Component Ontology Research Articles

Approach to Reasoning about Uncertain Temporal Data in OWL 2

Abstract In this paper, we propose an ontology-based approach for representing and reasoning about certain and uncertain temporal data. It handles temporal data in terms of quantitative time intervals and points and the qualitative relations between them (e.g., “before”). It includes three parts. (1) We extend the 4D-fluents approach with certain ontological components to represent the handled temporal data in OWL 2. (2) We extend the Allen’s interval algebra to reason about certain and uncertain time intervals. We adapt these relations to allow relating a time interval and a time point, and two time points. All relations can be used for temporal reasoning by means of transitivity tables. (3) The extended Allen’s algebra instantiates the 4D-fluents-based representation. Inferences are based on SWRL rules. Based on this ontology, a prototype is implemented and integrated into an ontology-based memory prosthesis for Alzheimer’s patients to handle certain and uncertain temporal data inputs.

Design of framework for ontological component retrieval from software component repositories

Modern component retrieval approaches are based on the context and domain of the software component in addition to using various classification and retrieval techniques like keyword search, attribute-based search and semantic search. This work proposes ontological retrieval framework for software components that makes the use of ontology for effective retrieval of components. Ontological component retrieval framework has been created to facilitate the users and developers to retrieve software components matching precisely to their needs. A well-framed set of queries ranging from little to specific knowledge about the component requirement has been used to validate the results.

How Save Aquinas’s “Intellectus essentiae Argument” for the Real Distinction between Essence and Esse?

Aquinas’ so-called “Intellectus essentiae Argument” for the distinction between being and essence is notoriously suspect, including among defenders of Aquinas’ distinction. For the paper in this volume, I take as my starting point the recent defense of the argument by Fr. Lawrence Dewan, O.P. Fr. Dewan’s project is unsuccessful. Pointing out some shortcomings in his readings allows me to take up his call to highlight the “formal” or “quidditative side” of Aquinas’ metaphysics, in this case in regards to the proofs of the “real distinction.” Accordingly, the second half of this paper sets forth a way in which the famous “Intellectus essentiae Argument” of De Ente et Essentia 4 can succeed as a proof of the real distinction. Aquinas’ argument presupposes the prior real distinction between essence and supposit or individual substance. Esse is the ontological component that makes true our judgments that substances actually are: Obama exists. By contrast, this “truth-maker” cannot be predicated of humanity, although it is in Obama as really distinct from him. If Aquinas’ reasoning in this most contentious of his proofs can be saved, so, perhaps, can most of his other proofs.

Aggregating the syntactic and semantic similarity of healthcare data towards their transformation to HL7 FHIR through ontology matching

Background and objectiveHealthcare systems deal with multiple challenges in releasing information from data silos, finding it almost impossible to be implemented, maintained and upgraded, with difficulties ranging in the technical, security and human interaction fields. Currently, the increasing availability of health data is demanding data-driven approaches, bringing the opportunities to automate healthcare related tasks, providing better disease detection, more accurate prognosis, faster clinical research advance and better fit for patient management. In order to share data with as many stakeholders as possible, interoperability is the only sustainable way for letting systems to talk with one another and getting the complete image of a patient. Thus, it becomes clear that an efficient solution in the data exchange incompatibility is of extreme importance. Consequently, interoperability can develop a communication framework between non-communicable systems, which can be achieved through transforming healthcare data into ontologies. However, the multidimensionality of healthcare domain and the way that is conceptualized, results in the creation of different ontologies with contradicting or overlapping parts. Thus, an effective solution to this problem is the development of methods for finding matches among the various components of ontologies in healthcare, in order to facilitate semantic interoperability. MethodsThe proposed mechanism promises healthcare interoperability through the transformation of healthcare data into the corresponding HL7 FHIR structure. In more detail, it aims at building ontologies of healthcare data, which are later stored into a triplestore. Afterwards, for each constructed ontology the syntactic and semantic similarities with the various HL7 FHIR Resources ontologies are calculated, based on their Levenshtein distance and their semantic fingerprints accordingly. Henceforth, after the aggregation of these results, the matching to the HL7 FHIR Resources takes place, translating the healthcare data into a widely adopted medical standard. ResultsThrough the derived results it can be seen that there exist cases that an ontology has been matched to a specific HL7 FHIR Resource due to its syntactic similarity, whereas the same ontology has been matched to a different HL7 FHIR Resource due to its semantic similarity. Nevertheless, the developed mechanism performed well since its matching results had exact match with the manual ontology matching results, which are considered as a reference value of high quality and accuracy. Moreover, in order to furtherly investigate the quality of the developed mechanism, it was also evaluated through its comparison with the Alignment API, as well as the non-dominated sorting genetic algorithm (NSGA-III) which provide ontology alignment. In both cases, the results of all the different implementations were almost identical, proving the developed mechanism’s high efficiency, whereas through the comparison with the NSGA-III algorithm, it was observed that the developed mechanism needs additional improvements, through a potential adoption of the NSGA-III technique. ConclusionsThe developed mechanism creates new opportunities in conquering the field of healthcare interoperability. However, according to the mechanism’s evaluation results, it is almost impossible to create syntactic or semantic patterns for understanding the nature of a healthcare dataset. Hence, additional work should be performed in evaluating the developed mechanism, and updating it with respect to the results that will derive from its comparison with similar ontology matching mechanisms and data of multiple nature.

