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Nowadays, research challenges - often based on the collaborative analysis of a large amount of data - require suitable infrastructures and user-facing solutions promoting multidisciplinary collaboration and appropriate communication and sharing of data, processes, and outcomes. The D4Science infrastructure and its virtual research environments proved to be a viable and effective solution for many communities of practice and use cases.

La scienza aperta è un paradigma che influenza le pratiche di produzione e condivisione di conoscenza. Obiettivo di questa roadmap è delineare un percorso per la realizzazione e diffusione di pratiche e politiche di scienza aperta all'interno del Consiglio Nazionale delle Ricerche.

In December 2019, an initial cluster of interstitial bilateral pneumonia emerged in Wuhan, China. A human-to-human transmission was assumed and a previously unrecognized entity, termed coronavirus disease-19 (COVID-19) due to a novel coronavirus (SARS-CoV-2) was described. The infection has rapidly spread out all over the world and Italy has been the first European country experiencing the endemic wave with unexpected clinical severity in comparison with Asian countries. It has been shown that SARS-CoV-2 utilizes angiotensin converting enzyme 2 (ACE2) as host receptor and host proteases for cell surface binding and internalization. Thus, a predisposing genetic background can give reason for interindividual disease susceptibility and/or severity. Taking advantage of the Network of Italian Genomes (NIG), here we mined whole-exome sequencing data of 6930 Italian control individuals from five different centers looking forACE2variants. A number of variants with a potential impact on protein stability were identified. Among these, three more common missense changes, p.(Asn720Asp), p.(Lys26Arg), and p.(Gly211Arg) were predicted to interfere with protein structure and stabilization. Rare variants likely interfering with the internalization process, namely p.(Leu351Val) and p.(Pro389His), predicted to interfere with SARS-CoV-2 spike protein binding, were also observed. Comparison ofACE2WES data between a cohort of 131 patients and 258 controls allowed identifying a statistically significant (Pvalue

InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2021 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, eScience, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, i.e. D4Science and OpenAIRE. During 2021 InfraScience members contributed to the publishing of 25 papers, to the research and development activities of 18 research projects (15 funded by EU), to the organization of conferences and training events, to several working groups and task forces.

The open science paradigm is increasingly praised and encouraged for improving efficiency through deduplication of efforts and for ultimately accelerating scientific discoveries. Such shift towards a collaborative and inclusive scientific process implies an alteration of the traditional research workflows to include the different dimensions that characterise the new paradigm, from open access to new assessment metrics. This systematic study analyses the open science research workflows proposed so far, highlighting (i) their distribution over time, (ii) the various means and approaches used for communicating them, (iii) the terminology used for denominating them, and (iv) the scientific domains where workflows were proposed. Moreover, the workflows were analysed and compared concerning a set of open science aspects deriving from the UNESCO Recommendation on Open Science. Overall, a total of 40 relevant studies were identified and analysed, corresponding to 33 unique workflows. The findings highlight (a) the limited effort spent by the research community to propose and communicate workflows oriented to match open science requirements, and (b) the different nuances of the meaning and understanding of open science and the resulting gap between its theoretical aspects and its practical application to the research processes.

Federations are an effective mechanism for jointly contributing to a service offering, integrating resources provided by the different federation members. As the open science and the open innovation paradigms are increasingly pursued at the European level, the European Open Science Cloud (EOSC) has been envisaged as a federation of systems for creating a solution fully supporting the research data life cycle across borders and disciplines. This study analyses the federation approaches and solutions adopted by 11 of the major European federated research infrastructures (CLARIN, D4Science, EGI, ELIXIR, ENVRI, EPOS, Gaia-X, GEANT, GEOSS, OpenAIRE and PaNOSC) selected for their representativity following their service offering type and thematic area of expertise. A classification of federated and federating services is proposed in order to highlight the action areas that are to be considered when pursuing the creation of a federated infrastructure with the objective of enabling open science and open innovation.

