Ontological Foundations Research Articles

Ecosystem integration: the use of ontologies in integrating knowledge across manufacturing value networks

One of the greatest challenges in creating effective decision-making systems for connected enterprises is the management of cross-domain information. In manufacturing value networks where supply chains are increasingly intertwined, and closed-loop lifecycle management requires traversing several domains, ontologies are proving to be a reliable reference for cross-domain semantic interoperability. However, ontology development, implementation, and management are fragmented and difficult for new users of ontologies to grasp. This is a significant challenge in environments where ontologies are vital for managing effective data exchanges in complex industrial processes. The OntoCommons project has evolved an ontology ecosystem that aims to lower the entry barrier to using ontologies. Building on this ambition, we present a holistic approach to the integration and management of ontologies horizontally across manufacturing ecosystems, including the creation of reference documentation for manufacturing value networks and related standards, available tools for working with ontologies, and examples of vertical integration of knowledge from application level with domain-level and top-level ontology reference documentation. As a novel research direction, we propose a meta-level approach to ontology-driven knowledge management in manufacturing ecosystems. Based on evidence from recent breakthroughs, we present future and emerging research directions.

Цивилизационная основа бытийственности институционального человека

Introduction. Atheistic literature insists that religious faith owes its origin to human ignorance. In its turn, this ‘ignorance’ of a person is closely connected with the ontological foundations of an institutional person determining the civilizational basis of his or her beingness. Theoretical analysis. Overcoming intellectual limitation the study of the ontological foundations of the formation of social being is now acquiring important scientific and socio-political significance in the development of social space. Considering the existence of a person through the category of an institutional person the philosophical concept of an institutional person involves diverse studies including both the analysis of the civilizational basis of the beingness of the social space and the living space of a person as mutually conditioned categories connected with historical tasks. Empirical analysis. Despite the perfect understanding of the laws of dialectics, the effect of the laws of the development of social being in the context of the tasks of history remains a poorly developed problem at the present time. Revealing the interdependence of the laws of self-organization and organization of being a new knowledge is born, and the civilizational basis of the beingness of an institutional person expands. Conclusion. The expanding possibilities of the civilization that has entered the space entail changes in the organization of social life. New meanings of an institutional person – a person of the universe system – are emerging.

When one logic is not enough: Integrating first-order annotations in OWL ontologies

In ontology development, there is a gap between domain ontologies which mostly use the Web Ontology Language, OWL, and foundational ontologies written in first-order logic, FOL. To bridge this gap, we present Gavel, a tool that supports the development of heterogeneous ‘FOWL’ ontologies that extend OWL with FOL annotations, and is able to reason over the combined set of axioms. Since FOL annotations are stored in OWL annotations, FOWL ontologies remain compatible with the existing OWL infrastructure. We show that for the OWL domain ontology OBI, the stronger integration with its FOL top-level ontology BFO via our approach enables us to detect several inconsistencies. Furthermore, existing OWL ontologies can benefit from FOL annotations. We illustrate this with FOWL ontologies containing mereotopological axioms that enable additional, useful inferences. Finally, we show that even for large domain ontologies such as ChEBI, automatic reasoning with FOL annotations can be used to detect previously unnoticed errors in the classification.

Speaking of what is not: Hatibzâde and Taşköprizâde Kâsım on the existential import of negative propositions

ABSTRACT This paper undertakes an in-depth examination of the intriguing argument for the existential import of negative propositions by the fifteenth-century Ottoman scholar Hatibzâde Mehmed (d. 1496) and the counterarguments by his disciple, Taşköprizâde Kâsım (d. 1513). It argues that this discussion is a significant example of Ottoman scholars engaging in long-standing disputes concerning the nature and ontological ground of negative propositions, which date back to Plato and Aristotle. It is also intended to underline the need for considering not only logic texts but also works primarily associated with other disciplines in order to attain a comprehensive picture of logical discussions in the post-classical period of Islamic thought.

Modeling competences in enterprise architecture: from knowledge, skills, and attitudes to organizational capabilities

Competence-based approaches have received increased attention, as the demand for qualified people with the right combination of competences establishes itself as a major factor of organizational performance. This paper examines how competences can be incorporated into Enterprise Architecture modeling: (i) we identify a key set of competence-related concepts such as knowledge, skills, and attitudes, (ii) analyze and relate them using a reference ontology (grounded on the Unified Foundational Ontology), and (iii) propose a representation strategy for modeling competences and their constituent elements leveraging the ArchiMate language, discussing how the proposed models can fit in enterprise competence-based practices. Our approach is intended to cover two tasks relevant to the combined application of Enterprise Architecture and Competence Modeling: ‘zooming in’ on competences, revealing the relations between competences, knowledge, skills, attitudes and other personal characteristics that matter in organizational performance, and ‘zooming out’ of competences, placing them in the wider context of other personal competences and overall organizational capabilities. An assessment of the representation is offered in the form of an empirical survey.

