scholarly journals ‘openDS’ – Progress on the New Standard for Digital Specimens

2020 ◽  
Vol 4 ◽  
Author(s):  
Wouter Addink ◽  
Alex Hardisty
Keyword(s):  
Dna Sequences ◽  
Technical Specification ◽  
Logical Structure ◽  
Scientific Data ◽  
Object Model ◽  
Health Food ◽  
Scientific Content ◽  
Data Infrastructure ◽  
Regulatory Processes ◽  
Definition Of

In a Biodiversity_Next 2019 symposium, a vision of Digital Specimens based on the concept of a Digital Object Architecture (Kahn and Wilensky 2006) (DOA) was discussed as a new layer between data infrastructure of natural science collections and user applications for processing and interacting with information about specimens and collections. This vision would enable the transformation of institutional curatorial practises into joint community curation of the scientific data by providing seamless global access to specimens and collections spanning multiple collection-holding institutions and sources. A DOA-based implementation (Lannom et al. 2020) also offers wider, more flexible, and ‘FAIR’ (Findable, Accessible, Interoperable, Reusable) access for varied research and policy uses: recognising curatorial work, annotating with latest taxonomic treatments, understanding variations, working with DNA sequences or chemical analyses, supporting regulatory processes for health, food, security, sustainability and environmental change, inventions/products critical to the bio-economy, and educational uses. To make this vision a reality, a specification is needed that describes what a Digital Specimen is, and how to technically implement it. This specification is named 'openDS' for open Digital Specimen. It needs to describe how machines and humans can act on a Digital Specimen and gain attribution for their work; how the data can be serialized and packaged; and it needs to describe the object model (the scientific content part and its structure). The object model should describe how to include the specimen data itself as well as all data derived from the specimen, which is in principle the same as what the Extended Specimen model aims to describe. This part will therefore be developed in close collaboration with people working on that model. After the Biodiversity_Next symposium, the idea of a standard for Digital Specimens has been further discussed and detailed in a MOBILISE Workshop in Warsaw, 2020, with stakeholders like the GBIF, iDigBio, CETAF and DiSSCo. The workshop examined the technical basis of the new specification, agreed on scope and structure of the new specification and laid groundwork for future activities in the Research Data Alliance (RDA), Biodiversity Information Standards (TDWG), and technical workshops. A working group in the DiSSCo Prepare project has begun on the technical specification of the ‘open Digital Specimen’ (openDS). This specification will provide the definition of what a Digital Specimen is, its logical structure and content, and the operations permitted on that. The group is also working on a document with frequently asked questions. Realising the vision of Digital Specimen on a global level requires openDS to become a new TDWG standard and to be aligned with the vision for Extended Specimens. A TDWG Birds-of-a-Feather working session in September 2020 discusses and plans this further. The object model will include concepts from ABCD 3.0 and EFG extension for geo-sciences, and also extend from bco:MaterialSample in the OBO Foundry’s Biological Collection Ontology (BCO), which is linked to Darwin Core and from iao:InformationContentEntity in OBO Foundry's Information Artifact Ontology (IAO). openDS will also make use of the RDA/TDWG attribution metadata recommendation and other RDA recommendations. A publication is in preparation that describes the relationship with RDA recommendations in more detail, which will also be presented in the TDWG symposium.

scholarly journals Making Heterogeneous Specimen Data ‘FAIR’: Implementing a digital specimen repository

2019 ◽  
Vol 3 ◽  
Author(s):  
Abraham Nieva de la Hidalga ◽  
Alex Hardisty
Keyword(s):  
Dna Sequences ◽  
Heterogeneous Data ◽  
Primary Data ◽  
Object Model ◽  
Digital Object ◽  
Data Types ◽  
Resource Manager ◽  
Digital Objects ◽  
Definition Of ◽  
Rapid Deployment

