Semantic Artifacts Research Articles

Modeling and Accessing Smart Materials with Integrity Constraints in the Shapes Constraint Language and Ontologies—The SmaDi Way

Various types of semantic artifacts play a vital role in developing software systems, for example, information systems for materials scientists that adhere to the findability, accessibility, interoperability, reusability principles for digital assets. Among them, integrity constraints (ICs) are essential artifacts as they orthogonally add to the representation capabilities of ontologies a means to enforce consistency and completeness of given data. An IC language recommended by the worldwide web consortium (W3C) for use with linked open data is Shapes Constraint Language (SHACL). This article discusses the algorithm and evaluation results for a new SHACL validator developed in the context of SmaDi, a project for digitalizing smart materials associated with MaterialDigital. The new validator reduces SHACL constraints to SPARQL Protocol and RDF Query Language (SPARQL) queries, that is, queries in the W3C recommended query language over repositories represented in the standard syntax for linked open data, RDF. Hence, in contrast to off‐the‐shelf validators, it can be used with any SPARQL endpoint, even if there is only a (virtual) view of the RDF data. The article demonstrates the use of SHACL ICs for modeling some simple constraints over smart materials. The evaluation shows that our SHACL validator has processing times comparable to off‐the‐shelf SHACL validators.

The reuse of electronic health records information models in the oncology domain: Studies with the bioframe framework

Objective:The reuse of Electronic Health Records (EHR) information models (e.g., templates and archetypes) may bring various benefits, including higher standardization, integration, interoperability, increased productivity in developing EHR systems, and unlock potential Artificial Intelligence applications built on top of medical records. The literature presents recent advances in standards for modeling EHR, in Knowledge Organization Systems (KOS) and EHR data reuse. However, methods, development processes, and frameworks to improve the reuse of EHR information models are still scarce. This study proposes a software engineering framework, named BioFrame, and analyzes how the reuse of EHR information models can be improved during the development of EHR systems. Methods:EHR standards and KOS, including ontologies, identified from systematic reviews were considered in developing the BioFrame framework. We used the structure of the OpenEHR to model templates and archetypes, as well as its relationship to international KOS used in the oncology domain. Our framework was applied in the context of pediatric oncology. Three data entry forms concerning nutrition and one utilized during the first pediatric oncology consultations were analyzed to measure the reuse of information models. Results:There was an increase in the adherence rate to international KOS of 18% to the original forms. There was an increase in the concepts reused in all 12 scenarios analyzed, with an average reuse of 6.55% in the original forms compared to 17.1% using BioFrame, resulting in significant differences. Conclusions:Our results point to higher reuse rates achieved due to an engineering process that provided greater adherence to EHR standards combined with semantic artifacts. This reveals the potential to develop new methods and frameworks aimed at EHR information model reuse. Additional research is needed to evaluate the impacts of the reuse of the EHR information model on interoperability, EHR data reuse, and data quality and assess the proposed framework in other health domains.

Bridging the Narrative Gap in Healthcare: One Framework at a Time

The goal of this study is to develop a semantic artifact for capturing and inferencing medically significant information from the patient narration. The motivation for such a framework emerges from the understanding of the significance of patient narration and its underutilization. The ontology which borrows from the theories of narration and its components, supports the capture of the narrative detail in medicine. Existing ontology-based narrative models also contributed to this study. A phased approach was adopted to fulfill the objective. A foundational framework was established during the initial phase, while the subsequent phase involved data modeling. A three-way evaluation was also performed to validate the model.

