scholarly journals FAIR Digital Objects and Natural Science Collection Data

2020 ◽  
Vol 4 ◽  
Author(s):  
Sharif Islam
Keyword(s):  
Natural Science ◽  
Large Scale ◽  
Building Blocks ◽  
Fragmented Landscape ◽  
Data Infrastructure ◽  
Collection Data ◽  
Digital Objects ◽  
New Research ◽  
Scientific Collections ◽  
Access Policies

The Distributed System of Scientific Collections (DiSSCo) is a new Research Infrastructure that is working towards the unification of all European natural science collections under common curation, access policies, and practices (Addink et al. 2019). The physical specimens in the collections and the vast amount of data derived from and linked to these specimens are important building blocks for this unification process. Primarily coming from large scale digitization projects (Blagoderov et al. 2012) along with new types of data collection, curation, and sharing methods (e.g. Kays et al. 2020), these specimens hold data that are critical for different scientific endeavours (Cook et al. 2020, Hedrick et al. 2020). Therefore it is important that the data infrastructure and the relevant services can provide a long-term sustainable and reliable access to these data. To that end, DiSSCo is working towards transforming a fragmented landscape of the natural science collections into an integrated data infrastructure that can ensure that these data can be easily Findable, more Accessible, Interoperable and Reusable – in other words, comply with the FAIR Guiding Principles (Wilkinson et al. 2016). A key decision for the design of this FAIR data infrastructure was to adopt FAIR Digital Objects (Wittenburg and Strawn 2019) that will enable the creation of Digital Specimen—a machine-actionable digital twin of the physical specimen (Lannom et al. 2020). This FAIR Digital Object by design, ensures FAIRness of the data (De Smedt et al. 2020) and thus will allow DiSSCo to provide services that are essential for natural science collection-based research. This talk summarises the motivation behind this adoption by showing how design decisions and best practices were influenced by the FAIR data principles, global discussions around FAIR Digital Objects and outputs from the Research Data Alliance (RDA) interest and working groups.

scholarly journals DiSSCo as a New Regional Model for Scientific Collections in Europe

2019 ◽  
Vol 3 ◽  
Author(s):  
Wouter Addink ◽  
Dimitrios Koureas ◽  
Ana Rubio
Keyword(s):  
Natural History ◽  
Natural Science ◽  
Large Scale ◽  
Advisory Board ◽  
Political Support ◽  
Research Infrastructure ◽  
Morphological Data ◽  
Natural History Museums ◽  
History Museums ◽  
Scientific Collections

European Natural Science Collections (NSC) are part of the global natural and cultural capital and represent 80% of the world bio-and geo-diversity. Data derived from these collections underpin thousands of scholarly publications and official reports (used to support legislative and regulatory processes relating to health, food, security, sustainability and environmental change) and let to inventions and products that today play an important role in our bio-economy. In the last decades, the research practice in natural sciences changed dramatically. Advances in digital, genomic and information technologies enable natural science collections to provide new insights but also ask for changing the current operational and business models of individual collections held at local natural history museums and universities. A new business model that provides unified access to collection objects and all scientific data derived from them. Although aggregating infrastructures like the Global Biodiversity Information Facility, GenBank and Catalogue of Life now successfully aggregate data on specific data classes, the landscape remains fragmented with limited capacity to bring together this information in a systematic and robust manner and with scattered access to the physical objects. The Distributed System of Scientific Collections (DiSSCo) represents a pan-European initiative, and the largest ever agreement of natural science museums, to jointly address the fragmentation of European collections. DiSSCo is unifying European natural science collections into a coherent new research infrastructure, able to provide bio- and geo-diversity data at the scale, form and precision required by a multi-disciplinary user base in science. DiSSCo is harmonising digitisation, curation and publication processes and workflows across the scientific collections in Europe and enables linking of occurrence, genomic, chemical and morphological data classes as well as publications and experts to the physical object. In this paper we will present the socio-cultural and governance aspects of this research infrastructure. DiSSCo is receiving political support from 11 countries in Europe and will gradually change its funding model from institutional to national funding, with temporary funding from the EC to support the preparation and development. Solutions to achieve large scale digitisation are currently designed in the EC funded ICEDIG project to underpin the future large scale digitisation carried out by the countries. Unified virtual (digitisation on demand) and transnational physical access to the collections is over the next four years being developed in the EC funded SYNTHESYS+ project. The governance of DiSSCo is designed to gradually change from a steering committee composed of a few large natural history museums contributing in cash to initiate the development into a legal entity in which national consortia are represented, with a central coordination office for daily management. Each country individually decides how its entities (scientific collection facilities, research councils, governmental bodies) are organised in their national consortium. A stakeholder and user forum, Scientific Advisory Board and International Advisory Board will ensure that DiSSCo will be functional in enabling science across disciplines and within the international landscape of infrastructures. Training and short scientific missions are being developed in the MOBILISE COST Action to build capacity in FAIR data production, publication and usage of scientific collection-derived data in Europe and to initiate the socio-cultural changes needed in the collection-holding institutes. A Helpdesk is being constructed in the SYNTHESYS+ and DiSSCo Prepare projects to further facilitate the use and scientific use cases have been collected in ICEDIG to develop and facilitate e-services tailored to scientific needs.

