Archives des mots-clés : research data

Vers une culture de la donnée en SHS : Une étude à l’Université de Lille

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Auteur/Author : Joachim Schöpfel

La science ouverte figure parmi les priorités de l’Etat français. Dans la continuité des chantiers engagés par le gouvernement français sur la transformation numérique de l’Etat et sa modernisation, le deuxième plan d’action national 2018-2020 “Pour une action publique transparente et collaborative” précise que la France « soutient la mise en œuvre des principes du gouvernement ouvert pour renforcer (…) l’accès aux matériaux et résultats de la recherche ».

Le plan national pour la science ouverte, présenté début juillet 2018, a confirmé cette ambition. L’objectif est que les données produites par la recherche publique soient progressivement structurées en conformité avec les principes FAIR, préservées et, quand cela est possible, ouvertes.

Notre étude “Vers une culture de la donnée en SHS” souhaite contribuer à la mise en œuvre de l’écosystème de la science ouverte sur le terrain d’un campus universitaire.

L’étude a été réalisée dans le cadre du projet structurant D4Humanities, avec un financement de la MESHS et du Conseil Régional Hauts-de-France, et elle fait suite à des travaux de recherche menés depuis 2013 par le laboratoire GERiiCO.

Conduite sous forme d’entretiens avec 51 chercheurs, doctorants, responsables de laboratoires, chefs de projets et ingénieurs en charge de données, l’étude poursuit trois objectifs :

  1. (Re)Mettre les enseignants-chercheurs au cœur de la mise en œuvre de l’écosystème de la science ouverte sur le campus, avec leurs besoins, priorités et interrogations.
  2. Identifier des opportunités et verrous pour une politique de données.
  3. Recommander dix actions à mettre en place pour développer la culture de données sur le campus.

Menée comme un audit sur un terrain particulier et dans le domaine des sciences humaines et sociales, l’étude a une portée pragmatique: dégager les éléments indispensables pour une politique cohérente de la production, gestion et réutilisation des données de la recherche sur un campus en sciences humaines et sociales, et contribuer ainsi à l’appropriation du concept de la science ouverte par une « mise en culture de la donnée, qui effectue une mise en sens d’usages disséminés et spécialisés de données ouvertes ».

Une première partie (« Constats préalables ») s’appuie sur deux études (Rennes 2, Lille 3) pour mieux cerner le concept de la donnée de recherche et son caractère de « longue traîne » ; cette partie synthétise les pratiques, motivations et attentes des enseignants-chercheurs dans ce domaine, en SHS.

Elle aborde également d’une manière générale la question des services et dispositifs de données. Une deuxième partie (« Observations ») décrit un paysage contrasté à partir des entretiens menés en 2017 et 2018 sur le campus SHS de l’Université de Lille.

Les besoins prioritaires des chercheurs sont la sécurité des données et systèmes, et la communication au sein des projets. L’image qui se dégage est un continuum de pratiques plus ou moins efficaces, formalisées et adéquates, avec une gouvernance parfois incertaine, au niveau des projets aussi bien qu’au niveau des structures.

Ces pratiques sont liées aux communautés disciplinaires mais plus encore, aux méthodes, équipements et thématiques scientifiques. La troisième partie (« Vers une culture de la donnée ») liste d’une manière succincte dix recommandations qui, ensemble, définissent un cadre de référence pour la mise en œuvre d’une politique de données sur un campus SHS :

  1. Mettre en place un pilotage scientifique
  2. Investir d’une manière ciblée
  3. Viser les projets, pas les laboratoires
  4. Utiliser les plans de gestion comme levier
  5. Apporter des réponses aux contraintes de sécurité
  6. Apporter des réponses aux besoins de communication
  7. Apporter des réponses aux besoins de curation
  8. Proposer plusieurs solutions pour la conservation des données
  9. Institutionnaliser le lien avec la TGIR Huma-Num
  10. Soutenir les bonnes pratiques

URL : Vers une culture de la donnée en SHS : Une étude à l’Université de Lille

Alternative location : https://hal.archives-ouvertes.fr/GERIICO/hal-01846849v1

Health Sciences Libraries Advancing Collaborative Clinical Research Data Management in Universities

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Authors : Tania P. Bardyn, Emily F. Patridge, Michael T. Moore, Jane J. Koh

Purpose

Medical libraries need to actively review their service models and explore partnerships with other campus entities to provide better-coordinated clinical research management services to faculty and researchers. TRAIL (Translational Research and Information Lab), a five-partner initiative at the University of Washington (UW), explores how best to leverage existing expertise and space to deliver clinical research data management (CRDM) services and emerging technology support to clinical researchers at UW and collaborating institutions in the Pacific Northwest.

Methods

The initiative offers 14 services and a technology-enhanced innovation lab located in the Health Sciences Library (HSL) to support the University of Washington clinical and research enterprise.

Sharing of staff and resources merges library and non-library workflows, better coordinating data and innovation services to clinical researchers. Librarians have adopted new roles in CRDM, such as providing user support and training for UW’s Research Electronic Data Capture (REDCap) instance.

Results

TRAIL staff are quickly adapting to changing workflows and shared services, including teaching classes on tools used to manage clinical research data. Researcher interest in TRAIL has sparked new collaborative initiatives and service offerings. Marketing and promotion will be important for raising researchers’ awareness of available services.

Conclusions

Medical librarians are developing new skills by supporting and teaching CRDM. Clinical and data librarians better understand the information needs of clinical and translational researchers by being involved in the earlier stages of the research cycle and identifying technologies that can improve healthcare outcomes.

At health sciences libraries, leveraging existing resources and bringing services together is central to how university medical librarians will operate in the future.