Knowledge Organisation Systems in the Humanities—Semantic Interoperability in Practice

ABSTRACTWe observe a growing universe of machine‐readable knowledge organisation systems (KOS) or even wider ‘semantic artifacts. We see at the same time, various attempts to bring semantic artifacts together via registries, catalogues and via cross‐walks among ontologies. This poster reflects how newest research on semantic interoperability informs current practice for research data repositories and registry service providers. We focus on the domain of humanities and cultural heritage, using different examples from Europe and the Netherlands: The European Archaeological Data Infrastructure Ariadne, services of the Dutch Cultural Heritage Network and two Data Stations (for Archaeology and for SSH) hosted at DANS‐KNAW. For those cases we report on current efforts to include ‘semantic artifacts’, together with opportunities and challenges. This poster is a practice report combined with an invitation to reflect about the context of semantic interoperability itself.

Mapping.bio: Piloting FAIR semantic mappings for biodiversity digital twins

Biodiversity research has a strong focus on the links between environment and functional traits, e.g., to assess how anthropogenic drivers of change impact ecological systems (Díaz et al. 2013). Interoperable exchange and integration of such data is enabled through the use of ontologies that provide ”meaning” to data and enable downstream processing involving learning and inference over graph-structured models of these data (Kulmanov et al. 2020). However, the development of thematically similar semantic artifacts, e.g., the Environmental Ontology (ENVO, Buttigieg et al. 2016) and the Semantic Web for Earth and Environment Technology Ontology (SWEET, DiGiuseppe et al. 2014), in biodiversity-related disciplines (e.g., environmental genomics and earth observation) can introduce substantial conceptual overlaps, and highlights the need for bridging technologies to facilitate reuse of biodiversity data across those knowledge fields (Karam et al. 2020). A recent design study, funded by the European Open Science Cloud (EOSC), proposes a framework to create, document and publish mappings and crosswalks linking different semantic artifacts within a particular scientific community and across scientific domains under the label of "Flexible Semantic Mapping Framework" (SEMAF, Broeder et al. 2021). SEMAF puts a strong emphasis on so-called pragmatic mappings, i.e., mappings that are driven by specific interoperability goals such as translations between specific observation measurements (e.g., sensor configurations) and metadata descriptions. Within the Horizon Europe Project “Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities" (BioDT), a mapping tool leveraging SEMAF is currently under development: Mapping.bio provides a lightweight web service to read semantic artifacts, visualize them, add mappings as graphical connections and store the mappings as FAIR (Findable, Accessible, Interoperable Reusable) Digital Objects (FDOs, De Smedt et al. 2020) in a repository. To foster reusability, sustainably and long-term availability of digital objects, mapping.bio features mappings compliant with the Simple Standard for Sharing Ontological Mappings (SSSOM, Matentzoglu et al. 2022), a machine-interpretable and extensible vocabulary enabling the self-contained exploration and processing of annotated mappings by machines (machine actionability, Jacobsen et al. 2020).

Ontology extension with NLP-based concept extraction for domain experts in catalytic sciences

Ontologies store semantic knowledge in a machine-readable way and represent domain knowledge in controlled vocabulary. In this work, a workflow is set up to derive classes from a text dataset using natural language processing (NLP) methods. Furthermore, ontologies and thesauri are browsed for those classes and corresponding existing textual definitions are extracted. A base ontology is selected to be extended with knowledge from catalysis science, while word similarity is used to introduce new classes to the ontology based on the class candidates. Relations are introduced to automatically reference them to already existing classes in the selected ontology. The workflow is conducted for a text dataset related to catalysis research on methanation of CO_2 and seven semantic artifacts assisting ontology extension by domain experts. Undefined concepts and unstructured relations can be more easily introduced automatically into existing ontologies. Domain experts can then revise the resulting extended ontology by choosing the best fitting definition of a class and specifying suggested relations between concepts of catalyst research. A structured extension of ontologies supported by NLP methods is made possible to facilitate a Findable, Accessible, Interoperable, Reusable (FAIR) data management workflow.

Aligning Semantic Interoperability Frameworks with the FOXS Stack for FAIR Health Data.