Molecular signal communication during arbuscular mycorrhizal formation induces significant transcriptional reprogramming of wheat (Triticum aestivum) roots.

Arbuscular mycorrhizal (AM) symbiosis begins with molecular signal communication (MSC) between AM fungi and the roots of the host plant. We aimed to test the hypothesis that the transcriptional profiles of wheat roots can be changed significantly by AM symbiotic signals, without direct contact. Non-mycorrhizal (NM) and MSC treatments involved burying filter membrane bags containing sterilized and un-sterilized inoculum of the AM fungus Rhizophagus irregularis, respectively. The bags physically separated roots and AM structures but allowed molecular signals to pass through. Extracted RNA from wheat roots was sequenced by high-throughput sequencing. Shoot total nitrogen and phosphorus content of wheat plants was decreased by the MSC treatment. A total of 2360 differentially expressed genes (DEGs), including 1888 up-regulated DEGs and 472 down-regulated DEGs, were found dominantly distributed on chromosomes 2A, 2B, 2D, 3B, 5B and 5D. The expression of 59 and 121 genes was greatly up- and down-regulated, respectively. Only a portion of DEGs could be enriched into known terms during gene ontology analysis, and were mostly annotated to 'catalytic activity', 'protein metabolic process' and 'membrane' in the molecular function, biological process and cellular component ontology categories, respectively. More than 120 genes that may be involved in key processes during AM symbiosis development were regulated at the pre-physical contact stages. The transcriptional profiles of wheat roots can be changed dramatically by MSC. Much of the information provided by our study is of great importance for understanding the mechanisms underlying the development of AM symbiosis.

Extracting and applying evaluation criteria for ontology quality assessment

PurposeThe purpose of this paper is to formulate apposite criteria for ontology evaluation and test them through assessments of existing ontologies.Design/methodology/approachA literature review provided the basis from which to extract the categories relevant to an evaluation of internal ontology components. According to the ontology evaluation categories, a panel of experts provided the evaluation criteria for each category via Delphi survey. Reliability was gauged by applying the criteria to assessments of existing smartphone ontologies.FindingsExisting research tends to approach ontology evaluation through comparison with well-engineered ontologies, implementation in target applications and appropriateness/interconnection appraisals in relation to raw data, but such methodologies fall short of shedding light on the internal workings of ontologies, such as structure, semantic representation and interoperability. This study adopts its evaluation categories from previous research while also collecting concrete evaluation criteria from an expert panel and verifying the reliability of the resulting 53 criteria.Originality/valueThis is the first published study to extract ontology evaluation criteria in terms of syntax, semantics and pragmatics. The results can be used as an evaluation index following ontology construction.