scholarly journals A Unique Research Data Infrastructure for Educational Research and Beyond: The National Educational Panel Study

2016 ◽  
Vol 236 (4) ◽  
Author(s):  
Daniel Fuß ◽  
Jutta von Maurice ◽  
Hans-Günther Roßbach
Keyword(s):  
Educational Research ◽  
Large Scale ◽  
Panel Study ◽  
Data Access ◽  
Research Data ◽  
Data Availability ◽  
Background Information ◽  
Data Infrastructure ◽  
Collection Data ◽  
Set Up

AbstractThe article provides an insight into the conceptual and methodological framework as well as the research data infrastructure of the German National Educational Panel Study (NEPS). The NEPS study has been set up to build a profound empirical basis for the description and analysis of educational processes and competence development across the life span. Its large-scale database consists of longitudinal information from more than 60,000 target respondents – distributed over six different starting cohorts ranging from newborns to adults – and from relevant context persons such as parents or teachers. The complex multicohort sequence design schedules annual or even semiannual survey waves including a broad spectrum of competence assessments. All data are thoroughly prepared, documented, and disseminated free of charge in the form of regularly expanded Scientific Use Files. In addition to some background information about NEPS in general, this paper primarily focuses on issues of data collection, data structure, data availability, and the requirements for different types of data access. The number of more than 1,000 data users involved in over 700 research projects so far serves to highlight the potential of NEPS as a unique research data infrastructure for educational research and beyond.

scholarly journals Technical capacities of digitisation centres within ICEDIG participating institutions

2020 ◽  
Vol 6 ◽  
Author(s):  
Naomi Cocks ◽  
Laurence Livermore ◽  
Vincent Smith ◽  
Matt Woodburn
Keyword(s):  
Distributed System ◽  
Natural Science ◽  
Large Scale ◽  
Practical Reasons ◽  
Institutional Collaboration ◽  
Level Of Aggregation ◽  
Scientific Collections ◽  
Future Work

DiSSCo, the Distributed System of Scientific Collections, is seeking to centralise certain infrastructure and activities relating to the digitisation of natural science collections. Deciding what activities to distribute, what to centralise, and what geographic level of aggregation (e.g. regional, national or pan European) is most appropriate for each task, was one of the challenges set out within the EC-funded ICEDIG project. In this paper we present the results of a survey of several European collections to establish current digitisation capacity, strengths and skills associated with existing digitisation infrastructure. Our results indicate that most of the institutions surveyed are engaged in large-scale digitisation of collections and that this is usually being undertaken by dedicated teams of digitisers within each institution. Some cross institutional collaboration is happening, but this is still the exception for a variety of funder and practical reasons. These results inform future work that establishes a set of principles to determine how digitisation infrastructure might be most efficiently organised across European organisations in order to maximise progress on the digitisation of the estimated 1.5 billion specimens held within European natural science collections.

scholarly journals Open access at the national level: A comprehensive analysis of publications by Finnish researchers

2020 ◽  
Vol 1 (4) ◽  
pp. 1396-1428
Author(s):  
Janne Pölönen ◽  
Mikael Laakso ◽  
Raf Guns ◽  
Emanuel Kulczycki ◽  
Gunnar Sivertsen
Keyword(s):  
Open Access ◽  
Large Scale ◽  
National Level ◽  
Building Blocks ◽  
Research Information ◽  
Data Infrastructure ◽  
For Profit ◽  
Large Scale Data ◽  
Publication Data ◽  
Assessment And Monitoring