The ever-growing availability of research artefacts of potential interest for users calls for helpers to assist their discovery. Artefacts of interest vary for the typology, e.g., papers, datasets, software. User interests are multifaceted and evolving. This paper analyses and classifies studies on recommender systems exploited to suggest research artefacts to researchers regarding the type of algorithm, users and their representations, item typologies and their representation, and evaluation methods used to assess the effectiveness of the recommendations. This study found that most of the current scientific artefacts recommender system focused only on recommending paper to individual researchers, just a few papers focused on dataset recommendation and software recommender system is unprecedented.

The FAIR principles have drawn a lot of attention since their publication in 2016. A broad range of stakeholders is confronting the implementation of these guiding principles in diverse contexts. This paper identifies and discusses the tools and approaches emerging from stakeholders' experiences adopting the FAIR principles in practice. In particular, 225 open access grey literature papers (namely, deliverables, milestones and data management plans) on FAIRification have been scrutinised to infer tools and approaches in use. The wealth of emerging tools (477) has been carefully analysed and organised into a comprehensive map highlighting the significant classes of instruments supporting FAIRification. A critical discussion on this collection of tools and approaches and the FAIRification completes the paper.

D4Science is an IT infrastructure specifically conceived to support the development and operation of Virtual Research Environments by the as-a-Service provisioning mode. This report documents the activities performed in 2022 to develop this infrastructure and support several projects and exploitations.

ObjectivesSubspecies pathogen typing is a pivotal tool to detect the emergence of high-risk clones in hospital settings and to limit their spreading among patients. Unfortunately, the most used subspecies typing methods (i.e. Pulsed-field Gel Electrophoresis - PFGE, Multi-Locus Sequence Typing - MLST and Whole Genome Sequencing - WGS) are too expensive and time consuming to be suitable for real-time surveillance. Here we present Hypervariable-Locus Melting Typing (HLMT), a novel subspecies typing approach based on High Resolution Melting (HRM) analysis, which allows pathogen typing in a few hours and with ∼5 euros per sample.MethodsHLMT types the strains by clustering them using melting temperatures (HLMT-clustering) and/or by assigning them to Melting Types (MTs) on the basis of a reference dataset (HLMT-assignment). We applied HLMT (clustering and typing) to 134 Klebsiella pneumoniae strains collected during outbreaks or surveillance programs in four hospitals. Then, we compared HLMT typing results to PFGE, MLST and WGS.ResultsHLMT-clustering distinguishes most of the K. pneumoniae high-risk clones with a sensitivity comparable to PFGE and MLST. It also drawed surveillance epidemiological curves comparable to those obtained by MLST, PFGE and WGS typing. Furthermore, the results obtained by HLMT-assignment were coherent to MLST for 96% of the typed strains with a Jaccard index of 0.912.ConclusionsHLMT is a fast and scalable method for pathogen typing, suitable for real-time hospital microbiological surveillance. HLMT is also inexpensive and thus it is applicable to infection control programs in low-middle income countries.

InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2020 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, e\-Sci\-ence, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, \ie D4Science and OpenAIRE. During 2020 InfraScience members contributed to the publishing of 30 papers, to the research and development activities of 12 research projects (11 funded by EU), to the organization of conferences and training events, to several working groups and task forces.

The enhancements in IT solutions and the open science movement are injecting changes in the practices dealing with data collection, collation, processing and analytics, and publishing in all the domains, including agri-food. However, in implementing these changes one of the major issues faced by the agri-food researchers is the fragmentation of the “assets” to be exploited when performing research tasks, e.g. data of interest are heterogeneous and scattered across several repositories, the tools modellers rely on are diverse and often make use of limited computing capacity, the publishing practices are various and rarely aim at making available the “whole story” with datasets, processes, workflows. This paper presents the AGINFRA PLUS endeavour to overcome these limitations by providing researchers in three designated communities with Virtual Research Environments facilitating the use of the “assets” of interest and promote collaboration.