Karakteristik Sains dalam Pemikiran Filosofis Kontemporer (Tinjauan Filsafat Ilmu-Ilmu Keislaman)

Science becomes a furqon/criterion, distinguishing between the quality of the creature, even the quality of the man himself. Science is intended as an appetizer reality, then the name is a reality not only in the form of objects, phenomena, facts, data concrete empirical. So, we need approaches or different methods, and not enough to just rely on the senses, instinct and sheer human rationality. Moreover, basically humans also have the potential tool if used optimally can understand and uncover the whole truth of reality. Philosophy of Science today is better known as a vehicle for interactive dialogue between philosophy and science. Science is "fertile ground" for the study of philosophy (Philosophy of Science), and the philosophy is the foundation that is very useful for science in progress-progress. Hence the development and progress of the Philosophy of Science is inseparable from the development and progress of science, and vice versa.Philosophy of Science arable fields more focused on the components of ontology, epistemology, and axiology science. Similarly to the sciences of Islamic understanding of the construction philosophy can not be separated from these three components (ontology, epistemology, and axiology) can provide the basis for the review and development of sciences of Islamic.

Adaptive Scientific Visualization Tools for a Smart Paleontological Museum

This paper is devoted to the development of tools that allow museum workers to create interactive exhibits by using the Internet of Things (IoT) technology. We propose a unified software and hardware solution that enables the users who do not have deep knowledge in electronics and programming to assemble and interconnect various devices by the principle of a construction set. This, in turn, makes it possible to implement the concept of Smart Museum without the involvement of third-party IT specialists and large investments. The hardware part of the proposed solution is based on the ESP8266 programmable microcontroller with a built-in WiFi module. Peripheral devices can be connected to this microcontroller via expansion boards, the so-called shields. The software part of the solution is based on the SciVi adaptive multiplatform scientific visualization system. This system is fully controlled by the ontological knowledge base and provides the user with a high-level graphical interface that allows him or her to describe visualization algorithms by using data flow diagrams (DFDs). In this work, the SciVi system is supplemented with a mechanism that automatically generates firmware for IoT devices. It is based on an electronic component ontology that describes these devices and their programming methods. The firmware code generator controlled by this ontology automates the creation of lightweight embedded SciVi copies, which are installed on IoT devices and act as servers for data collection, processing, and visualization. To test the proposed solution, we created an interactive exhibit of Dimetrodon grandis, an extinct species of synapsids that lived during the Early Permian.

Transcriptome-based analysis of carotenoid accumulation-related gene expression in petals of Chinese cabbage (Brassica rapa L.).

To identify genes associated with carotenoid accumulation in petals of Chinese cabbage, the composition and content of carotenoids were analyzed, and comparative transcriptome sequencing was performed between the yellow flower line, 92S105, and the orange flower line, 94C9. High-performance liquid chromatography (HPLC) revealed that petals of 92S105 were high in violaxanthin as well as lutein, whereas petals of 94C9 showed considerable levels of lutein and β-carotene. Transcriptome analysis showed that 3534 and 3833 genes were up- and down-regulated in 94C9, respectively. Among these differentially expressed genes (DEGs), many related to carotenoid accumulation were identified, including 12 carotenoid biosynthesis pathway genes, 4 transcription factor genes, and 1028 specifically expressed genes. β-carotene hydroxylase 1 (BrBCH1), BrBCH2, zeaxanthin epoxidase (BrZEP), and MYB transcription factor gene (BrGAMYB) were down-regulated in petals of 94C9 when compared with petals of 92S105, which caused β-carotene accumulation and may lead to orange petal color in 94C9. Expression levels of 20 DEGs were verified by qPCR and the results were highly consistent with those of transcriptome sequencing. Moreover, Gene Ontology (GO) enrichment analysis revealed that membrane, binding, and metabolic processes were the most significantly enriched GO terms in cellular component, molecular function, and biological process ontologies, respectively. In conclusion, our study analyzed the differences in composition and content of carotenoids between 92S105 and 94C9 and identified potential candidate genes related to carotenoid accumulation in petals, thereby creating a solid foundation for future studies on the mechanism regulating carotenoid accumulation in petals of Chinese cabbage.

