scholarly journals Technical capacities of digitisation centres within ICEDIG participating institutions

2020 ◽  
Vol 6 ◽  
Author(s):  
Naomi Cocks ◽  
Laurence Livermore ◽  
Vincent Smith ◽  
Matt Woodburn

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.

Author(s):  
Wouter Addink ◽  
Dimitrios Koureas ◽  
Ana Rubio

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.


2020 ◽  
Vol 6 ◽  
Author(s):  
Niels Raes ◽  
Ana Casino ◽  
Hilary Goodson ◽  
Sharif Islam ◽  
Dimitrios Koureas ◽  
...  

The Distributed System of Scientific Collections (DiSSCo) Research Infrastructure (RI) is presently in its preparatory phase. DiSSCo is developing a new distributed RI to operate as a one-stop-shop for the envisaged European Natural Science Collection (NSC) and all its derived information. Through mass digitisation, DiSSCo will transform the fragmented landscape of NSCs, including an estimated 1.5 billion specimens, into an integrated knowledge base that will provide interconnected evidence of the natural world. Data derived from European NSCs underpin countless discoveries and innovations, including tens of thousands of scholarly publications and official reports annually (supporting legislative and regulatory processes on sustainability, environmental change, land use, societal infrastructure, health, food, security, etc.); base-line biodiversity data; inventions and products essential to bio-economy; databases, maps and descriptions of scientific observations; educational material for students; and instructive and informative resources for the public. To expand the user community, DiSSCo will strengthen capacity building across Europe for maximum engagement of stakeholders in the biodiversity-related field and beyond, including industry and the private sector, but also policy-driving entities. Hence, it is opportune to reach out to relevant stakeholders in the European environmental policy domain represented by the European Environment Agency (EEA). The EEA aims to support sustainable development by helping to achieve significant and measurable improvement in Europe's environment, through the provision of timely, targeted, relevant and reliable information to policy-making agents and the public. The EEA provides information through the European Environment Information and Observation System (Eionet). The aim of this white paper is to open the discussion between DiSSCo and the EEA and identify the common service interests that are relevant for the European environmental policy domain. The first section describes the significance of (digital) Natural Science Collections (NHCs). Section two describes the DiSSCo programme with all DiSSCo aligned projects. Section three provides background information on the EEA and the biodiversity infrastructures that are developed and maintained by the EEA. The fourth section illustrates a number of use cases where the DiSSCo consortium sees opportunities for interaction between the DiSSCo RI and the Eionet portal of the EEA. Opening the discussion with the EEA in this phase of maturity of DiSSCo will ensure that the infrastructural design of DiSSCo and the development of e-Services accommodate the present and future needs of the EEA and assure data interoperability between the two infrastructures. The aim of this white paper is to present benefits from identifying the common service interests of DiSSCo and the EEA. A brief introduction to natural science collections as well as the two actors is given to facilitate the understanding of the needs and possibilities in the alignment of DiSSCo with the EEA.


2020 ◽  
Vol 6 ◽  
Author(s):  
Katherine Dixey ◽  
Matt Woodburn ◽  
Helen Hardy ◽  
Laurence Livermore ◽  
Vincent Smith

Digitisation of natural science collections is fundamental to the vision for the Distributed System of Scientific Collections (DiSSCo), and given the low proportion of collections digitally accessible, it is proposed that ‘Centres of Excellence’ be developed to accelerate the creation of digital copies of original specimens. Within the ICEDIG project, a team of scientists from across the consortium explored the concept of Centres of Excellence and have constructed a toolset to help identify these centres to support the development of DiSSCo. This report documents this process and describes the toolset.


2018 ◽  
Vol 2 ◽  
pp. e25474
Author(s):  
Dimitrios Koureas ◽  
Wouter Addink ◽  
Alex Hardisty

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.


Author(s):  
Sharif Islam

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.


2021 ◽  
Vol 7 ◽  
Author(s):  
Alex Hardisty ◽  
Wouter Addink ◽  
Falko Glöckler ◽  
Anton Güntsch ◽  
Sharif Islam ◽  
...  