The enhancements in IT solutions and the open science movement are injecting changes in the practices dealing with data collection, collation, processing, analytics, and publishing in all the domains, including agri-food. However, in implementing these changes one of the major issues faced by the agri-food researchers is the fragmentation of the “assets” to be exploited when performing research tasks, for example, data of interest are heterogeneous and scattered across several repositories, the tools modelers rely on are diverse and often make use of limited computing capacity, the publishing practices are various and rarely aim at making available the “whole story” including datasets, processes, and results. This paper presents the AGINFRA PLUS endeavor to overcome these limitations by providing researchers in three designated communities with Virtual Research Environments facilitating the use of the “assets” of interest and promote collaboration. © 2020 John Wiley & Sons Ltd

This chapter is describing the ISTI-CNR vision and contribution towards the implementation of Digital science infrastructures as collaborative, community-driven resources for Food & Agriculture. In particular, it stress the contribution Virtual Research Environments can give in terms of open science enablers.

This document summarises the views expressed by the Italian Computing and Data Initiative (ICDI) in response to the open consultation for the EOSC Strategic Research and Innovation Agenda (SRIA), closed on the 31st of August. It provides insightful input and suggestions about the current draft of the SRIA document shared with the wider EOSC community, with the aim of helping to shape the future vision of the European Open Science Cloud.

This paper aims to give some insights on how the European Open Science Cloud (EOSC) will be able to influence the Social Sciences and Humanities (SSH) sector, thus paving the way towards innovation. Points of discussion on how the LRs and RIs community can contribute to the revolution in the practice of research areas are provided.

On Thursday 26th of November the InfraEOSC-5 FAIR data and infrastructure Task Force, set-up by the projects in the INFRAEOSC-05-2018-2019 call: EOSC-synergy, EOSC-Pillar, EOSC-Nordic, NI4OS-Europe, ExPaNDS, FAIRsFAIR, and EOSCsecretariat.eu, organised a special edition of its usual monthly meeting to present to the European Commission the key work being carried out on the topic of FAIR data assessment and certification by the InfraEOSC-5 call funded initiatives. The event was co-organised by the EOSCsecretariat.eu and the FAIRsFAIR initiative and engaged all the InfraEOSC-5 call projects actively involved in the FAIR Task Force with the aim to provide an overview on the tools, challenges, lessons learned and recommendations towards FAIR Assessment and certification of digital objects and data repositories. The meeting also gave a deep-dive into practical use cases that demonstrate the impact of applying the current tools to different communities across Europe and the priorities for the stakeholders involved.

The objective of the EOSCpilot data interoperability task (6.2) is to demonstrate how to ensure availability of research data to services and users through an open cloud infrastructure. To do so, this task has produced a set of recommendations driving a coherent strategy, as well as a set of technical solutions to help users and programmatic services to find and access datasets across several disciplines, enabling the EOSC to be built around a more coordinated and aligned data ecosystem. The six recommendations driving our proposed strategy are: - The data guidelines and technical solutions proposed by the EOSC should be specific, common, simple, lightweight and collaborative. - All the data resources contributing to the EOSC should expose structured metadata. - The EOSC should reuse or build upon existing standards and formats, and promote the use of common best practices across scientific domains. - The EOSC should propose minimum information guidelines across scientific domains especially targeting key operational metadata which is important for services consuming data. - The EOSC should support an interconnected ecosystem of metadata catalogues as a fundamental service component to facilitate data discovery. - The EOSC should implement a monitoring service to validate standards and recommendations proposed by the EOSC. The four technical solutions that comprise the data strategy are: - A common minimum information metadata guideline for datasets in the EOSC. - Recommendations to establish a coordinated and interconnected ecosystem of dataset metadata catalogues. - Adoption of ResearchSchemas as a means to drive research data discoverability and accessibility. - A set of recommendations for common properties across multiple data types.