FAIR Guiding Principles present a synergy with the use cases for digital health records, in that clinical data need to be found, accessible within a range of environments, and data must interoperate between systems and subsequently reused. The use of HL7 FHIR, openEHR, IHE XDS, and SNOMED CT (FOXS) together represents a specification to create an open digital health platform for modern health care applications. To describe where logical FOXS components align to the European Open Science Cloud Interoperability Framework (EOSC-IF) reference architecture for semantic interoperability. This should provide a means of defining if FOXS aligns to FAIR principles and to establish the data models and structures that support longitudinal care records as being fit to underpin scientific research. The EOSC-IF Semantic View is a representation of semantic interoperability where meaning is preserved between systems and users. This was analyzed and cross-referenced with FOXS architectural components, mapping concepts, and objects that describe content such as catalogues and semantic artifacts. Majority of conceptual Semantic View components were featured within the FOXS architecture. Semantic Business Objects are composed of a range of elements such as openEHR archetypes and templates, FHIR resources and profiles, SNOMED CT concepts, and XDS document identifiers. Semantic Functional Content comprises catalogues of metadata that were also supported by openEHR and FHIR tools. Despite some elements of EOSC-IF being vague (e.g., FAIR Digital Object), there was a broad conformance to the framework concepts and the components of a FOXS platform. This work supports a health-domain-specific view of semantic interoperability and how this may be achieved to support FAIR data for health research via a standardized framework.

A Pixel–Channel Hybrid Attention Model for Image Processing

In the field of image processing, better results can often be achieved through the deepening of neural network layers involving considerably more parameters. In image classification, improving classification accuracy without introducing too many parameters remains a challenge. As for image conversion, the use of the conversion model of the generative adversarial network often produces semantic artifacts, resulting in images with lower quality. Thus, to address the above problems, a new type of attention module is proposed in this paper for the first time. This proposed approach uses the pixel–channel hybrid attention (PCHA) mechanism, which combines the attention information of the pixel and channel domains. The comparative results of using different attention modules on multiple-image data verify the superiority of the PCHA module in performing classification tasks. For image conversion, we propose a skip structure (S-PCHA model) in the up- and down-sampling processes based on the PCHA model. The proposed model can help the algorithm identify the most distinctive semantic object in a given image, as this structure effectively realizes the intercommunication of encoder and decoder information. Furthermore, the results showed that the attention model could establish a more realistic mapping from the source domain to the target domain in the image conversion algorithm, thus improving the quality of the image generated by the conversion model.

FAIR Digital Twins for Data-Intensive Research.

Although all the technical components supporting fully orchestrated Digital Twins (DT) currently exist, what remains missing is a conceptual clarification and analysis of a more generalized concept of a DT that is made FAIR, that is, universally machine actionable. This methodological overview is a first step toward this clarification. We present a review of previously developed semantic artifacts and how they may be used to compose a higher-order data model referred to here as a FAIR Digital Twin (FDT). We propose an architectural design to compose, store and reuse FDTs supporting data intensive research, with emphasis on privacy by design and their use in GDPR compliant open science.

ArEnAlg: A Pedagogical Mobile Application for Algorithms Linguistics Based on a Semantic Bilingual Ontology

Ontologies are knowledge structures that serve as the foundation for semantic applications. These semantic artifacts organize and classify knowledge to define the semantic relations among the concepts. Some ontologies are constructed for a single natural language, whereas others are built for dual or multi-natural languages. The goal of this study is to design and implement a mobile educational application to help students learn more effectively and to increase the learner’s acquisition of computational linguistics in the Algorithm domain. The methodology is to develop an application with unique features that can display the terms and the concepts in both Arabic and English languages in two different layouts: a list form and a flashcard form. The created app “ArEnAlg” can generate the terms in the algorithm domain. The major objective of the exercise modules is to examine the user’s knowledge of the concepts in the domain of algorithms. The evaluation results tested three factors: the learner’s enjoyment, the acquisition of the computational linguistics, and the application presentation, which showed that behavioral responses support the purpose of the developed application with a max-min range of 99% -81%.

