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16 Research products

  • DARIAH EU
  • 2013-2022
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  • DARIAH EU

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Berg, Hannes; Wirtz Martin, Maria A.; Altincekic, Nadide; Alshamleh, Islam; +20 Authors

    SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. Angewandte Chemie. International Edition, 61 (46) ISSN:0570-0833 ISSN:1433-7851 ISSN:1521-3773

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      Article . 2022
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Hannes Berg; Maria A. Wirtz Martin; Nadide Altincekic; Islam Alshamleh; +79 Authors

    Work at BMRZ is supported by the state of Hesse. Work in Covid19-NMR was supported by the Goethe Corona Funds, by the IWBEFRE-program 20007375 of state of Hesse, the DFG through CRC902: “Molecular Principles of RNA-based regulation.” and through infrastructure funds (project numbers: 277478796, 277479031, 392682309, 452632086, 70653611) and by European Union’s Horizon 2020 research and innovation program iNEXT-discovery under grant agreement No 871037. BY-COVID receives funding from the European Union’s Horizon Europe Research and Innovation Programme under grant agreement number 101046203. “INSPIRED” (MIS 5002550) project, implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co-financed by Greece and the EU (European Regional Development Fund) and the FP7 REGPOT CT-2011-285950—“SEE-DRUG” project (purchase of UPAT’s 700 MHz NMR equipment). The support of the CERM/CIRMMP center of Instruct-ERIC is gratefully acknowledged. This work has been funded in part by a grant of the Italian Ministry of University and Research (FISR2020IP_02112, ID-COVID) and by Fondazione CR Firenze. A.S. is supported by the Deutsche Forschungsgemeinschaft [SFB902/B16, SCHL2062/2-1] and the Johanna Quandt Young Academy at Goethe [2019/AS01]. M.H. and C.F. thank SFB902 and the Stiftung Polytechnische Gesellschaft for the Scholarship. L.L. work was supported by the French National Research Agency (ANR, NMR-SCoV2-ORF8), the Fondation de la Recherche Médicale (FRM, NMR-SCoV2-ORF8), FINOVI and the IR-RMN-THC Fr3050 CNRS. Work at UConn Health was supported by grants from the US National Institutes of Health (R01 GM135592 to B.H., P41 GM111135 and R01 GM123249 to J.C.H.) and the US National Science Foundation (DBI 2030601 to J.C.H.). Latvian Council of Science Grant No. VPP-COVID-2020/1-0014. National Science Foundation EAGER MCB-2031269. This work was supported by the grant Krebsliga KFS-4903-08-2019 and SNF-311030_192646 to J.O. P.G. (ITMP) The EOSC Future project is co-funded by the European Union Horizon Programme call INFRAEOSC-03-2020—Grant Agreement Number 101017536. Open Access funding enabled and organized by Projekt DEAL SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. 12 pags., 4 figs., 3 tabs. Peer reviewed

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Angewandte Chemie In...arrow_drop_down
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    Angewandte Chemie International Edition
    Other literature type . Article . 2022 . Peer-reviewed
    License: CC BY
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    Angewandte Chemie
    Article . 2022 . Peer-reviewed
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    https://doi.org/10.26083/tupri...
    Article . 2024
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Angewandte Chemie In...arrow_drop_down
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      Angewandte Chemie International Edition
      Other literature type . Article . 2022 . Peer-reviewed
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      Angewandte Chemie
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      https://doi.org/10.26083/tupri...
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Daga, Enrico; Asprino, Luigi; Damiano, Rossana; Diaz Agudo, Belen; +9 Authors