A dataset without a code book: ethnography and open science.

This paper reflects upon calls for "open data" in ethnography, drawing on our experiences doing research on sexual violence. The core claim of this paper is not that open data is undesirable; it is that there is a lot we must know before we presume its benefits apply to ethnographic research. The epistemic and ontological foundation of open data is grounded in a logic that is not always consistent with that of ethnographic practice. We begin by identifying three logics of open data-epistemic, political-economic, and regulatory-which each address a perceived problem with knowledge production and point to open science as the solution. We then evaluate these logics in the context of the practice of ethnographic research. Claims that open data would improve data quality are, in our assessment, potentially reversed: in our own ethnographic work, open data practices would likely have compromised our data quality. And protecting subject identities would have meant creating accessible data that would not allow for replication. For ethnographic work, open data would be like having the data set without the codebook. Before we adopt open data to improve the quality of science, we need to answer a series of questions about what open data does to data quality. Rather than blindly make a normative commitment to a principle, we need empirical work on the impact of such practices - work which must be done with respect to the different epistemic cultures' modes of inquiry. Ethnographers, as well as the institutions that fund and regulate ethnographic research, should only embrace open data after the subject has been researched and evaluated within our own epistemic community.

ONTOLOGI ILMU PENGETAHUAN PERSPEKTIF ISLAM (Hirarki Wujud Menurut Al-Farabi dan Perbandingannya dengan Barat)

The ontological foundations of science in the western and Islamic views have differences. This has an impact on different classifications of science. One of the Muslim philosophers who classified science was al-Farabi. This article aims to review or explain the ontological foundations of Science in Islamic and Western views, and the herarchy of existence according to al-Farabi. The study in this study uses qualitative methods, the source of data is in the form of ideas from Al-Farabi, which are obtained from secondary sources in the form of books, journals, and scientific articles. Based on the results of this research, it was revealed that in the Islamic view ontological studies are not only limited to physical-empirical matters so that the classification of science according to al-Farabi includes all parts of both the physical and metaphysical fields. One of the important points of the classification of sciences according to al-Farabi's view is that he has classified sciences that depart from the division of the hierarchy of maujudat (ontological status) at 4 (four) levels, namely: Allah, as obligatory al-being, then angels, celestial bodies (celestial) and earth bodies (terrestrial).

Ontology-based security modeling in ArchiMate

Enterprise Risk Management involves the process of identification, evaluation, treatment, and communication regarding risks throughout the enterprise. To support the tasks associated with this process, several frameworks and modeling languages have been proposed, such as the Risk and Security Overlay (RSO) of ArchiMate. An ontological investigation of this artifact would reveal its adequacy, capabilities, and limitations w.r.t. the domain of risk and security. Based on that, a language redesign can be proposed as a refinement. Such analysis and redesign have been executed for the risk elements of the RSO grounded in the Common Ontology of Value and Risk. The next step along this line of research is to address the following research problems: What would be the outcome of an ontological analysis of security-related elements of the RSO? That is, can we identify other semantic deficiencies in the RSO through an ontological analysis? Once such an analysis is provided, can we redesign the security elements of the RSO accordingly, in order to produce an improved artifact? Here, with the aid of the Reference Ontology for Security Engineering (ROSE) and the ontological theory of prevention behind it, we address the remaining gap by proceeding with an ontological analysis of the security-related constructs of the RSO. The outcome of this assessment is an ontology-based redesign of the ArchiMate language regarding security modeling. In a nutshell, we report the following contributions: (1) an ontological analysis of the RSO that identifies six limitations concerning security modeling; (2) because of the key role of the notion of prevention in security modeling, the introduction of the ontological theory of prevention in ArchiMate; (3) a well-founded redesign of security elements of ArchiMate; and (4) ontology-based security modeling patterns that are logical consequences of our proposal of redesign due to its underlying ontology of security. As a form of evaluation, we show that our proposal can describe risk treatment options, according to ISO 31000. Finally, besides presenting multiple examples, we proceed with a real-world illustrative application taken from the cybersecurity domain.