Drivers for the development of an Animal Health Surveillance Ontology (AHSO)

Comprehensive reviews of syndromic surveillance in animal health have highlighted the hindrances to integration and interoperability among systems when data emerge from different sources. Discussions with syndromic surveillance experts in the fields of animal and public health, as well as computer scientists from the field of information management, have led to the conclusion that a major component of any solution will involve the adoption of ontologies. Here we describe the advantages of such an approach, and the steps taken to set up the Animal Health Surveillance Ontological (AHSO) framework. The AHSO framework is modelled in OWL, the W3C standard Semantic Web language for representing rich and complex knowledge. We illustrate how the framework can incorporate knowledge directly from domain experts or from data-driven sources, as well as by integrating existing mature ontological components from related disciplines. The development and extent of AHSO will be community driven and the final products in the framework will be open-access.

Research on Learning OWL Ontology from Relational Database

Ontology learning is the pivotal technology to construct knowledge base efficiently, and the data of existing knowledge systems are mostly organized in relational mode. In order to reuse and share knowledge in existing knowledge systems, it is necessary to construct ontology for existing knowledge systems. After comparing and analyzing the formal definitions of relational data schema and ontology, this paper proposes a method of extracting knowledge ontology from relational data model. This method builds OWL ontology knowledge base architecture based on metadata of relational data schema, maps different data elements into components of OWL ontology, and implements with prototype tool based on Java platform. As a case study, this method is applied to transform the database of online examination system into OWL ontology model. The method proposed in this paper can be applied to the practice of transferring the widely existing relational-based knowledge base system to the knowledge base system based on OWL ontology framework.

A Review on Ontology Learning Approaches of Creating a Topic Map of Cybercrime Research

Conducting an academic research requires getting a firm grasp of ongoing research issues as well as locating research materials effectively. Often research in different fields on a similar topic can assume diverse approaches due to different objectives and research goals in their own fields. Especially in an interdisciplinary research field like cybercrime, many research topics overlap with those of other research fields. Researchers in such a field, therefore, can benefit from understanding the related domains of one’s own research. Topic maps provide methods for understanding research domain and managing relevant information resources at the same time. In this paper, we review a topic map solution to acquire knowledge structure and to locate information resources effectively. We address current problems of cybercrime research, review previous studies that use automated methods for topic map creation, and examine existing sets of methods for automatically extracting topic map components. Especially, the methods we discuss here are text mining techniques for extracting ontology components, denoted as ontology learning.

Конституційний судовий процес: методологія та філософсько-правові засади

The purpose of the scientific article is to summarize and develop theoretical and methodological knowledge about the nature, nature and features of the constitutional judicial process, as well as to invent a system of measures to: defining the philosophical and legal content of constitutional judicial control as a multifaceted philosophical and legal category; understanding of methodological and procedural principles of its application; identification of the relationship between the structural and functional specifics of the judicial control institute and the characteristic features of social relations in the main spheres of life of the society. The methodological basis of scientific search is a set of philosophical and philosophical principles of scientific cognition, methodological approaches, general methods of thinking, philosophical, general scientific and specifically scientific methods, the use of which has provided the validity and reliability of the results of the study of the laws of constitutional judicial process formation. The scientific novelty of the publication is that for the first time it was proposed to use special methodological tools in the course of developing the theory of constitutional litigation; have further developed scientific ideas about the genesis of the theory of proof and its prospects in domestic law. The conclusions of the scientific article are as follows: The philosophical and legal nature of the judicial constitutional process as a socio-political category and legal phenomenon is based on the achievements of the centuries-old history of the national state-making in ensuring human rights and freedoms, decent living conditions and the desire to develop and strengthen a democratic, social, and legal state. In this context, the powers of the Constitutional Court of Ukraine are not only an important function from the point of view of compliance with constitutional law, but also have special significance as an activity aimed at determining the essential principles of the constitutional process and reflecting the socio-cultural status of society and indicators of the real level of relations between society and the individual. , the government and the citizen, the mechanism of state power and the institutions of civil society in their unity and contradiction (opposites). Thus, «unity of opposites» means their interdependence, that is, the existence of one opposition implies the necessary existence of another opposite, in our case it concerns the categories of «letter» (positivist component) and «spirit» (axiological and ontological components) of law. Keywords: evidence base; constitutional litigation; methodological tools; theory of proof.

