Archives des mots-clés : open science

Open science, reproducibility, and transparency in ecology

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Authors : Stephen M. Powers, Stephanie E. Hampton

Reproducibility is a key tenet of the scientific process that dictates the reliability and generality of results and methods. The complexities of ecological observations and data present novel challenges in satisfying needs for reproducibility and also transparency.

Ecological systems are dynamic and heterogeneous, interacting with numerous factors that sculpt natural history and that investigators cannot completely control. Observations may be highly dependent on spatial and temporal context, making them very difficult to reproduce, but computational reproducibility can still be achieved.

Computational reproducibility often refers to the ability to produce equivalent analytical outcomes from the same data set using the same code and software as the original study.

When coded workflows are shared, authors and editors provide transparency for readers and allow other researchers to build directly and efficiently on primary work. These qualities may be especially important in ecological applications that have important or controversial implications for science, management, and policy.

Expectations for computational reproducibility and transparency are shifting rapidly in the sciences.

In this work, we highlight many of the unique challenges for ecology along with practical guidelines for reproducibility and transparency, as ecologists continue to participate in the stewardship of critical environmental information and ensure that research methods demonstrate integrity.

URL : Open science, reproducibility, and transparency in ecology

DOI : https://doi.org/10.1002/eap.1822

Someone has to pay: The global sustainability coalition for open science services (SCOSS)

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Authors : Martin Borchert, Vanessa Proudman

The Open Access (OA) and Open Science (OS) movement is gaining momentum with an increasing number of scholarly outputs openly and freely available to researchers and the community. OA and OS cannot however, be free for everyone.

Someone has to pay for the infrastructure and there has to be a supporting economy. While many commercial publishers are charging for OA, there are many OA and OS infrastructure providers baring the cost of providing infrastructure. Without funding, essential services that many are dependent upon to implement government and funder OA policies worldwide, are at risk of service degradation, reduced availability and even survival. Something had to be done.

In response, the Global Sustainable Coalition for Open Science Services (SCOSS) was formed in 2017 as a result of collaborations between key global stakeholders, with SPARC Europe as the co-ordinator.

It aims to develop and apply a rigorous proposal and assessment process to provide guidance to the OA and OS community on what to fund.

It uses a new financial crowdfunding contribution model seeking a three-year commitment for funding for the services it recommends. This will help improve the financial position, resilience and sustainability of these OA / OS infrastructure services and will help them on their way to find a mid to long-term sustainable solution for years to come.

The first open science services to receive assistance were Sherpa RoMEO which is operated by the Joint Information Steering Committee (Jisc, UK) and provides summary information of journal and publisher OA polices; and the Directory of Open Access Journals (DOAJ) which provides a list of over 10,000 peer-reviewed open access journals.

Since launching in November 2017, a growing number of university libraries from across the globe are committing to fund Sherpa/Romeo and DOAJ for the next there years.

This paper will provide an introduction to SCOSS and its purpose, governance, processes, and challenges and will give an update on institutional financial commitments to date.

URL : https://docs.lib.purdue.edu/cgi/viewcontent.cgi?article=2229&context=iatul

Open science and codes of conduct on research integrity

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Author : Heidi Laine

The purpose of this article is to examine the conceptual alignment between the ethical principles of research integrity and open science. Research integrity is represented in this study by four general codes of conduct on responsible conduct of research (RCR), three of them international in scope, and one national.

A representative list of ethical principles associated with open science is compiled in order to create categories for assessing the content of the codes. According to the analysis, the current understanding of RCR is too focused on traditional publications and the so called FFP definition of research misconduct to fully support open science.

The main gaps include recognising citizen science and societal outreach and supporting open collaboration both among the research community and beyond its traditional borders.

Updates for both the content of CoCs as well as the processes of creating such guidelines are suggested.

URL : Open science and codes of conduct on research integrity

DOI : https://doi.org/10.23978/inf.77414

Text data mining and data quality management for research information systems in the context of open data and open science

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Authors : Otmane Azeroual, Gunter Saake, Mohammad Abuosba, Joachim Schöpfel

In the implementation and use of research information systems (RIS) in scientific institutions, text data mining and semantic technologies are a key technology for the meaningful use of large amounts of data.

It is not the collection of data that is difficult, but the further processing and integration of the data in RIS. Data is usually not uniformly formatted and structured, such as texts and tables that cannot be linked.

These include various source systems with their different data formats such as project and publication databases, CERIF and RCD data model, etc. Internal and external data sources continue to develop.

On the one hand, they must be constantly synchronized and the results of the data links checked. On the other hand, the texts must be processed in natural language and certain information extracted.

Using text data mining, the quality of the metadata is analyzed and this identifies the entities and general keywords. So that the user is supported in the search for interesting research information.

The information age makes it easier to store huge amounts of data and increase the number of documents on the internet, in institutions’ intranets, in newswires and blogs is overwhelming.

Search engines should help to specifically open up these sources of information and make them usable for administrative and research purposes. Against this backdrop, the aim of this paper is to provide an overview of text data mining techniques and the management of successful data quality for RIS in the context of open data and open science in scientific institutions and libraries, as well as to provide ideas for their application. In particular, solutions for the RIS will be presented.

URL : https://arxiv.org/abs/1812.04298

The principles of tomorrow’s university

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Authors : Daniel S. Katz, Gabrielle Allen, Lorena A. Barba, Devin R. Berg, Holly Bik, Carl Boettiger, Christine L. Borgman, C. Titus Brown, Stuart Buck, Randy Burd, Anita de Waard, Martin Paul Eve, Brian E. Granger, Josh Greenberg, Adina Howe, Bill Howe, May Khanna, Timothy L. Killeen, Matthew Mayernik, Erin McKiernan, Chris Mentzel, Nirav Merchant, Kyle E. Niemeyer, Laura Noren, Sarah M. Nusser, Daniel A. Reed, Edward Seidel, MacKenzie Smith, Jeffrey R. Spies, Matt Turk, John D. Van Horn, Jay Walsh

In the 21st Century, research is increasingly data- and computation-driven. Researchers, funders, and the larger community today emphasize the traits of openness and reproducibility.

In March 2017, 13 mostly early-career research leaders who are building their careers around these traits came together with ten university leaders (presidents, vice presidents, and vice provosts), representatives from four funding agencies, and eleven organizers and other stakeholders in an NIH- and NSF-funded one-day, invitation-only workshop titled “Imagining Tomorrow’s University.”

Workshop attendees were charged with launching a new dialog around open research – the current status, opportunities for advancement, and challenges that limit sharing.

The workshop examined how the internet-enabled research world has changed, and how universities need to change to adapt commensurately, aiming to understand how universities can and should make themselves competitive and attract the best students, staff, and faculty in this new world.

During the workshop, the participants re-imagined scholarship, education, and institutions for an open, networked era, to uncover new opportunities for universities to create value and serve society.

They expressed the results of these deliberations as a set of 22 principles of tomorrow’s university across six areas: credit and attribution, communities, outreach and engagement, education, preservation and reproducibility, and technologies.

Activities that follow on from workshop results take one of three forms. First, since the workshop, a number of workshop authors have further developed and published their white papers to make their reflections and recommendations more concrete.

These authors are also conducting efforts to implement these ideas, and to make changes in the university system.

Second, we plan to organise a follow-up workshop that focuses on how these principles could be implemented.

Third, we believe that the outcomes of this workshop support and are connected with recent theoretical work on the position and future of open knowledge institutions.

URL : The principles of tomorrow’s university

DOI : https://doi.org/10.12688/f1000research.17425.1

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