Semantic applications for ontological information theory

Information theory is a field that has applications in several scientific domains. This field, which was initially proposed by Claude Shannon, is interdisciplinary; it combines probability, electrical engineering, information engineering, computer science, and statistics. Representing knowledge in information theory provides scientific scholars a resourceful reference for the filed. By learning the precise terminology used in information theory, researchers can discover documents in the domain. In addition, they can communicate knowledge and ideas by using the accurate jargon. A scientific ontology representing knowledge corpus can be implemented digitally by articulating the concepts in the domain of information theory using semantic graphs. These scientific semantic artifacts are valuable with Web 3 technologies. They facilitate searching documents online by providing precise related results. In addition, it is expected that the semantic knowledge to be applicable in Web service applications based on information theory as Web services are software components that communicate information. This work presents an ontology for the Information theory. The ontology conceptualizes the knowledge of information domain by identifying the main concepts, principles, equations, metrics, and history of information theory. The ontology composed of classes, instances, and properties is built using protege, an ontology editor, and is stored in OWL format. Educational applications for the built ontology are indicated.

A data warehouse hybrid design framework using domain ontologies for local good-governance assessment

Purpose Most local governance assessment tools are entirely or partially based on stakeholders’ surveys, focus groups and benchmarks of different local governments in the world. These tools remain a subjective way of local governance evaluation. To measure the performance of local good-governance using an unbiased assessment technique, the authors have developed a framework to help automate the design process of a data warehouse (DW), which provides local and central decision-makers with factual, measurable and accurate local government data to help assess the performance of local government. The purpose of this paper is to propose the extraction of the DW schema based on a mixed approach that adopts both i* framework for requirements-based representation and domain ontologies for data source representation, to extract the multi-dimensional (MD) elements. The data was collected from various sources and information systems (ISs) deployed in different municipalities. Design/methodology/approach The authors present a framework for the design and implementation of a DW for local good-governance assessment. The extraction of facts and dimensions of the DW’s MD schema is done using a hybrid approach, where the extraction of requirement-based DW schema and source-based DW schema are done in parallel followed by the reconciliation of the obtained schemas to obtain the good-governance assessment DW final design. Findings The authors developed a novel framework to design and implement a DW for local good-governance assessment. The framework enables the extraction of the DW MD schema by using domain ontologies to help capture semantic artifacts and minimize misconceptions and misunderstandings between different stakeholders. The introduction and use of domain ontologies during the design process serves the generalization and automation purpose of the framework. Research limitations/implications The presently conducted research faced two main limitations as follows: the first is the full automation of the design process of the DW and the second, and most important, is access to local government data as it remains limited because of the lack of digitally stored data in municipalities, especially in developing countries in addition to the difficulty of accessing the data because of regulatory aspects and bureaucracy. Practical implications The local government environment is among the public administrations most subject to change-adverse cultures and where the authors can face high levels of resistance and significant difficulties during the implementation of decision support systems, despite the commitment/engagement of decision-makers. Access to data sources stored by different ISs might be challenging. While approaching the municipalities for data access, it was done in the framework of a research project within one of the most notorious universities in the country, which gave more credibility and trust to the research team. There is also a need for further testing of the framework to reveal its scalability and performance characteristics. Originality/value Compared to other local government assessment ad hoc tools that are partially or entirely based on subjectively collected data, the framework provides a basis for automated design of a comprehensive local government DW using e-government domain ontologies for data source representation coupled with the goal, rationale and business process diagrams for user requirements representations, thus enabling the extraction of the final DW MD schema.

An Ontology for Specifying and Tracing Requirements Engineering Artifacts and Test Artifacts

This paper proposes an ontology that defines and integrates the concepts adopted for use cases and test cases specification. These concepts belong to the metamodels of different Requirements Engineering and testing management supporting tools, and their formalization in an ontology language prevents using concepts ambiguously and enables interoperability among the involved tools, in order to achieve semantic consistency and artifacts tracing.