La noción de criatura viva en el naturalismo cultural de John Dewey

The term ‘naturalism’ is problematic in the current context since it comprises a set of very different philosophical traditions and thinkers. Some contemporary authors, such as David Papineau, have proposed grouping them according to two different components: the ontological component, which is concerned with the contents of reality; and the methodological one, which is concerned with the way of investigating reality. In general terms, John Dewey’s naturalism, the same as Perice’s and Rorty’s ones, has been defined as methodological. However, through the analysis of the notion of living creature, this article attempts to show how Deweyan naturalism also needs to be understood from its ontological dimension. First, it deals with the different philosophical currents and authors which contribute to the evolution from the Deweyan term of organism to the living creature. Then, it outlines the continuity between the creature and its surroundings that affirms Dewey’s emergent ontology and the potential of this interaction.

JsonToOnto: Building Owl2 Ontologies from Json Documents

The amount of data circulating through the web has grown rapidly recently. This data is available as semi-structured or unstructured documents, especially JSON documents. However, these documents lack semantic description. In this paper, we present a method to automatically extract an OWL2 ontology from a JSON document. We propose a set of transformation rules to transform JSON elements to ontology components. Our approach also allows analyzing the content of JSON documents to discover categorization in order to generate class hierarchy. Finally, we evaluate our approach by conducting experiments on several JSON documents. The results show that the obtained ontologies are rich in terms of taxonomic relationships.

Constructive realism: advantages of ontology and methodology

This article attempts to reveal and analyse the advantages of constructive realism as a methodological framework of contemporary science. Comparing realism and constructivism as two divergent positions in epistemology in their extreme forms, we mention their downsides. These are the epistemological component for extreme realism and the ontological component for radical constructivism. We indicate that the concept of our study is characterized with the best balance of ontology and gnoseology and it allows overcoming ontological and epistemological difficulties associated with constructivism and realism correspondingly. We conclude that constructive realism may facilitate the development of the scientific worldview pertinent to modern knowledge and ready to respond the inherent methodological challenges that science faces.

Limitations of the Western Scientific Worldview for the Study of Metaphysically Inclusive Peoples

The study and understanding of peoples whose worldviews include metaphysical phenomena and explanations are undermined by the strict adherence of many social scientists to the Western scientific worldview which acknowledges only physical phenomena and explanations. The effect of employing Western science in studying the material and practiced cultures of these peoples is to reduce them to constituent ontological components, strip away and discard their metaphysical aspects, and then take what can be readily extracted while leaving what is not understood and therefore not valued. This disrespects the knowledge and alternative worldviews of the very peoples that social scientists seek to more fully understand. One solution is not only to acknowledge the existence of and study alternative worldviews, but also to include and even operationally adopt them when appropriate or necessary to more fully appreciate the metaphysical perspectives of other cultures. In anthropology, for example, this approach could be accomplished by extending the rationale for and methodology of participant observation to include worldview pluralism, and employing the most appropriate worldview for a subject or aspect of a subject under study. In archaeology, this approach is consistent with the goals of the growing Indigenous archaeology movement. Specifically, if the subject has a metaphysical aspect, then a non-Western scientific worldview should be employed in studying that aspect rather than simply dismissing it as unimportant or even non-existent. This paper summarizes the philosophical framework underlying Western science and the evolution and current state of the Western scientific worldview in the social sciences, compares and contrasts Western science with Indigenous peoples’ way of knowing, and presents an example of how the limits of the Western scientific worldview can negatively impact the study of metaphysically inclusive peoples.

Artifact Metaphors as Verbal Means of Objectivization of the Concept "Language" in the Philosophical Discourse of W. von Humboldt

