Interoperability and FAIRness through a novel combination of Web technologies

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs

Knowledge Organization Systems (KOS) in the Semantic Web: A Multi-Dimensional Review

Since the Simple Knowledge Organization System (SKOS) specification and its SKOS eXtension for Labels (SKOS-XL) became formal W3C recommendations in 2009 a significant number of conventional knowledge organization systems (KOS) (including thesauri, classification schemes, name authorities, and lists of codes and terms, produced before the arrival of the ontology-wave) have made their journeys to join the Semantic Web mainstream. This paper uses "LOD KOS" as an umbrella term to refer to all of the value vocabularies and lightweight ontologies within the Semantic Web framework. The paper provides an overview of what the LOD KOS movement has brought to various communities and users. These are not limited to the colonies of the value vocabulary constructors and providers, nor the catalogers and indexers who have a long history of applying the vocabularies to their products. The LOD dataset producers and LOD service providers, the information architects and interface designers, and researchers in sciences and humanities, are also direct beneficiaries of LOD KOS. The paper examines a set of the collected cases (experimental or in real applications) and aims to find the usages of LOD KOS in order to share the practices and ideas among communities and users. Through the viewpoints of a number of different user groups, the functions of LOD KOS are examined from multiple dimensions. This paper focuses on the LOD dataset producers, vocabulary producers, and researchers (as end-users of KOS).Comment: 31 pages, 12 figures, accepted paper in International Journal on Digital Librarie

Metadata enrichment for digital heritage: users as co-creators

This paper espouses the concept of metadata enrichment through an expert and user-focused approach to metadata creation and management. To this end, it is argued the Web 2.0 paradigm enables users to be proactive metadata creators. As Shirky (2008, p.47) argues Web 2.0’s social tools enable “action by loosely structured groups, operating without managerial direction and outside the profit motive”. Lagoze (2010, p. 37) advises, “the participatory nature of Web 2.0 should not be dismissed as just a popular phenomenon [or fad]”. Carletti (2016) proposes a participatory digital cultural heritage approach where Web 2.0 approaches such as crowdsourcing can be sued to enrich digital cultural objects. It is argued that “heritage crowdsourcing, community-centred projects or other forms of public participation”. On the other hand, the new collaborative approaches of Web 2.0 neither negate nor replace contemporary standards-based metadata approaches. Hence, this paper proposes a mixed metadata approach where user created metadata augments expert-created metadata and vice versa. The metadata creation process no longer remains to be the sole prerogative of the metadata expert. The Web 2.0 collaborative environment would now allow users to participate in both adding and re-using metadata. The case of expert-created (standards-based, top-down) and user-generated metadata (socially-constructed, bottom-up) approach to metadata are complementary rather than mutually-exclusive. The two approaches are often mistakenly considered as dichotomies, albeit incorrectly (Gruber, 2007; Wright, 2007) . This paper espouses the importance of enriching digital information objects with descriptions pertaining the about-ness of information objects. Such richness and diversity of description, it is argued, could chiefly be achieved by involving users in the metadata creation process. This paper presents the importance of the paradigm of metadata enriching and metadata filtering for the cultural heritage domain. Metadata enriching states that a priori metadata that is instantiated and granularly structured by metadata experts is continually enriched through socially-constructed (post-hoc) metadata, whereby users are pro-actively engaged in co-creating metadata. The principle also states that metadata that is enriched is also contextually and semantically linked and openly accessible. In addition, metadata filtering states that metadata resulting from implementing the principle of enriching should be displayed for users in line with their needs and convenience. In both enriching and filtering, users should be considered as prosumers, resulting in what is called collective metadata intelligence

Research and Development Workstation Environment: the new class of Current Research Information Systems