    Digital archives of memory institutions are typically concerned with the cataloguing of artefacts of artistic, historical, and cultural value. Recently, new forms of citizen participation in cultural heritage have emerged, producing a wealth of material spanning from visitors’ experiential feedback on exhibitions and cultural artefacts, to digitally mediated interactions like the ones happening on social media platforms. Citizen curation is proposed in the context of the European project SPICE - Social Participation, Cohesion, and Inclusion through Cultural Engagement - as a methodology for producing, collecting, interpreting, and archiving people’s responses to cultural objects, with the aim of favouring the emergence of multiple, sometimes conflicting viewpoints, and motivating users and memory institutions to reflect upon them. We argue that citizen curation urges to rethink the nature of computational infrastructures supporting data management of memory institutions, bringing novel challenges that include issues of distribution, authoritativeness, interdependence, privacy, and rights management. To approach these issues, we survey relevant literature towards a distributed, Linked Data infrastructure, with a focus on identifying the roles and requirements involved in such an infrastructure. We show how existing research can contribute significantly in facing the challenges raised by citizen curation, and discuss challenges and opportunities from the socio-technical standpoint.

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    ZENODO
    Article . 2021
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Archivio Istituziona...arrow_drop_down
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      ZENODO
      Article . 2021
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  • Authors: Tahko, Tuuli; Zehavi, Ora; Lhotak, Martin; Romanova, Natasha; +3 Authors

    The DESIR project sets out to strengthen the sustainability of DARIAH and firmly establish it as a long-term leader and partner within arts and humanities communities. The project was designed to address six core infrastructural sustainability dimensions and one of these was dedicated to training and education, which is also one of the four pillars identified in the DARIAH Strategic Plan 2019-2026. In the framework of Work Package 7: Teaching, DESIR organised dedicated workshops in the six DARIAH accession countries (Czech Republic, Finland, Israel, Spain, Switzerland and the United Kingdom) to introduce them to the DARIAH infrastructure and related services, and to develop methodological research skills. The topic of each workshop was decided by accession countries representatives according to the training needs of the national communities of researchers in the (Digital) Humanities. Training topics varied greatly: on the one hand, some workshops had the objective to introduce participants to specific methodological research skills; on the other hand, a different approach was used, and some events focused on the infrastructural role of training and education. The workshops organised in the context of Work Package 7: Teaching are listed below:• CZECH REPUBLIC: “A series of fall tutorials 2019 organized by LINDAT/CLARIAHCZ, tutorial #3 on TEI Training”, November 28, 2019, Prague;• FINLAND: “Reuse & sustainability: Open Science and social sciences and humanities research infrastructures”, 23 October 2019, Helsinki;• ISRAEL: “Introduction to Text Encoding and Digital Editions”, 24 October 2019, Haifa;• SPAIN: “DESIR Workshop: Digital Tools, Shared Data, and Research Dissemination”, 3 July 2019, Madrid;• SWITZERLAND: “Sharing the Experience: Workflows for the Digital Humanities”, 5-6 December 2019, Neuchâtel;• UNITED KINGDOM: “Research Software Engineering for Digital Humanities: Role of Training in Sustaining Expertise”, 9 December, London.

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    Authors: John A. Walsh; Peter J. Cobb; Wayne de Fremery; Koraljka Golub; +9 Authors

    AbstractThe interdisciplinary field known as digital humanities (DH) is represented in various forms in the teaching and research practiced in iSchools. Building on the work of an iSchools organization committee charged with exploring digital humanities curricula, we present findings from a series of related studies exploring aspects of DH teaching, education, and research in iSchools, often in collaboration with other units and disciplines. Through a survey of iSchool programs and an online DH course registry, we investigate the various education models for DH training found in iSchools, followed by a detailed look at DH courses and curricula, explored through analysis of course syllabi and course descriptions. We take a brief look at collaborative disciplines with which iSchools cooperate on DH research projects or in offering DH education. Next, we explore DH careers through an analysis of relevant job advertisements. Finally, we offer some observations about the management and administrative challenges and opportunities related to offering a new iSchool DH program. Our results provide a snapshot of the current state of digital humanities in iSchools which may usefully inform the design and evolution of new DH programs, degrees, and related initiatives.