Open access (OA) has mostly been studied by relying on publication data from selective international databases, notably Web of Science (WoS) and Scopus. The aim of our study is to show that it is possible to achieve a national estimate of the number and share of OA based on institutional publication data providing a comprehensive coverage of the peer-reviewed outputs across fields, publication types, and languages. Our data consists of 48,177 journal, conference, and book publications from 14 Finnish universities in 2016–2017, including information about OA status, as self-reported by researchers and validated by data-collection personnel through their Current Research Information System (CRIS). We investigate the WoS, Scopus, and DOI coverage, as well as the share of OA outputs between different fields, publication types, languages, OA mechanisms (gold, hybrid, and green), and OA information sources (DOAJ, Bielefeld list, and Sherpa/Romeo). We also estimate the role of the largest international commercial publishers compared to the not-for-profit Finnish national publishers of journals and books. We conclude that institutional data, integrated at national and international level, provides one of the building blocks of a large-scale data infrastructure needed for comprehensive assessment and monitoring of OA across countries, for example at the European level.

scholarly journals Digital Object Cloud for linking natural science collections information; The case of DiSSCo 

2018 ◽  
Vol 2 ◽  
pp. e25474
Author(s):  
Dimitrios Koureas ◽  
Wouter Addink ◽  
Alex Hardisty
Keyword(s):  
Natural Science ◽  
Large Scale ◽  
Digital Object ◽  
Science Museums ◽  
Large Scale Data ◽  
Governance Model ◽  
Different Types ◽  
Types Of Information ◽  
Scientific Collections ◽  
Fragmented Data

DiSSCo(The Distributed System of Scientific Collections) is a Research Infrastructure (RI) aiming at providing unified physical (transnational), remote (loans) and virtual (digital) access to the approximately 1.5 billion biological and geological specimens in collections across Europe. DiSSCo represents the largest ever formal agreement between natural science museums (114 organisations across 21 European countries). With political and financial support across 14 European governments and a robust governance model DiSSCo will deliver, by 2025, a series of innovative end-user discovery, access, interpretation and analysis services for natural science collections data. As part of DiSSCo's developing data model, we evaluate the application of Digital Objects (DOs), which can act as the centrepiece of its architecture. DOs have bit-sequences representing some content, are identified by globally unique persistent identifiers (PIDs) and are associated with different types of metadata. The PIDs can be used to refer to different types of information such as locations, checksums, types and other metadata to enable immediate operations. In the world of natural science collections, currently fragmented data classes (inter alia genes, traits, occurrences) that have derived from the study of physical specimens, can be re-united as parts in a virtual container (i.e., as components of a Digital Object). These typed DOs, when combined with software agents that scan the data offered by repositories, can act as complete digital surrogates of the physical specimens. In this paper we: investigate the architectural and technological applicability of DOs for large scale data RIs for bio- and geo-diversity, identify benefits and challenges of a DO approach for the DiSSCo RI and describe key specifications (incl. metadata profiles) for a specimen-based new DO type.

scholarly journals Towards a Global Collection Description Standard

2019 ◽  
Vol 3 ◽  
Author(s):  
Niels Raes ◽  
Emily van Egmond ◽  
Ana Casino ◽  
Matt Woodburn ◽  
Deborah L Paul
Keyword(s):  
Natural History ◽  
Large Scale ◽  
The United States ◽  
Fragmented Landscape ◽  
Global Biodiversity Information Facility ◽  
Classification Schemes ◽  
Natural History Collections ◽  
Natural History Collection ◽  
World Collection ◽  
Scientific Collections

