Archives des mots-clés : research data

Towards FAIR protocols and workflows: the OpenPREDICT use case

Posté le par

Authors : Remzi Celebi, Joao Rebelo Moreira, Ahmed A. Hassan, Sandeep Ayyar, Lars Ridder, Tobias Kuhn, Michel Dumontier

It is essential for the advancement of science that researchers share, reuse and reproduce each other’s workflows and protocols. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize the importance of making digital objects findable and reusable by others.

The question of how to apply these principles not just to data but also to the workflows and protocols that consume and produce them is still under debate and poses a number of challenges. In this paper we describe a two-fold approach of simultaneously applying the FAIR principles to scientific workflows as well as the involved data.

We apply and evaluate our approach on the case of the PREDICT workflow, a highly cited drug repurposing workflow. This includes FAIRification of the involved datasets, as well as applying semantic technologies to represent and store data about the detailed versions of the general protocol, of the concrete workflow instructions, and of their execution traces.

We propose a semantic model to address these specific requirements and was evaluated by answering competency questions. This semantic model consists of classes and relations from a number of existing ontologies, including Workflow4ever, PROV, EDAM, and BPMN.

This allowed us then to formulate and answer new kinds of competency questions. Our evaluation shows the high degree to which our FAIRified OpenPREDICT workflow now adheres to the FAIR principles and the practicality and usefulness of being able to answer our new competency questions.

URL : Towards FAIR protocols and workflows: the OpenPREDICT use case

DOI : https://doi.org/10.7717/peerj-cs.281

What drives and inhibits researchers to share and use open research data? A systematic literature review to analyze factors influencing open research data adoption

Posté le par

Authors : Anneke Zuiderwijk, Rhythima Shinde, Wei Jeng

Both sharing and using open research data have the revolutionary potentials for forwarding scientific advancement. Although previous research gives insight into researchers’ drivers and inhibitors for sharing and using open research data, both these drivers and inhibitors have not yet been integrated via a thematic analysis and a theoretical argument is lacking.

This study’s purpose is to systematically review the literature on individual researchers’ drivers and inhibitors for sharing and using open research data. This study systematically analyzed 32 open data studies (published between 2004 and 2019 inclusively) and elicited drivers plus inhibitors for both open research data sharing and use in eleven categories total that are: ‘the researcher’s background’, ‘requirements and formal obligations’, ‘personal drivers and intrinsic motivations’, ‘facilitating conditions’, ‘trust’, ‘expected performance’, ‘social influence and affiliation’, ‘effort’, ‘the researcher’s experience and skills’, ‘legislation and regulation’, and ‘data characteristics.’

This study extensively discusses these categories, along with argues how such categories and factors are connected using a thematic analysis. Also, this study discusses several opportunities for altogether applying, extending, using, and testing theories in open research data studies.

With such discussions, an overview of identified categories and factors can be further applied to examine both researchers’ drivers and inhibitors in different research disciplines, such as those with low rates of data sharing and use versus disciplines with high rates of data sharing plus use. What’s more, this study serves as a first vital step towards developing effective incentives for both open data sharing and use behavior.

URL : What drives and inhibits researchers to share and use open research data? A systematic literature review to analyze factors influencing open research data adoption

DOI : https://doi.org/10.1371/journal.pone.0239283

Research data management policy and practice in Chinese university libraries

Posté le par

Authors : Yingshen Huang, Andrew M. Cox, Laura Sbaffi

On April 2, 2018, the State Council of China formally released a national Research Data Management (RDM) policy “Measures for Managing Scientific Data”. In this context and given that university libraries have played an important role in supporting RDM at an institutional level in North America, Europe, and Australasia, the aim of this article is to explore the current status of RDM in Chinese universities, in particular how university libraries have been involved in taking the agenda forward.

This article uses a mixed‐methods data collection approach and draws on a website analysis of university policies and services; a questionnaire for university librarians; and semi‐structured interviews. Findings indicate that Research Data Service at a local level in Chinese Universities are in their infancy.

There is more evidence of activity in developing data repositories than support services. There is little development of local policy. Among the explanations of this may be the existence of a national‐level infrastructure for some subject disciplines, the lack of professionalization of librarianship, and the relatively weak resonance of openness as an idea in the Chinese context.

URL : Research data management policy and practice in Chinese university libraries

DOI : https://doi.org/10.1002/asi.24413

Données à penser. Enjeux pratiques et éthiques autour des données dans le montage de projets de recherche européens

Posté le par

Auteurs/Authors : Delphine Cavallo, Camille Noûs

Cet article prend la forme d’un retour d’expérience sur le montage de projets de recherche européens, en déroulant les enchaînements entre objectifs, contraintes et prises de décisions autour de deux cas concrets.