This deliverable is the second and final release of the EOSC Service Architecture. It sets the foundations characterising the EOSC System:(i) Its functionalities are provisioned as-a-Service; (ii) It is a highly distributed, evolving and heterogeneous hybrid cloud; (iii)Its operation and development is regulated by a set of Rules of Participation; (iv) It is modelled as an open and evolving System of Systems (SoS) where the component systems providing services include existing and emerging Research Infrastructures (including e-Infrastructures) and other types of Service Providers; (v) EOSC services provision is based on an open and evolving set of EOSC Nodes spread across several organisations and regions; (vi) EOSC Services should promote and support FAIRness. The deliverable identifies 47 classes of services that can be considered at this stage of development as the "Minimal Viable Product" able to match the EOSC overall goal. Such services include cross-cutting services together with services specifically envisaged to serve researchers, research administrators, third-party service providers as well as EOSC managers, service providers and service suppliers. This deliverable briefly highlights major contextual aspects already introduced in D5.1 and then describes the identified classes of services. The deliverable also discusses aspects related to "how" the system can/should be developed. The notions of "federation" and "interoperability" related to the building of this EOSC System are addressed highlighting the importance of dealing with these two concepts per-single service rather than from the perspective of EOSC as a whole.

In deep and cold subduction such as that experienced by the UHP Units of the Western Alps, carbon dissolution is a relevant mechanism for carbon transfer from the slab into the mantle. The UHP impure Cal-Dol-marbles from the Dora-Maira Massif are studied to investigate the poorly known evolution of dolomite during deep subduction. Dolomite shows four stages of growth, from pre-Alpine to early-retrograde Alpine, coupled with chemical variations and distinct included mineral assemblages. To explain the evidence for growth and partial reabsorption of dolomite through HP prograde, UHP peak, and UHP early-retrograde Alpine metamorphism, a chemically simple marble (Cal, Dol, Di, Fo, and retrograde Atg, Tr, Mg-Chl) has been studied in detail. Microstructural relationships, coupled with mineral chemistry, indicate the growth of the assemblage dolomite+diopside+forsterite±aragonite during HP prograde, UHP peak, and UHP early-retrograde evolution. Mixed-volatile P-T projection modeled in the simple CaO-(FeO)-MgO-SiO 2 -H 2 O-CO 2 system and T - P - X CO 2 petrogenetic grids and pseudosections predict the prograde (1.7 GPa, 560 °C) growth of dolomite in equilibrium with diopside and forsterite through the breakdown of antigorite+aragonite. In a H 2 O-CO 2 -saturated system, the subsequent HP-UHP evolution is predicted in the Di+Fo+Dol+Arg stability field in equilibrium with a dominantly aqueous COH fluid [ 0 . 0003 X CO 2 0 . 0008 ], whose composition is internally buffered by the equilibrium assemblage. Thermodynamic modeling indicates that neither the consumption nor the growth of new dolomite generations at UHP conditions can have been induced by metamorphic reactions. The abundant primary H 2 O+Cal+Dol+Cl-rich Tr+Cl-rich Tlc±chloride fluid inclusions present in UHP Cpx indicate that a dominantly aqueous, saline (salinity >26.3 wt% of NaCl eq ) COH fluid, containing Ca, Mg, and Si as dissolved cations was present during the growth of the UHP assemblage Dol+Cpx+Ol+Arg. The complex zoning of dolomite is therefore interpreted as due to protracted episodes of dissolution and precipitation in saline aqueous fluids at HP/UHP conditions. Kinetics of dolomite dissolution in aqueous fluids is poorly known, and experimental and thermodynamic data under HP conditions are still lacking. Data on calcite indicate that dissolution at HP is enhanced by a prograde increase in both P and T , by high salinity in aqueous fluids, and/or low-pH conditions. In the studied marble, the P-T path and the occurrence of free high-saline fluids represent favorable conditions: (1) for the inferred dissolution-precipitation processes of the stable dolomite in a closed system, and (2) for possible migration of the dissolved carbonate, if the system would have been open during subduction.

This deliverable outlines a minimal set of Rules of Participation for Service Providers and Users in EOSC, and aims at feeding decisions within future discussions on EOSC Governance. The proposed organisational Rules of Participation for EOSC embrace the principles of openness, transparency and inclusiveness. They have been designed after deep analysis of widely accepted working practices in already established European infrastructures and organisations, and iterative consultations of EOSC Stakeholders. The deliverable presents a main Rule of Participation for all EOSC service providers, complemented by a series of 7 specific requirements which could be applied depending on the needs of each scientific field. The main rule is that "EOSC services shall be registered in an EOSC compliant or compatible service catalogue visible to the global EOSC gateway".