HiGHmed - An Open Platform Approach to Enhance Care and Research across Institutional Boundaries.

Summary Introduction: This article is part of the Focus Theme of Methods of Information in Medicine on the German Medical Informatics Initiative. HiGHmed brings together 24 partners from academia and industry, aiming at improvements in care provision, biomedical research and epidemiology. By establishing a shared information governance framework, data integration centers and an open platform architecture in cooperation with independent healthcare providers, the meaningful reuse of data will be facilitated. Complementary, HiGHmed integrates a total of seven Medical Informatics curricula to develop collaborative structures and processes to train medical informatics professionals, physicians and researchers in new forms of data analytics. Governance and Policies: We describe governance structures and policies that have proven effective during the conceptual phase. These were further adapted to take into account the specific needs of the development and networking phase, such as roll-out, carerelated aspects and our focus on curricula development in Medical Inform atics. Architectural Framework and Methodology: To address the challenges of organizational, technical and semantic interoperability, a concept for a scalable platform architecture, the HiGHmed Platform, was developed. We outline the basic principles and design goals of the open platform approach as well as the roles of standards and specifications such as IHE XDS, openEHR, SNOMED CT and HL7 FHIR. A shared governance framework provides the semantic artifacts which are needed to establish semantic interoperability. Use Cases: Three use cases in the fields of oncology, cardiology and infection control will demonstrate the capabilities of the HiGHmed approach. Each of the use cases entails diverse challenges in terms of data protection, privacy and security, including clinical use of genome sequencing data (oncology), continuous longitudinal monitoring of physical activity (cardiology) and cross-site analysis of patient movement data (infection control). Discussion: Besides the need for a shared governance framework and a technical infrastructure, backing from clinical leaders is a crucial factor. Moreover, firm and sustainable commitment by participating organizations to collaborate in further development of their information system architectures is needed. Other challenges including topics such as data quality, privacy regulations, and patient consent will be addressed throughout the project.

¿Trascendiendo la arquitectura o arquitectura trascendente?

En esta ponencia se consideran las oportunidades y riesgos de obras arquitectónicas que buscan la trascendencia. Tras una corta discusión sobre cómo lograr la trascendencia a través de un acercamiento ético o estético de la arquitectura, la conversación es dirigida hacia la ambigüedad del término trascender. Esto permite una reflexión sutil y profunda al hacer que nos preguntemos: ¿qué o quién está realizando la trascendencia?; y exactamente, ¿qué es lo que está siendo trascendido? Quizá esta vaguedad no sea sólo algo semántico, sino que se apoye en la realidad (al menos fenomenológica) de las experiencias arquitectónicas trascendentes. Ciertamente, esta línea de estudio prohibe toda conclusión, asegura la humildad y nos anima a encontrar nuevas interpretaciones, incluso de las ya interpretadas. La presente comunicación es una reelaboración del capítulo introductorio al libro Transcending Architecture. Contemporary Views on Sacred Space, editado por el autor y publicado por la CUA Press (Washington DC, 2015).

EHR Systems - Future Developments

For a long period of time of more than 35 years Electronic Health Record (EHR) system are developed and used. There is no dispute whether patient data that is kept in an EHR-system has many advantages such as: a safe and full documentation of the healthcare provided, exchange between co-operating healthcare providers, generation of invoices or reports, education, clinical decision support, support of clinical pathways, clinical and other re-use for research, etc. Many of the potential benefits have not been realised. There has to be a missing piece of the puzzle. This position paper will answer the question why and will point out the solution: at least a European or preferably a worldwide supporting INFO structure as a publicly financed organisation that produces, maintains and publishes semantic interoperability artifacts.