Managing Provenance Data in Knowledge Graph Management Platforms

Knowledge Graphs (KGs) present factual information about domains of interest. They are used in a wide variety of applications and in different domains, serving as powerful backbones for organizing and extracting knowledge from complex data. In both industry and academia, a variety of platforms have been proposed for managing Knowledge Graphs. To use the full potential of KGs within these platforms, it is essential to have proper provenance management to understand where certain information in a KG stems from. This plays an important role in increasing trust and supporting open science principles. It enables reproducibility and updatability of KGs. In this paper, we propose a framework for provenance management of KG generation within a web portal. We present how our framework captures, stores, and retrieves provenance information. Our provenance representation is aligned with the standardized W3C Provenance Ontology. Through our framework, we can rerun the KG generation process over the same or different source data. With this, we support four applications: reproducibility, altered rerun, undo operation, and provenance retrieval. In summary, our framework aligns with the core principles of open science. By promoting transparency and reproducibility, it enhances the reliability and trustworthiness of research outcomes.

Toward an ontology for EA modeling and EA model quality

Models have long since been used, in different shapes and forms, to understand, communicate about, and (re)shape, the world around us; including many different social, economic, biological, chemical, physical, and digital aspects. This is also the case in the context of enterprise architecture (EA), where we see a wide range of models in many different shapes and forms being used as well. Researchers in EA modeling usually introduce their own lexicon, and perspective of what a model actually is, while accepting (often implicitly) the accompanying ontological commitments. Similarly, practitioners of EA modeling implicitly also commit to (different) ontologies, resulting in models that have an uncertain ontological standing. This is because, for the subject domain of enterprise architecture models (as opposed to the content of such models), no single ontology has gained major traction. As a result, studies into aspects of enterprise architecture models, such as “model quality” and “return on modeling effort”, are fragmented, and cannot readily be compared or combined. This paper proposes a comprehensive applied ontology, specifically geared to enterprise architecture modeling. Ontologies represent structured knowledge about a particular subject domain. It allows for study into, and reasoning about, that subject domain. Our ontology is derived from a theory of modeling, while clarifying concepts such as “enterprise architecture model”, and introduces novel concepts such as “model audience” and “model objective”. Furthermore, the relevant interrelations between these different concepts are identified and defined. The resulting ontology for enterprise architecture models is represented in OntoUML, and shown to be consistent with the foundational ontology for modeling, Unified Foundational Ontology.

Landasan Ontologis dalam Pengembangan Kurikulum Pendidikan Agama Islam pada Madrasah Ibtidaiyah

The current moral decadence is a major concern in the field of education, particularly in Islamic Religious Education (PAI) subjects, which are responsible for instilling moral and religious values in students. This study aims to examine the ontological foundations in the development of the PAI curriculum for the Aqidah Akhlak subject at MI Muhammadiyah 01 Cakru Jember. Utilizing a qualitative method with a case study design, this research involves interviews and observations as the primary data collection techniques, supported by literature reviews. The findings indicate that a curriculum developed based on ontological foundations can serve as an effective reference for educators in implementing Aqidah Akhlak teaching. Key findings include the positive impact of a well-planned curriculum on personal changes in students and the broader community. The implications of this study emphasize the importance of continuous evaluation and monitoring to ensure the curriculum remains on track and supports the development of students' strong and integral character.

Landasan Ontologis dalam Pengembangan Kurikulum PAI pada Mata Pelajaran Al-Qur’an Hadist di Madrasah Tsanawiyah

This study examines the critical role of ontological foundations in the development of the Islamic Religious Education (PAI) curriculum, specifically for Qur'an and Hadith subjects in Madrasah Tsanawiyah (MTs). Recognizing the importance of a strong philosophical underpinning in religious education, this research aims to explore how integrating ontological principles into the PAI curriculum can enhance students' comprehension of Islamic values and their engagement in the learning process. Employing a qualitative research design, data were collected through in-depth interviews, observations, and document analysis at several MTs in Yogyakarta over a two-month period. The findings reveal that embedding ontological concepts in the curriculum not only deepens students' understanding of Islamic teachings but also fosters greater spiritual and character development. The study suggests that a more philosophically integrated approach to curriculum design can significantly contribute to the holistic development of students, aligning educational practices with the core values of Islam. The implications of this research highlight the need for educational institutions to adopt and implement curricula that emphasize deep, reflective learning, which is essential for cultivating both intellectual and spiritual growth in students.