Persistent identifiers (PID) to identify digital representations of physical specimens in natural science collections (i.e., digital specimens) unambiguously and uniquely on the Internet are one of the mechanisms for digitally transforming collections-based science. Digital Specimen PIDs contribute to building and maintaining long-term community trust in the accuracy and authenticity of the scientific data to be managed and presented by the Distributed System of Scientific Collections (DiSSCo) research infrastructure planned in Europe to commence implementation in 2024. Not only are such PIDs valid over the very long timescales common in the heritage sector but they can also transcend changes in underlying technologies of their implementation. They are part of the mechanism for widening access to natural science collections. DiSSCo technical experts previously selected the Handle System as the choice to meet core PID requirements. Using a two-step approach, this options appraisal captures, characterises and analyses different alternative Handle-based PID schemes and the possible operational modes of use. In a first step a weighting and ranking the options has been applied followed by a structured qualitative assessment of social and technical compliance across several assessment dimensions: levels of scalability, community trust, persistence, governance, appropriateness of the scheme and suitability for future global adoption. The results are discussed in relation to branding, community perceptions and global context to determine a preferred PID scheme for DiSSCo that also has potential for adoption and acceptance globally. DiSSCo will adopt a ‘driven-by DOI’ persistent identifier (PID) scheme customised with natural sciences community characteristics. Establishing a new Registration Agency in collaboration with the International DOI Foundation is a practical way forward to support the FAIR (findable, accessible interoperable, reusable) data architecture of DiSSCo research infrastructure. This approach is compatible with the policies of the European Open Science Cloud (EOSC) and is aligned to existing practices across the global community of natural science collections.


Information ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 14
Author(s):  
Aluizio Rocha Neto ◽  
Thiago P. Silva ◽  
Thais Batista ◽  
Flávia C. Delicato ◽  
Paulo F. Pires ◽  
...  

In smart city scenarios, the huge proliferation of monitoring cameras scattered in public spaces has posed many challenges to network and processing infrastructure. A few dozen cameras are enough to saturate the city’s backbone. In addition, most smart city applications require a real-time response from the system in charge of processing such large-scale video streams. Finding a missing person using facial recognition technology is one of these applications that require immediate action on the place where that person is. In this paper, we tackle these challenges presenting a distributed system for video analytics designed to leverage edge computing capabilities. Our approach encompasses architecture, methods, and algorithms for: (i) dividing the burdensome processing of large-scale video streams into various machine learning tasks; and (ii) deploying these tasks as a workflow of data processing in edge devices equipped with hardware accelerators for neural networks. We also propose the reuse of nodes running tasks shared by multiple applications, e.g., facial recognition, thus improving the system’s processing throughput. Simulations showed that, with our algorithm to distribute the workload, the time to process a workflow is about 33% faster than a naive approach.


Author(s):  
C. Nataraj

Abstract A single link robotic manipulator is modeled as a rotating flexible beam with a rigid mass at the tip and accurate energy expressions are derived. The resulting partial differential equations are solved using an approximate method of weighted residuals. From the solutions, coupling between axial and flexural deformations and the interactions with rigid body motions are rigorously analyzed. The emphasis in the current paper is not on an exhaustive analysis of existing systems but it is rather intended to compare and highlight the various flexibility effects in a relatively simple system. Hence, a nondimensional parametric analysis is performed to determine the effect of several parameters (including the rotating speed) on the errors and the individual interaction effects are discussed. Comparison with previous work in the field shows important phenomena often ignored or buried in large scale numerical analyses. Future work including application to multi-link robots is outlined.


2020 ◽  
Vol 6 (1) ◽  
pp. 5-12
Author(s):  
J.B. Zhang ◽  
J.K. Tomberlin ◽  
M.M. Cai ◽  
X.P. Xiao ◽  
L.Y. Zheng ◽  
...  

The larvae of the black soldier fly (BSF), Hermetia illucens L., are commonly associated with decaying organic wastes. Over the past 15 years, investigators in China have conducted extensive research exploring the use of BSF larvae to recycle organic materials as a means to protect the environment, while producing products of value, such as protein and bioenergy. Initial efforts were based on a BSF strain from the USA. However, since then, H. illucens strains from specimens collected in Hubei and Guangdong Provinces have been established and used as models to explore the use of this species in sustainable agriculture. China has played an instrumental role in developing an in-door breeding method using a quartz-iodine lamp rather than depend on natural sunlight. This discovery has allowed the establishment of in-door BSF colonies in regions throughout the world where abiotic conditions (i.e. cold temperatures) are preventative. Researchers in China paved the way for using microbes as a means to enhance BSF production including, enhancing BSF egg-laying as well as waste reduction. Furthermore, bacteria from BSF gut or waste can be cultured and used to promote BSF growth, shorten conversion time, and enhanced conversion efficacy. Recent efforts have demonstrated BSF larvae can degrade antibiotics as well as suppress noxious odours in livestock manure. Due to the efforts of research on BSF in China, numerous companies that recycle organic waste at a large scale (>20 tonnes waste digested/day), have been established. Resulting products include insect powder, and live BSFL that can be used as animal feed ingredients for livestock (e.g. eels and frogs), while protecting the environment. Future work will decipher the mechanisms regulating BSF larval conversion of organic waste so that the system can be optimised. However, efforts are still needed at the government level to establish quality assurance standards if this process is truly to become established as an industry in China.


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