The definition of a digital specimen is proposed to encompass the digital representation(s) of physical specimens from natural science collections. The digital specimen concept is intended to define a representation (digital object) that brings together an array of heterogeneous data types, which are themselves alternative physical specimen representations. In this case, the digital specimen (DS) holds references to specimen data from a collection management system, images, 3D models, research articles, DNA sequences, collector information, among many other data types. The proposal is to create persistent relationships between the DS and other categories of digital objects (e.g. resource types mentioned above, collections, storage platforms, organisations, databases, and provenance data). Complying with FAIR data principles (findability, accessibility, interoperability, and reuse), i.e., achieving data ‘FAIRness’, eases data integration, which is needed for cross-disciplinary linking and combination of data from different domains, making the DS as a comprehensive package of information about a specimen. Implementation and access to a digital specimen repository (DSR) as a Digital Object Architecture (Sharp 2016) component demonstrates the alignment of the DS concept and FAIR data principles (Wilkinson et al. 2016, Kahn and Wilensky 2006). The DSR fulfills four roles: data producer, resource manager, data publisher, and collaboration space. As data producer, the DSR allows acquisition and curation (indexing, storage) of DSs linking primary data, models, analyses, and other digital object types. As resource manager, the DSR manages access to distributed platforms, ranging from acquisition networks (digitisation stations, museums, herbariums) to processing services, advanced computational resources, data asset storage systems, and specialised servers. As data publisher, the DSR provides access to data assets from national and transnational data archives. As collaboration space, the DSR supports users’ accessing, sharing and (re)using data assets, and derived data products and services. Adopting the collaboration space and data publisher roles, the DSR implements interfaces that expose the DSs to the research community, fulfilling the FAIR findability, accessibility, and reuse principles. Adopting the data producer and resource manager roles, the DSR creates meaningful and persistent relationships required to link DSs and other types of digital objects, fulfilling the FAIR interoperability principle. A prototype DSR based on the Cordra digital object repository has been deployed (Corporation for National Research Initiatives (CNRI) 2018, Reilly and Tupelo-Schneck 2010). The advantages of Cordra are: rapid deployment, customisable object model, creation of relations between digital objects, and application program interfaces for programmatic access. Rapid deployment of the DSR provides a tangible target for discussing the implementation of the DS concept. The customisable object model enables the refinement and enhancing of the definition of DS in response to feedback from colleagues who have accessed the DSR and used its contents. Creating relations between digital objects enables flexible linking to digital objects stored in different repositories. Accessing the DSR programmatically through APIs enables extending the use of the repository in different platforms (e.g. mobile devices) as well as integration with other repositories and services. As well as supporting a HTTP-oriented API, Cordra implements Digital Object Interface Protocol (DONA Foundation 2018), allowing the definition of operations to act directly on selected DSs in the repository. The DSR prototype has been demonstrated by providing access to the repository administrative interface and with a custom interface designed to facilitate access by different user groups, such as collection curators, researchers, teachers, and students. The client interface has been designed to demonstrate a subset of the functionalities derived from user stories, which describe software features from the end-user perspective. Demonstrating the DSR capabilities as proposed, will inform the refinement of the design of the DS model and provide early feedback about the needed software features.

scholarly journals A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

2008 ◽  
Vol 191 (1) ◽  
pp. 91-99 ◽  
Author(s):  
Marc Deloger ◽  
Meriem El Karoui ◽  
Marie-Agnès Petit
Keyword(s):  
Dna Sequences ◽  
Dna Content ◽  
Core Genome ◽  
Biological Diversity ◽  
Bacterial Species ◽  
Genomic Distance ◽  
The Core ◽  
Intraspecies Diversity ◽  
Genome Level ◽  
Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

Current approaches to comprehensive assessment of child and adolescent health in hygiene and clinical practice

2020 ◽  
pp. 47-52
Author(s):  
Olga Pavlovna Gritsina ◽  
Anna Konstantinovna Yatsenko ◽  
Lidiya Viktorovna Trankovskaya ◽  
Oksana Valerievna Perelomova
Keyword(s):  
Computer Program ◽  
Children And Adolescents ◽  
Integrated Assessment ◽  
Technical Specification ◽  
Health Indicators ◽  
Comprehensive Assessment ◽  
Medical Surveillance ◽  
Human Welfare ◽  
Software Product ◽  
Definition Of

The relevance of improving the quality of preventive medical surveillance of children and adolescents is undeniable, which provides the basis for the search for methodologically sound approaches to an integrated assessment of the health of the child population. The purpose of the study was to develop and create the software product «Computer Program «Comprehensive Assessment of the Health of Children and Adolescents». For realization of the purpose, patent search, compilation of a technical specification on the basis of criteria of assessment of children’s health and assignment to a particular group of health, writing of a software product using modern programming libraries, as well as preparation of accompanying documents for registration of an intellectual property object were performed. The result of the work was the «Computer Program «Comprehensive Assessment of the Health of Children and Adolescents», designed for the integrated assessment of the state of health of children and adolescents during screening and preventive examinations. After filling in all fields, the program processes the received data and displays the final result — assessment of the child’s health status with the definition of the health group. Information about the examined patient is sent to the program database. The built-in database allows you to systematize the data obtained, analyze the health indicators of the surveyed contingents both in one-step and in longitudinal studies. This program product can be used in the work of medical organizations, higher educational institutions of a medical profile, physical education organizations and institutions of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare in the Russian Federation.

