As it was not presented properly at the international level before, this article presents the case of Vilnius University Library which actively cooperates with other Lithuanian academic institutions, works in creating and coordinating policies, conducts research on the improvements and services of eLABa and MIDAS, and suggests and implements the integral solutions for opening science.

URL : Opening Science with Institutional Repository: A Case Study of Vilnius University Library

DOI : http://doi.org/10.18352/lq.10217