Philosophy of Mathematics in Primary Education Mathematics Learning: Ontological, Epistemological, and Methodological

The purpose of this study is to examine the relationship, position, and role of the philosophy of mathematics in learning mathematics in basic education through the perspective of the scope of philosophy, namely ontological mathematics, epistemological mathematics, and methodological mathematics. This research is a qualitative descriptive research with a literature study approach. Data collection techniques are carried out through the documentation method of articles originating from the Google Scholar database, as well as books related to the philosophy of mathematics. Data analysis techniques consist of data reduction, data presentation, and conclusion. The results highlight three main aspects within the scope of the philosophy of mathematics: ontological, epistemological, and methodological. Ontological mathematics addresses the ontological foundations of mathematics for teaching, including the role of mathematics in various contexts. The epistemology of mathematics emphasizes the importance of understanding the discipline from multiple perspectives to enhance learning and curriculum design. Meanwhile, the methodology of mathematics highlights the role of specific methods in determining mathematical solutions. In conclusion, understanding the philosophy of mathematics in these three aspects is important for educators to improve the learning process of mathematics at the primary level comprehensively and optimally.

Towards an Ontology for Generating Behaviors for Socially Assistive Robots Helping Young Children

Socially assistive robots (SARs) have the potential to revolutionize educational experiences by providing safe, non-judgmental, and emotionally supportive environments for children's social development. The success of SARs relies on the synergy of different modalities, such as speech, gestures, and gaze, to maximize interactive experiences. This paper presents an approach for generating SAR behaviors that extend an upper ontology. The ontology may enable flexibility and scalability for adaptive behavior generation by defining key assistive intents, turn-taking, and input properties. We compare the generated behaviors with hand-coded behaviors that are validated through an experiment with young children. The results demonstrate that the automated approach covers the majority of manually developed behaviors while allowing for significant adaptations to specific circumstances. The technical framework holds the potential for broader interoperability in other assistive domains and facilitates the generation of context-dependent and socially appropriate robot behaviors.

Coordinating virus research: The Virus Infectious Disease Ontology.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.

Collaborative Semantic Annotation Tooling (CoAT) to Improve Efficiency and Plug-and-Play Semantic Interoperability in the Secondary Use of Medical Data: Concept, Implementation, and First Cross-Institutional Experiences

The cross-institutional secondary use of medical data benefits from structured semantic annotation, which ideally enables the matching and merging of semantically related data items from different sources and sites. While numerous medical terminologies and ontologies, as well as some tooling, exist to support such annotation, cross-institutional data usage based on independently annotated datasets is challenging for multiple reasons: the annotation process is resource intensive and requires a combination of medical and technical expertise since it often requires judgment calls to resolve ambiguities resulting from the non-uniqueness of potential mappings to various levels of ontological hierarchies and relational and representational systems. The divergent resolution of such ambiguities can inhibit joint cross-institutional data usage based on semantic annotation since data items with related content from different sites will not be identifiable based on their respective annotations if different choices were made without further steps such as ontological inference, which is still an active area of research. We hypothesize that a collaborative approach to the semantic annotation of medical data can contribute to more resource-efficient and high-quality annotation by utilizing prior annotational choices of others to inform the annotation process, thus both speeding up the annotation itself and fostering a consensus approach to resolving annotational ambiguities by enabling annotators to discover and follow pre-existing annotational choices. Therefore, we performed a requirements analysis for such a collaborative approach, defined an annotation workflow based on the requirement analysis results, and implemented this workflow in a prototypical Collaborative Annotation Tool (CoAT). We then evaluated its usability and present first inter-institutional experiences with this novel approach to promote practically relevant interoperability driven by use of standardized ontologies. In both single-site usability evaluation and the first inter-institutional application, the CoAT showed potential to improve both annotation efficiency and quality by seamlessly integrating collaboratively generated annotation information into the annotation workflow, warranting further development and evaluation of the proposed innovative approach.

Ontologies of Herbal Medicine: A thematic review analysis from 2011-2022

This study examines various approaches for ontology construction and evaluation in medicinal plant ontology, focusing on the challenges associated with this domain. Thirty review articles on three databases revealed five alternative approaches for ontology generation in herbal medicine: well-structured methodology, customized methodology, semiautomatic approach, socio-technical approach, domain expert techniques, and top-level approach. However, 68% of the research did not include ontology evaluation. Ontology quality was often assessed using competency questions, expert opinion, and automated error detection. The study provides ontology developers with a better understanding of established methodologies for developing and evaluating standard ontologies in this area and identifies gaps in existing research for future studies.