Against the backdrop of the development of modern technologies in the field of scientific research the new class of Current Research Information Systems (CRIS) and related intelligent information technologies has arisen. It was called - Research and Development Workstation Environment (RDWE) - the comprehensive problem-oriented information systems for scientific research and development lifecycle support. The given paper describes design and development fundamentals of the RDWE class systems. The RDWE class system's generalized information model is represented in the article as a three-tuple composite web service that include: a set of atomic web services, each of them can be designed and developed as a microservice or a desktop application, that allows them to be used as an independent software separately; a set of functions, the functional filling-up of the Research and Development Workstation Environment; a subset of atomic web services that are required to implement function of composite web service. In accordance with the fundamental information model of the RDWE class the system for supporting research in the field of ontology engineering - the automated building of applied ontology in an arbitrary domain area, scientific and technical creativity - the automated preparation of application documents for patenting inventions in Ukraine was developed. It was called - Personal Research Information System. A distinctive feature of such systems is the possibility of their problematic orientation to various types of scientific activities by combining on a variety of functional services and adding new ones within the cloud integrated environment. The main results of our work are focused on enhancing the effectiveness of the scientist's research and development lifecycle in the arbitrary domain area.Comment: In English, 13 pages, 1 figure, 1 table, added references in Russian. Published. Prepared for special issue (UkrPROG 2018 conference) of the scientific journal "Problems of programming" (Founder: National Academy of Sciences of Ukraine, Institute of Software Systems of NAS Ukraine

OHMI: The Ontology of Host-Microbiome Interactions

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results

Metadata and ontologies for organizing students’ memories and learning: standards and convergence models for context awareness

Este artículo trata de las ontologías que sirven para la comprensión en contexto y la Gestión de la Información Personal (PIM)y su aplicabilidad al proyecto Memex Metadata(M2). M2 es un proyecto de investigación de la Universidad de Carolina del Norte en Chapel Hill para mejorar la memoria digital de los alumnos utilizando tablet PC, la tecnología SenseCam de Microsoft y otras tecnologías móviles(p.ej. un dispositivo de GPS) para capturar el contexto del aprendizaje. Este artículo presenta el proyecto M2, dicute el concepto de los portafolios digitales en las actuales tendencias educativas, relacionándolos con las tecnologías emergentes, revisa las ontologías relevantes y su relación con el proyecto CAF (Context Awareness Framework), y concluye identificando las líneas de investigación futuras.This paper focuses on ontologies supporting context awareness and Personal Information Management (PIM) and their applicability in Memex Metadata (M2) project. M2 is a research project of the University of North Carolina at Chapel Hill to improve student digital memories using the tablet PC, Microsoft’s SenseCam technology, and other mobile technologies (e.g., a GPS device) to capture context. The M2 project offers new opportunities studying students’ learning with digital technologies. This paper introduces the M2 project; discusses E-portfolios and current educational trends related to pervasive computing; reviews relevant ontologies and their relationship to the projects’ CAF (context awareness framework), and concludes by identifying future research directions

Systematic Analysis of COVID-19 Ontologies

This comprehensive study conducts an in-depth analysis of existing COVID-19 ontologies, scrutinizing their objectives, classifications, design methodologies, and domain focal points. The study is conducted through a dual-stage approach, commencing with a systematic review of relevant literature and followed by an ontological assessment utilizing a parametric methodology. Through this meticulous process, twenty-four COVID-19 Ontologies (CovOs) are selected and examined. The findings highlight the scope, intended purpose, granularity of ontology, modularity, formalism, vocabulary reuse, and extent of domain coverage. The analysis reveals varying levels of formality in ontology development, a prevalent preference for utilizing OWL as the representational language, and diverse approaches to constructing class hierarchies within the models. Noteworthy is the recurrent reuse of ontologies like OBO models (CIDO, GO, etc.) alongside CODO. The METHONTOLOGY approach emerges as a favored design methodology, often coupled with application-based or data-centric evaluation methods. Our study provides valuable insights for the scientific community and COVID-19 ontology developers, supplemented by comprehensive ontology metrics. By meticulously evaluating and documenting COVID-19 information-driven ontological models, this research offers a comparative cross-domain perspective, shedding light on knowledge representation variations. The present study significantly enhances understanding of CovOs, serving as a consolidated resource for comparative analysis and future development, while also pinpointing research gaps and domain emphases, thereby guiding the trajectory of future ontological advancements.Comment: 16 pages, accepted for publication in 17th International Conference on Metadata and Semantics Research (MTSR2023), University of Milano-Bicocca, Milan, Italy, October 23-27, 202