La trattazione vetero-stoica dell’ira: componenti logiche e caratteri fisiologici

Elenchos ◽  
2018 ◽  
Vol 39 (2) ◽  
pp. 323-347
Author(s):  
Francesca Alesse
Keyword(s):  
Logical Structure ◽  
Human Soul ◽  
Definition Of

Abstract The paper compares the two components of the Stoic definition of pathos, the logico-linguistic component and the physiological, ‘pneumatic’ one, in order to examine the role that each of them plays in the onset of pathos, its persistence in the human soul, its possible eradication. The analysis is focused on anger (ὀργή) which reveals some peculiarities, especially as regards its logical structure, due to the fact that this passion seems to be the combination of two different feelings. The anger indeed is classified as a species of desire but the description of its onset also includes pain.

Organic Hits the Mainstream

2016 ◽  
Author(s):  
Connor J. Fitzmaurice ◽  
Brian J. Gareau
Keyword(s):  
Organic Farming ◽  
Consumer Choice ◽  
Organic Foods ◽  
Regulatory Processes ◽  
Federal Recognition ◽  
Chemical Inputs ◽  
Consistent Basis ◽  
Definition Of ◽  
Chemical Pesticides ◽  
The U.S

With the passage of the U.S. Organic Foods Production Act (OFPA) of 1990, organic food left the fringes of America’s agricultural economy and received federal recognition— and regulation. But how did organic farming become a niche market governed by regulations aimed at limiting the use of synthetic chemical pesticides and fertilizers, rather than by more holistic concerns about society and ecology? This chapter provides an overview of the regulatory processes that yielded both the OFPA and the final USDA organic standards implemented in 2000. While the federal government’s approach to organic farming began with a holistic, process-based definition of organic agriculture in the USDA’s 1980 “Report and Recommendations on Organic Farming,” the final standards came to focus on issues surrounding chemical inputs. This process served to settle the organic market by providing commensurability, offering a consistent basis for consumer choice, not broad agricultural sustainability.

scholarly journals Overall Introduction

2021 ◽  
pp. 1-7
Author(s):  
Wenzhong Shi ◽  
Michael F. Goodchild ◽  
Michael Batty ◽  
Mei-Po Kwan ◽  
Anshu Zhang
Keyword(s):  
Information Technologies ◽  
Interdisciplinary Approach ◽  
Urban Systems ◽  
Data Infrastructure ◽  
Urban Informatics ◽  
New Information ◽  
Wide Range ◽  
Urban Science ◽  
Definition Of

AbstractUrban informatics is an interdisciplinary approach to understanding, managing, and designing the city using systematic theories and methods based on new information technologies. Integrating urban science, geomatics, and informatics, urban informatics is a particularly timely way of fusing many interdisciplinary perspectives in studying city systems. This edited book aims to meet the urgent need for works that systematically introduce the principles and technologies of urban informatics. The book gathers over 40 world-leading research teams from a wide range of disciplines, who provide comprehensive reviews of the state of the art and the latest research achievements in their various areas of urban informatics. The book is organized into six parts, respectively covering the conceptual and theoretical basis of urban informatics, urban systems and applications, urban sensing, urban big data infrastructure, urban computing, and prospects for the future of urban informatics. This introductory chapter provides a definition of urban informatics and an outline of the book’s structure and scope.

scholarly journals Architecture of Component-based Information Systems over the J2EE Platform

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Daniel Perovich ◽  
Leonardo Rodrıguez Rodrıguez ◽  
Andres Vignaga
Keyword(s):  
Information Systems ◽  
Methodological Approach ◽  
Logical Structure ◽  
The Other ◽  
Model Driven ◽  
J2ee Platform ◽  
Component Based Development ◽  
Abstract Level ◽  
Definition Of ◽  
Different Levels