DOI : https://doi.org/10.7191/jeslib.2018.1130

Clinical Trial Participants’ Views of the Risks and Benefits of Data Sharing

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Authors : Michelle M. Mello, Van Lieou, Steven N. Goodman

Background

Sharing of participant-level clinical trial data has potential benefits, but concerns about potential harms to research participants have led some pharmaceutical sponsors and investigators to urge caution. Little is known about clinical trial participants’ perceptions of the risks of data sharing.

Methods

We conducted a structured survey of 771 current and recent participants from a diverse sample of clinical trials at three academic medical centers in the United States. Surveys were distributed by mail (350 completed surveys) and in clinic waiting rooms (421 completed surveys) (overall response rate, 79%).

Results

Less than 8% of respondents felt that the potential negative consequences of data sharing outweighed the benefits. A total of 93% were very or somewhat likely to allow their own data to be shared with university scientists, and 82% were very or somewhat likely to share with scientists in for-profit companies.

Willingness to share data did not vary appreciably with the purpose for which the data would be used, with the exception that fewer participants were willing to share their data for use in litigation.

The respondents’ greatest concerns were that data sharing might make others less willing to enroll in clinical trials (37% very or somewhat concerned), that data would be used for marketing purposes (34%), or that data could be stolen (30%). Less concern was expressed about discrimination (22%) and exploitation of data for profit (20%).

Conclusions

In our study, few clinical trial participants had strong concerns about the risks of data sharing. Provided that adequate security safeguards were in place, most participants were willing to share their data for a wide range of uses. (Funded by the Greenwall Foundation.)

URL : https://www.nejm.org/doi/full/10.1056/NEJMsa1713258

Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers

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Authors : John A. Borghi, Ana E. Van Gulick

Neuroimaging methods such as magnetic resonance imaging (MRI) involve complex data collection and analysis protocols, which necessitate the establishment of good research data management (RDM). Despite efforts within the field to address issues related to rigor and reproducibility, information about the RDM-related practices and perceptions of neuroimaging researchers remains largely anecdotal.

To inform such efforts, we conducted an online survey of active MRI researchers that covered a range of RDM-related topics. Survey questions addressed the type(s) of data collected, tools used for data storage, organization, and analysis, and the degree to which practices are defined and standardized within a research group.

Our results demonstrate that neuroimaging data is acquired in multifarious forms, transformed and analyzed using a wide variety of software tools, and that RDM practices and perceptions vary considerably both within and between research groups, with trainees reporting less consistency than faculty.

Ratings of the maturity of RDM practices from ad-hoc to refined were relatively high during the data collection and analysis phases of a project and significantly lower during the data sharing phase.

Perceptions of emerging practices including open access publishing and preregistration were largely positive, but demonstrated little adoption into current practice.

URL : Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers

DOI : https://doi.org/10.1371/journal.pone.0200562

The Modern Research Data Portal: a design pattern for networked, data-intensive science

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Authors : Kyle Chard, Eli Dart, Ian Foster​, David Shifflett, Steven Tuecke, Jason Williams

We describe best practices for providing convenient, high-speed, secure access to large data via research data portals. We capture these best practices in a new design pattern, the Modern Research Data Portal, that disaggregates the traditional monolithic web-based data portal to achieve orders-of-magnitude increases in data transfer performance, support new deployment architectures that decouple control logic from data storage, and reduce development and operations costs.

We introduce the design pattern; explain how it leverages high-performance data enclaves and cloud-based data management services; review representative examples at research laboratories and universities, including both experimental facilities and supercomputer sites; describe how to leverage Python APIs for authentication, authorization, data transfer, and data sharing; and use coding examples to demonstrate how these APIs can be used to implement a range of research data portal capabilities.

Sample code at a companion web site, https://docs.globus.org/mrdp, provides application skeletons that readers can adapt to realize their own research data portals.

URL : The Modern Research Data Portal: a design pattern for networked, data-intensive science

DOI : https://doi.org/10.7717/peerj-cs.144

Interoperability and FAIRness through a novel combination of Web technologies

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Authors : Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris A. Swertz, Fleur D.L. Kelpin, Alasdair J.G. Gray, Erik A. Schultes, Erik M. van Mulligen, Paolo Ciccarese, Arnold Kuzniar, Anand Gavai, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT).

These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not.

The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability.

Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings.

We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles.

The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs.

URL : Interoperability and FAIRness through a novel combination of Web technologies

DOI : https://doi.org/10.7717/peerj-cs.110

Enhancing the Research Data Management of Computer-Based Educational Assessments in Switzerland

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Authors : Catharina Wasner, Ingo Barkow, Fabian Odoni

Since 2006 the education authorities in Switzerland have been obliged by the Constitution to harmonize important benchmarks in the educational system throughout Switzerland. With the development of national educational objectives in four disciplines an important basis for the implementation of this constitutional mandate was created.

In 2013 the Swiss National Core Skills Assessment Program (in German: ÜGK – Überprüfung der Grundkompetenzen) was initiated to investigate the skills of students, starting with three of four domains: mathematics, language of teaching and first foreign language in grades 2, 6 and 9. ÜGK uses a computer-based test and a sample size of 25.000 students per year.

A huge challenge for computer-based educational assessment is the research data management process. Data from several different systems and tools existing in different formats has to be merged to obtain data products researchers can utilize.

The long term preservation has to be adapted as well. In this paper, we describe our current processes and data sources as well as our ideas for enhancing the data management.

URL : Enhancing the Research Data Management of Computer-Based Educational Assessments in Switzerland

DOI : http://doi.org/10.5334/dsj-2018-018