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    Journal of the Association for Information Science and Technology
    Article . 2021 . Peer-reviewed
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      Journal of the Association for Information Science and Technology
      Article . 2021 . Peer-reviewed
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  • Authors: Georgios Artopoulos;

    This article reports on the technical development and testing of the basic components of a virtual environment platform that could be used for the cross-disciplinary study of complex urban realities, such as the historic city of Nicosia, Cyprus - the last divided capital of Europe. This platform captures data of virtual visitors' movements in space, and the article suggests that these data could help better understand the impact of planning scenarios and design interventions in open public spaces that used to be popular among the citizens of the historic city. The article presents how this platform uses interaction and immersion opportunities to engage citizens and stakeholders in the management of public open spaces that are associated with built heritage. Crowd simulation is discussed as a computational technique that when is combined with the presented virtual environment platform, and under the right conditions, would contribute to a digital practice for small-scale urban modelling. However, it is beyond the scope of this technical note to provide a full empirical testing and validation of the presented immersive virtual environment.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Foka, Anna; Demiroglu, Osman Cenk; Barker, Elton; Mostofian, Nasrin; +4 Authors

    Abstract This progress article focuses on an overview of the potential and challenges of using contemporary Geographic Information System (GIS) applications for the visual rendering and analysis of textual spatial data. The case study is an ancient traveling narrative, Pausanias’s Description of Greece (Periegesis Hellados) which was written in the second century CE. First, we describe the process of converting the volumes to spatial data using a customized version of the open-source digital semantic annotation platform Recogito. Then the focus shifts to the implementation of collected and organized spatial data to a number of GIS applications: namely Google Maps, DARIAH Geo-Browser, Gephi, Palladio and ArcGIS. Through empirical experimentation with spatial data and their implementation in different platforms, our paper charts the ways in which contemporary GIS applications may be implemented to cast new light on ancient understandings of identity, space, and place.

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    Digital Scholarship in the Humanities
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  • Authors: Velloso-Lyons, Mae; Dombrowski, Quinn; Starkey, Kathryn;

    This paper introduces the Global Medieval Sourcebook (GMS), an online repository of medieval texts and translations with an open network of contributors. Drawing on our experience developing and building this project in two phases over six years, we reflect on questions regarding editorial, curatorial, and translation practices, and on technical issues involved in the preparation, display, and preservation of texts for online publication. As an example of a scholar-led digital project, the trajectory of the GMS has broad relevance for scholars planning digital curation work of their own. In particular, it offers a salutary example of the infrastructural barriers to sustaining collaborative digital work and a possible model for preserving a concluded project.

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  • Authors: Szprot, Jakub; Arpagaus, Brigitte; Ciula, Arianna; Clivaz, Claire; +14 Authors

    This report provides information about activities and progress towards establishing DARIAH membership in six countries: the Czech Republic, Finland, Israel, Spain, Switzerland, and the UK, which took place between July and December 2019. Previous activities were described in detail in the D3.2 - Regularly Monitor Country-Specific Progress in Enabling New DARIAH Membership. During the project lifetime, the Czech Republic joined DARIAH ERIC; in other countries, collaboration with DARIAH has been greatly strengthened and significant progress regarding DARIAH membership has been achieved. The report also outlines the next steps in the accession processes, building on the results of the DESIR project.

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    Authors: Riccardo Pozzo; Andrea Filippetti; Mario Paolucci; Vania Virgili;

    AbstractThis article introduces the notion of cultural innovation, which requires adapting our approach to co-creation. The argument opens with a first conceptualization of cultural innovation as an additional and autonomous category of the complex processes of co-creation. The dimensions of cultural innovation are contrasted against other forms of innovation. In a second step, the article makes an unprecedented attempt in describing processes and outcomes of cultural innovation, while showing their operationalization in some empirical case studies. In the conclusion, the article considers policy implications resulting from the novel definition of cultural innovation as the outcome of complex processes that involve the reflection of knowledge flows across the social environment within communities of practices while fostering the inclusion of diversity in society. First and foremost, cultural innovation takes a critical stance against inequalities in the distribution of knowledge and builds innovation for improving the welfare of individuals and communities.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Berg, Hannes; Wirtz Martin, Maria A.; Altincekic, Nadide; Alshamleh, Islam; +20 Authors

    SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. Angewandte Chemie. International Edition, 61 (46) ISSN:0570-0833 ISSN:1433-7851 ISSN:1521-3773

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    Authors: Hannes Berg; Maria A. Wirtz Martin; Nadide Altincekic; Islam Alshamleh; +79 Authors

    Work at BMRZ is supported by the state of Hesse. Work in Covid19-NMR was supported by the Goethe Corona Funds, by the IWBEFRE-program 20007375 of state of Hesse, the DFG through CRC902: “Molecular Principles of RNA-based regulation.” and through infrastructure funds (project numbers: 277478796, 277479031, 392682309, 452632086, 70653611) and by European Union’s Horizon 2020 research and innovation program iNEXT-discovery under grant agreement No 871037. BY-COVID receives funding from the European Union’s Horizon Europe Research and Innovation Programme under grant agreement number 101046203. “INSPIRED” (MIS 5002550) project, implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co-financed by Greece and the EU (European Regional Development Fund) and the FP7 REGPOT CT-2011-285950—“SEE-DRUG” project (purchase of UPAT’s 700 MHz NMR equipment). The support of the CERM/CIRMMP center of Instruct-ERIC is gratefully acknowledged. This work has been funded in part by a grant of the Italian Ministry of University and Research (FISR2020IP_02112, ID-COVID) and by Fondazione CR Firenze. A.S. is supported by the Deutsche Forschungsgemeinschaft [SFB902/B16, SCHL2062/2-1] and the Johanna Quandt Young Academy at Goethe [2019/AS01]. M.H. and C.F. thank SFB902 and the Stiftung Polytechnische Gesellschaft for the Scholarship. L.L. work was supported by the French National Research Agency (ANR, NMR-SCoV2-ORF8), the Fondation de la Recherche Médicale (FRM, NMR-SCoV2-ORF8), FINOVI and the IR-RMN-THC Fr3050 CNRS. Work at UConn Health was supported by grants from the US National Institutes of Health (R01 GM135592 to B.H., P41 GM111135 and R01 GM123249 to J.C.H.) and the US National Science Foundation (DBI 2030601 to J.C.H.). Latvian Council of Science Grant No. VPP-COVID-2020/1-0014. National Science Foundation EAGER MCB-2031269. This work was supported by the grant Krebsliga KFS-4903-08-2019 and SNF-311030_192646 to J.O. P.G. (ITMP) The EOSC Future project is co-funded by the European Union Horizon Programme call INFRAEOSC-03-2020—Grant Agreement Number 101017536. Open Access funding enabled and organized by Projekt DEAL SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. 12 pags., 4 figs., 3 tabs. Peer reviewed

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    Angewandte Chemie International Edition
    Other literature type . Article . 2022 . Peer-reviewed
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      Angewandte Chemie
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    Authors: Daga, Enrico; Asprino, Luigi; Damiano, Rossana; Diaz Agudo, Belen; +9 Authors

    Digital archives of memory institutions are typically concerned with the cataloguing of artefacts of artistic, historical, and cultural value. Recently, new forms of citizen participation in cultural heritage have emerged, producing a wealth of material spanning from visitors’ experiential feedback on exhibitions and cultural artefacts, to digitally mediated interactions like the ones happening on social media platforms. Citizen curation is proposed in the context of the European project SPICE - Social Participation, Cohesion, and Inclusion through Cultural Engagement - as a methodology for producing, collecting, interpreting, and archiving people’s responses to cultural objects, with the aim of favouring the emergence of multiple, sometimes conflicting viewpoints, and motivating users and memory institutions to reflect upon them. We argue that citizen curation urges to rethink the nature of computational infrastructures supporting data management of memory institutions, bringing novel challenges that include issues of distribution, authoritativeness, interdependence, privacy, and rights management. To approach these issues, we survey relevant literature towards a distributed, Linked Data infrastructure, with a focus on identifying the roles and requirements involved in such an infrastructure. We show how existing research can contribute significantly in facing the challenges raised by citizen curation, and discuss challenges and opportunities from the socio-technical standpoint.

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    ZENODO
    Article . 2021
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