OHDSI Standardized Vocabularies-a large-scale centralized reference ontology for international data harmonization.

The Observational Health Data Sciences and Informatics (OHDSI) is the largest distributed data network in the world encompassing more than 331 data sources with 2.1 billion patient records across 34 countries. It enables large-scale observational research through standardizing the data into a common data model (CDM) (Observational Medical Outcomes Partnership [OMOP] CDM) and requires a comprehensive, efficient, and reliable ontology system to support data harmonization. We created the OHDSI Standardized Vocabularies-a common reference ontology mandatory to all data sites in the network. It comprises imported and de novo-generated ontologies containing concepts and relationships between them, and the praxis of converting the source data to the OMOP CDM based on these. It enables harmonization through assigned domains according to clinical categories, comprehensive coverage of entities within each domain, support for commonly used international coding schemes, and standardization of semantically equivalent concepts. The OHDSI Standardized Vocabularies comprise over 10 million concepts from 136 vocabularies. They are used by hundreds of groups and several large data networks. More than 8600 users have performed 50 000 downloads of the system. This open-source resource has proven to address an impediment of large-scale observational research-the dependence on the context of source data representation. With that, it has enabled efficient phenotyping, covariate construction, patient-level prediction, population-level estimation, and standard reporting. OHDSI has made available a comprehensive, open vocabulary system that is unmatched in its ability to support global observational research. We encourage researchers to exploit it and contribute their use cases to this dynamic resource.

The Relation Between Mathematics Philosophy And Culture-Based Learning Model

The aim of this study is to study the correlation of mathematical philosophy with cultural-based learning models. The method of research used is the method of library research, i.e. conducting studies related to mathematical philosophy, philosophical mathematics learning, culture-based mathematic learning, the connection of mathematically philosopher with ethnomatematics, the relationship of mathematic philosophies with cultural-based learning models. The results of the research have been obtained that the philosofy of maths, the model of learning based on culture, and ethnomathematics have close connections in the context of understanding and teaching of Mathematics. Mathematical philosophy deals with the foundations of mathematical epistemology and ontology, while a culture-based learning model emphasizes the integration of values and cultural contexts in mathematics learning. Ethnomatematics refers to the study of mathematical ways of thinking in a particular culture. By understanding the cultures, traditions, and world views of a particular society, ethnomathematics can help develop more culturally relevant and meaningful learning models. Therefore, the interrelationship between mathematical philosophy, culture-based learning models, and ethnomathematics can create a more holistic and contextual approach to mathematics learning.
 Keywords: Mathematical Philosophy, Cultural Based Learning Model, Ethnomathematics

Архаика и гостеприимство в экофилософской перспективе

The article presents the results of an analysis of the logic and ethos responsible for the environmental crisis of our time, and the conditions for the possibility of exiting it through their transformation. Despite the fact that this problem has been repeatedly discussed by researchers, such a factor as “disenchantment of the world” (Max Weber) remains undeservedly ignored. On the one hand, its result is anthropocentrism, around the figure of which values and ethos strategies are subsequently formed, leading to the thoughtless use of natural resources and environmental pollution. On the other hand, there is the objectification of the “world” and the “other-alien”, which is deprived of its own ontological foundations. It is the communal practices of constructing the “other-alien” on a conventional basis that are largely responsible for the lack of effectiveness of environmental programs and initiatives. Thus, the subject-object episteme that dominates the “disenchanted” new European “world” not only initiates the environmental crisis of our time, but also creates an obstacle to exiting it. The idea of the reclamation of the “archaic” has analytical value for ecophilosophy, the “otherrationality” of which allows us to go beyond the boundaries of new European thinking, covered with a thick layer of technocratic illusions, political phantasms and value fictions. At the same time, archaic “other-rationality” is not exclusively a mental phenomenon, but is cast in ritual practices. The ritual of hospitality seems to unfold a symbolic map of “worlds” “here-now”, linking the past, present and future and inextricably connecting different “worlds” and their inhabitants. The subject-object matrix of vision and action is completely inappropriate in its execution, and therefore the ontic experience generated by it, in its constitutive principles, is very far from the experience of modern European man. As a symbolic “anthropotechnique”, hospitality can become a kind of provocation for a cognitive, existential and social turn, which will make responsible human interaction with the “world”, permeated with an attitude of participation and care, possible.