With digitisation of natural history collections over the past decades, their traditional roles — for taxonomic studies and public education — have been greatly expanded into the fields of biodiversity assessments, climate change impact studies, trait analyses, sequencing, 3D object analyses etc. (Nelson and Ellis 2019; Watanabe 2019). Initial estimates of the global natural history collection range between 1.2 and 2.1 billion specimens (Ariño 2010), of which 169 million (8-14% - as of April 2019) are available at some level of digitisation through the Global Biodiversity Information Facility (GBIF). With iDigBio (Integrated Digitized Biocollections) established in the United States and with the European DiSSCo (Distributed Systems of Scientific Collections) accepted on the ESFRI roadmap, it has become a priority to digitize natural history collections at an industrialized scale. Both iDigBio and DiSSCo aim at mobilising, unifying and delivering bio- and geo-diversity information at the scale, form and precision required by scientific communities, and thereby transform a fragmented landscape into a coherent and responsive research infrastructure. In order to prioritise digitisation based on scientific demand, and efficiency using industrial digitisation pipelines, it is required to arrive at a uniform and unambiguously accepted collection description standard that would allow comparing, grouping and analysing natural history collections at diverse levels. Several initiatives attempt to unambiguously describe natural history collections using taxonomic and storage classification schemes. These initiatives include One World Collection, Global Registry of Scientific Collections (GRSciColl), TDWG (Taxonomic Databases Working Group) Natural Collection Descriptions (NCD) and CETAF (Consortium of European Taxonomy Facilities) passports, among others. In a collaborative effort of DiSSCo, ICEDIG (Innovation and consolidation for large scale digitisation of natural heritage), iDigBio, TDWG and the Task Group Collection Digitisation Dashboards, the various schemes were compared in a cross-walk analysis to propose a preliminary natural collection description standard that is supported by the wider community. In the process, two main user groups of collection descriptions standards were identified; scientists and collection managers. The classification produced intends to meet requirements from them both, resulting in three classification schemes that exist in parallel to each other (van Egmond et al. 2019). For scientific purposes a ‘Taxonomic’ and ‘Stratigraphic’ classification were defined, and for management purposes a ‘Storage’ classification. The latter is derived from specimen preservation types (e.g. dried, liquid preserved) defining storage requirements and the physical location of specimens in collection holding facilities. The three parallel collection classifications can be cross-sectioned with a ‘Geographic’ classification to assign sub-collections to major terrestrial and marine regions, which allow scientists to identify particular taxonomic or stratigraphic (sub-)collections from major geographical or marine regions of interest. Finally, to measure the level of digitisation of institutional collections and progress of digitisation through time, the number of digitised specimens for each geographically cross-sectioned (sub-)collection can be derived from institutional collection management systems (CMS). As digitisation has different levels of completeness a ‘Digitisation’ scheme has been adopted to quantify the level of digitisation of a collection from Saarenmaa et al. 2019, ranging from ‘not digitised’ to extensively digitised, recorded in a progressive scale of MIDS (Minimal Information for Digital Specimen). The applicability of this preliminary classification will be discussed and visualized in a Collection Digitisation Dashboards (CDD) to demonstrate how the implementation of a collection description standard allows the identification of existing gaps in taxonomic and geographic coverage and levels of digitisation of natural history collections. This set of common classification schemes and dashboard design (van Egmond et al. 2019) will be contributed to the TDWG Collection Description interest group to ultimately arrive at the common goal of a 'World Collection Catalogue'.

scholarly journals The DiSSCo Knowledgebase: A trusted information hub for the natural science collection community worldwide

2021 ◽  
Vol 5 ◽  
Author(s):  
Mareike Petersen ◽  
Sabine von Mering ◽  
Julia Pim Reis ◽  
Falko Glöckler
Keyword(s):  
Natural Science ◽  
Single Point ◽  
Developmental Approach ◽  
Controlled Vocabularies ◽  
Domain Specific ◽  
Stakeholder Groups ◽  
Project Outcomes ◽  
New Research ◽  
Scientific Collections ◽  
Link Information

In the last two decades, various projects and initiatives have conducted research on how to share, exchange, and link information from natural science collection objects. This profound (technical) knowledge, standards, tools, and best practices are essential to the development of any new research infrastructure facilitating research on bio- and geodiversity. However, the knowledge and research results are usually not easily accessible at a single point and particularly not in a well-curated form. Here, the Knowledgebase developed for the Distributed System of Scientific Collections (DiSSCo) comes into play. This information hub will act as trusted source for project outcomes and other relevant resources (e.g., web services, Persistent Identifier Systems, controlled vocabularies, domain-specific ontologies and standards) for users and developers of DiSSCo and other research infrastructures worldwide. In this talk, we will present the current version of the DiSSCo Knowledgebase, its developmental approach, and the opportunity for this source to act as an e-service for various stakeholder groups interested in and working with natural science collections worldwide.