Reconocimiento y economía de la estima: La normatividad basal de los artefactos semánticos

In the structuring of the social moral grammar, Recognition [Anerkennung] plays a key role both as a subject's perception of the dignity of each psychic system, as well as of others as subjects worthy of decent treatment. Brennan and Pettit have rescued the value of the Economy of Esteem. It highlights that the subject's wishful structure involves not only the want of material goods and social power but also to seek esteem. That it is, economy would not only maximize the utility of goods or reputation through, for example, material goods and positional goods but also the competition by esteem. Persons, as semantic artifacts, compete and establish mechanisms for the distribution of esteem. Its possession or not, involve degrees of social inclusion or exclusion from a communicational perspective. Equal access to compete for it, would be a fundamental right. The present paper explores how far this entry to compete in equal conditions by Esteem is not conditioned by Recognition, which as Pettit and Brennan address, it is different from esteem. In that sense, it is possible to consider Recognition as the normative basal grammar and would constitute a conditioning element for fair democratic competition by esteem.

On inter-deriving small-step and big-step semantics: A case study for storeless call-by-need evaluation

Starting from the standard call-by-need reduction for the λ-calculus that is common to Ariola, Felleisen, Maraist, Odersky, and Wadler, we inter-derive a series of hygienic semantic artifacts: a reduction-free storeless abstract machine, a continuation-passing evaluation function, and what appears to be the first heapless natural semantics for call-by-need evaluation. Furthermore we observe that the evaluation function implementing this natural semantics is in defunctionalized form. The refunctionalized counterpart of this evaluation function implements an extended direct semantics in the sense of Cartwright and Felleisen.Overall, the semantic artifacts presented here are simpler than many other such artifacts that have been independently worked out, and which require ingenuity, skill, and independent soundness proofs on a case-by-case basis. They are also simpler to inter-derive because the inter-derivational tools (e.g., refocusing and defunctionalization) already exist.

Challenging the Limits of Critique in Education Through Morin’s Paradigm of Complexity

The position adopted in this paper is inspired by Edgar Morin’s paradigm of complexity and his critique of scientific and philosophical forms of reductionism. This paper is based on research focusing on the diversity of conceptions of critique developed in academic discourses. It aims to challenge the fragmentation and the reduction framing the understanding of this notion in educational sciences. The reflection begins with the introduction of some of Morin’s assumptions concerning the paradigm of complexity. The next section provides a definition of the idea of critique and explores some limits associated with contemporary references framing this notion. Theories of critique are at the core of several educational theories. Based on the literature identified in French-speaking and English-speaking critical traditions in education, several factors determining the way the idea of critique is reduced in education are highlighted. Stressing the tacit character of those variables challenges the limits of traditional conceptions of critique in contemporary education. The position adopted denounces therefore the fact that the current development of theories of critique in education does not provide a framework considering more systematically their conditions of emergence, their own limitations, as well as the antagonistic, complementary and contradictory relationships, which connect them to one another. Based on this position, this paper finally suggests that a distinction be made between “hypocritique” and “hypercritique” as a semantic artifact, stressing the importance of challenging existing theories of critique in education according to the level of complexity that one may attribute to them.

Inter-deriving semantic artifacts for object-oriented programming

We present a new abstract machine for Abadi and Cardelli's untyped non-imperative calculus of objects. This abstract machine mechanically corresponds to both the reduction semantics (i.e., small-step operational semantics) and the natural semantics (i.e., big-step operational semantics) specified in Abadi and Cardelli's monograph. To move closer to actual implementations, which use environments rather than actual substitutions, we then represent methods as closures and we present three new semantic artifacts for a version of Abadi and Cardelli's calculus with explicit substitutions: a reduction semantics, an environment-based abstract machine, and a natural semantics (i.e., an interpreter) with environments. These three new semantic artifacts mechanically correspond to each other, and the two abstract machines are bisimilar. Their significance lies in the fact that they have not been designed from scratch and then proved correct; instead, they have been inter-derived. To illustrate the inter-derivation and to make this article stand-alone, we also comprehensively treat the example of negational normalization over Boolean formulas, in appendix.