Component-based development can be addressed from two different fronts, or more precisely, from two different levels. One of them regards the technology used for system implementation, and the other is a previous and more abstract level, where the focus is set to the logical structure of the solution and where technological issues are not considered. Model Driven Architecture promotes such separation by distinguishing platform independent models from platform specific models. In alignment with this approach, this article proposes a mapping from the tiered and platform independent architecture for information systems resulting from the application of a widely known methodological approach, to the available constructs in the J2EE platform. This mapping allows the definition of transformations between platform independent models, resulting from the referred methodology where it is possible to abstractly reason about the solution, and platform specific models which are aligned with technological constructs and are directly implemented.

SIDS and Sleeping Position

PEDIATRICS ◽  
1993 ◽  
Vol 91 (2) ◽  
pp. 511-512
Author(s):  
DANIEL C. SHANNON ◽  
CARL E. HUNT
Keyword(s):  
Clinical History ◽  
Scientific Data ◽  
Statistical Association ◽  
Review Of The Literature ◽  
Sleeping Position ◽  
Death Scene ◽  
Death Scene Investigation ◽  
Prone Sleeping ◽  
Scene Investigation ◽  
Definition Of

In Reply.— Guntheroth and Spiers,1 displeased with our commentary in Pediatrics,2 have raised many issues. However, the key question is whether the scientific data incriminating the prone position as a contributor to SIDS warrant a recommendation to change sleeping position at this time. Based on our critical review of the literature, we conclude that this recommendation was premature and unwarranted. Accepting the current definition of SIDS as the sudden death of an infant that remains unexplained even after a thorough postmortem examination, death scene investigation, and review of the clinical history, one can decide which of the 15 published studies in which a statistical association is described between prone sleeping and SIDS is acceptable.

Learning Object Model and Framework Design for the Digital Modules Production

2013 ◽  
pp. 28-36
Author(s):  
Alicia García Holgado ◽  
Francisco José García-Peñalvo ◽  
Valentina Zangrando ◽  
Antonio M. Seoane Pardo
Keyword(s):  
Production Process ◽  
Learning Object ◽  
Object Model ◽  
Creation Process ◽  
Framework Design ◽  
Digital Contents ◽  
Innovative Tool ◽  
Definition Of ◽  
Landscape Geography ◽  
Multicultural Perspective

The MIH (Multicultural Interdisciplinary Handbook) project provides new tools for helping teachers and pupils plunge deeper into the culture and the language of another nation via its history and its landscape/geography. The Digital Modules are the most innovative tool of the project. Throughout the chapter, the authors present all stages to develop MIH Digital Modules: (1) the definition of the Learning Object Model based on IEEE LOM; (2) the framework design in order to provide quality digital contents; (3) the Digital Modules production process both during the project and after the end of the project; (4) the tutorials that support all the creation process; and last, but not least, and (5) the multicultural perspective of the Digital Modules.

scholarly journals Trust motivation: The self-regulatory processes underlying trust decisions

2019 ◽  
Vol 9 (2-3) ◽  
pp. 99-123 ◽  
Author(s):  
Lisa van der Werff ◽  
Alison Legood ◽  
Finian Buckley ◽  
Antoinette Weibel ◽  
David de Cremer
Keyword(s):  
Goal Setting ◽  
Feedback Loop ◽  
Future Research ◽  
Two Phase ◽  
Cognitive Trust ◽  
Regulatory Processes ◽  
Dynamic View ◽  
Definition Of ◽  
And Behavior ◽  
And Control

Theorizing about trust has focused predominantly on cognitive trust cues such as trustworthiness, portraying the trustor as a relatively passive observer reacting to the attributes of the other party. Using self-determination and control theories of motivation, we propose a model of trust motivation that explores the intraindividual processes involved in the volitional aspects of trust decision-making implied by the definition of trust as a willingness to be vulnerable. We distinguish between intrinsic and extrinsic drivers of trust and propose a two-phase model of trust goal setting and trust regulation. Our model offers a dynamic view of the trusting process and a framework for understanding how trust cognition, affect and behavior interact over time. Furthermore, we discuss how trust goals may be altered or abandoned via a feedback loop during the trust regulation process. We conclude with a discussion of potential implications for existing theory and future research.

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