New Models of Content Creation and Scholarship at the Intersection of Library Spaces, Technologies, and Expertise

2018 ◽  
Author(s):  
Mike Nutt ◽  
Gregory Raschke
Keyword(s):  
Large Scale ◽  
Interactive Media ◽  
Scholarly Communication ◽  
Three Dimensions ◽  
Organizational Capabilities ◽  
High Definition ◽  
Content Creation ◽  
Full Life Cycle ◽  
Digital Scholarship ◽  
Digital Objects

Library spaces that blend collaboration areas, advanced technologies, and librarian expertise are creating new modes of scholarly communication. These spaces enable scholarship created within high-definition, large-scale visual collaborative environments. This emergent model of scholarly communication can be experienced within those specific contexts or through digital surrogates on the networked Web. From experiencing in three dimensions the sermons of John Donne in 1622 to interactive media interpretations of American wars, scholars are partnering with libraries to create immersive digital scholarship. Viewing the library as a research platform for these emergent forms of digital scholarship presents several opportunities and challenges. Opportunities include re-engaging faculty in the use of library space, integrating the full life-cycle of the research enterprise, and engaging broad communities in the changing nature of digitally-driven scholarship. Issues such as identifying and filtering collaborations, strategically managing staff resources, creating surrogates of immersive digital scholarship, and preserving this content for the future present an array of challenges for libraries that require coordination across organizations. From engaging and using high-technology spaces to documenting the data and digital objects created, this developing scholarly communication medium brings to bear the multifaceted skills and organizational capabilities of libraries.

Bullying, School Violence, and Climate in Evolving Contexts

2018 ◽  
Author(s):  
Ron Avi Astor ◽  
Rami Benbenisthty
Keyword(s):  
School Violence ◽  
School Safety ◽  
Media Coverage ◽  
Large Scale ◽  
Ecological Model ◽  
Empirical Studies ◽  
Practical Applications ◽  
Teacher Student ◽  
Area Of Interest ◽  
New Research

Since 2005, the bullying, school violence, and school safety literatures have expanded dramatically in content, disciplines, and empirical studies. However, with this massive expansion of research, there is also a surprising lack of theoretical and empirical direction to guide efforts on how to advance our basic science and practical applications of this growing scientific area of interest. Parallel to this surge in interest, cultural norms, media coverage, and policies to address school safety and bullying have evolved at a remarkably quick pace over the past 13 years. For example, behaviors and populations that just a decade ago were not included in the school violence, bullying, and school safety discourse are now accepted areas of inquiry. These include, for instance, cyberbullying, sexting, social media shaming, teacher–student and student–teacher bullying, sexual harassment and assault, homicide, and suicide. Populations in schools not previously explored, such as lesbian, gay, bisexual, transgender, and queer students and educators and military- and veteran-connected students, become the foci of new research, policies, and programs. As a result, all US states and most industrialized countries now have a complex quilt of new school safety and bullying legislation and policies. Large-scale research and intervention funding programs are often linked to these policies. This book suggests an empirically driven unifying model that brings together these previously distinct literatures. This book presents an ecological model of school violence, bullying, and safety in evolving contexts that integrates all we have learned in the 13 years, and suggests ways to move forward.

scholarly journals A Comprehensive Review: Sphingolipid Metabolism and Implications of Disruption in Sphingolipid Homeostasis

2021 ◽  
Vol 22 (11) ◽  
pp. 5793
Author(s):  
Brianna M. Quinville ◽  
Natalie M. Deschenes ◽  
Alex E. Ryckman ◽  
Jagdeep S. Walia
Keyword(s):  
Nervous System ◽  
Large Scale ◽  
System Development ◽  
Building Blocks ◽  
Cell Types ◽  
Nervous System Development ◽  
Sphingolipid Metabolism ◽  
Lysosomal Storage ◽  
Bioactive Lipids ◽  
Comprehensive Review

Sphingolipids are a specialized group of lipids essential to the composition of the plasma membrane of many cell types; however, they are primarily localized within the nervous system. The amphipathic properties of sphingolipids enable their participation in a variety of intricate metabolic pathways. Sphingoid bases are the building blocks for all sphingolipid derivatives, comprising a complex class of lipids. The biosynthesis and catabolism of these lipids play an integral role in small- and large-scale body functions, including participation in membrane domains and signalling; cell proliferation, death, migration, and invasiveness; inflammation; and central nervous system development. Recently, sphingolipids have become the focus of several fields of research in the medical and biological sciences, as these bioactive lipids have been identified as potent signalling and messenger molecules. Sphingolipids are now being exploited as therapeutic targets for several pathologies. Here we present a comprehensive review of the structure and metabolism of sphingolipids and their many functional roles within the cell. In addition, we highlight the role of sphingolipids in several pathologies, including inflammatory disease, cystic fibrosis, cancer, Alzheimer’s and Parkinson’s disease, and lysosomal storage disorders.

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