Il montre comment les acteurs de ces projets – porteurs et porteuses scientifiques comme ingénieur-e-s – tentent de penser une réponse à la fois scientifique, documentaire, technologique et éthique aux exigences de la Commission européenne en matière de gestion des données de la recherche, à un moment où ces exigences ne correspondent ni à des métiers et pratiques intégrés dans les structures de recherche, ni à des routines ou des besoins identifiés parmi les équipes de recherche.

Il plaide pour la prise en compte conjointe entre chercheurs et chercheuses et ingénieur-e-s des enjeux éthiques liés à la gestion des données dès le montage des projets.

DOI : https://doi.org/10.4000/traces.10793

Ouverture des données de la recherche : les mutations juridiques récentes

Posté le par

Auteurs/Authors : Anne-Laure Stérin, Camille Noûs

Il est devenu « obligatoire » d’ouvrir les données de la recherche, ou plus précisément, certaines données de la recherche. Cette démarche d’ouverture suppose de mener, en amont du projet de recherche, une analyse fine et rigoureuse des données à collecter, avant de déterminer celles qui seront à ouvrir, et les modalités de leur ouverture (« aussi ouvertes que possible, aussi fermées que nécessaire »). Cette entreprise nécessite de faire collaborer des compétences diverses et d’y consacrer des moyens.

DOI : https://doi.org/10.4000/traces.10603

Models for Engaging Liaisons in Research Data Services

Posté le par

Authors : Megan Sapp Nelson, Abigail Goben

Research data services in academic libraries is often perceived as the purview of liaison librarians. A variety of models has emerged by which these services may be developed or implemented.

These include hierarchical models and those based more on individual interest. Of critical importance with any model, however, is the identification of support and opportunities for engagement from library administration and management in order to grow and assess the implementation of research data services.

URL : Models for Engaging Liaisons in Research Data Services

DOI : https://doi.org/10.7710/2162-3309.2382

Research methodology and characteristics of journal articles with original data, preprint articles and registered clinical trial protocols about COVID-19

Posté le par

Authors : Mahir Fidahic, Danijela Nujic, Renata Runjic, Marta Civljak, Zvjezdana Lovric Makaric, Livia Puljak

Background

The research community reacted rapidly to the emergence of COVID-19. We aimed to assess characteristics of journal articles, preprint articles, and registered trial protocols about COVID-19 and its causal agent SARS-CoV-2.

Methods

We analyzed characteristics of journal articles with original data indexed by March 19, 2020, in World Health Organization (WHO) COVID-19 collection, articles published on preprint servers medRxiv and bioRxiv by April 3, 2010.

Additionally, we assessed characteristics of clinical trials indexed in the WHO International Clinical Trials Registry Platform (WHO ICTRP) by April 7, 2020.

Results

Among the first 2118 articles on COVID-19 published in scholarly journals, 533 (25%) contained original data. The majority was published by authors from China (75%) and funded by Chinese sponsors (75%); a quarter was published in the Chinese language.

Among 312 articles that self-reported study design, the most frequent were retrospective studies (N = 88; 28%) and case reports (N = 86; 28%), analyzing patients’ characteristics (38%). Median Journal Impact Factor of journals where articles were published was 5.099.

Among 1088 analyzed preprint articles, the majority came from authors affiliated in China (51%) and were funded by sources in China (46%). Less than half reported study design; the majority were modeling studies (62%), and analyzed transmission/risk/prevalence (43%).

Of the 927 analyzed registered trials, the majority were interventional (58%). Half were already recruiting participants. The location for the conduct of the trial in the majority was China (N = 522; 63%).

The median number of planned participants was 140 (range: 1 to 15,000,000). Registered intervention trials used highly heterogeneous primary outcomes and tested highly heterogeneous interventions; the most frequently studied interventions were hydroxychloroquine (N = 39; 7.2%) and chloroquine (N = 16; 3%).

Conclusions

Early articles on COVID-19 were predominantly retrospective case reports and modeling studies. The diversity of outcomes used in intervention trial protocols indicates the urgent need for defining a core outcome set for COVID-19 research.

Chinese scholars had a head start in reporting about the new disease, but publishing articles in Chinese may limit their global reach. Mapping publications with original data can help finding gaps that will help us respond better to the new public health emergency.

URL : Research methodology and characteristics of journal articles with original data, preprint articles and registered clinical trial protocols about COVID-19

DOI : https://doi.org/10.1186/s12874-020-01047-2