The research features the metaphorical representations of the language in the individual author's worldview expressed by W. von Humboldt via artifact metaphors. The linguistic personality of the great scientist remains surprisingly understudied, so it seems important to study the language means of verbalizing the basic concepts in his philosophical discourse. The research concentrates on the verbalization of the phenomenon "Language" by means of artifact metaphors in W. von Humboldt’s "On the Difference of the Structure of Human Languages and its Influence on the Spiritual Development of Mankind" (Über die Verschiedenheit des menschlichen Sprachbaues und ihren Einfluss auf die geistige Entwicklung des Menschengeschlechts, 1836) [1]. The analysis of empirical material included the method of linguocognitive analysis, the method of component analysis based on dictionary definitions, the method of interpretative analysis of contexts, conceptual and semantic-cognitive analysis of artifact metaphors, etc. The article reveals some features of the cognitive structure of the phenomenon "Language" on the basis of artifact metaphors "language as tool" and "language as fabric". As a result of the research, the frame structure of the artifact metaphorical models of the language concept has been revealed, as well as the ontological components of the language structuring various types of slots. The basic frames "language as tool" and "language as fabric" objectify the concept "Language", represented by the metaphorical model "Artifact" in the philosophical discourse of W. van Humboldt. The "language as tool" metaphor explicates the correlation of Language with such phenomena such as Spirit, Thought, andMan.The metaphorical identification of language and instrument explores the mediatory power of language in relation to Nation and Spirit. The "language as fabric" metaphor objectifies language as a complex entity, whose relevant features are anthropological qualities dominated by intellectual and sensualistic components in the diversity of their manifestations. Individuality is one of the dominant epistemological features of the concept "Language", represented by the artifact metaphorical model in W. von Humboldt’s philosophical discourse. The study proves a high degree of metaphoricity of W.vonHumboldt's linguistic worldview as a whole. One of the important concepts in his philosophical discourse is the "character of language". The scientist metaphorically "humanizes" the language, giving it individual features inherent only to human. The character of the language emphasizes the inseparable interdependence of Spirit and Nation, in its turn, being influenced by the external (verbal) form of the language.

ITRAQ-Based Quantitative Proteomics Suggests Synaptic Mitochondrial Dysfunction in the Hippocampus of Rats Susceptible to Chronic Mild Stress.

Mounting studies show that hippocampal synaptic transmission and plasticity are abnormal in depression. It has been suggested that impairment of synaptic mitochondrial functions potentially occurs in the hippocampus. Thus, the synaptic mitochondria may be a crucial therapeutic target in the course of depression. Here, we investigated the potential dysregulation of synaptic mitochondrial proteins in the hippocampus of a chronic mild stress (CMS) rat model. Proteomic changes of hippocampal synaptosomes containing synaptic mitochondria were quantitatively examined using the isobaric tag for relative and absolute quantitation labeling combined with tandem mass spectrometry. 45 Proteins were identified to be differentially expressed, of which 21 were found to be putative synaptic mitochondrial proteins based on gene ontology component and SynaptomeDB analyses. Detailed investigations of protein functions and disease relevance support the importance of hippocampal synaptic mitochondria as a key substrate contributing to impairment in synaptic plasticity of stress-related disorders. Interestingly, eight synaptic mitochondrial proteins were specifically associated to the susceptible group, and might represent part of molecular basis of depression. Further analysis indicated that the synaptic mitochondrial oxidative phosphorylation (OXPHOS) system was heavily affected by CMS in the susceptible rats. The present results provide novel insights into the disease mechanism underlying the abnormal OXPHOS that is responsible for energy-demanding synaptic plasticity, and thereby increase our understanding of the role of hippocampal synaptic mitochondrial dysfunction in depression.

Personal Freedom and Identity Representation Performance in Modern Urban Subculture

Conglomerations of modern cities are becoming increasingly fractional/disintegrated. An urban person turns into a special type of a person called “homo urbis”, capable of living in a "stone jungle" of performance, in a dense concentration of urban culture objects and amongst the most heterogeneous human mass. The modern civilizational paradigm predetermines the dynamics of the processes of socio-cultural personal identity formation performance in urban culture environment, as well as its globalization and glocalization. The very phenomenon of personal identity in modern urban culture falls into the spectrum of multiple "identities", its evolutionary and critical performance processes. All socio-cultural and civilizational interactions of urban cultural environment are mixed up in existential contradictions. Clear and distinct bases of the traditional world are giving way to civilizationally complex chaos, diverse cultural multilayer and their intricate interlacement. The coexistence of numerous axiological patterns, stereotypes, narratives and metanarratives of the city result in colossal ideological and spiritual tension, where a person has been considered the core of the concentration of the crisis problems since the Socratic anthropological turn. In this connection, the problem of determination and creation of an urban personality, by all means, should be supplemented with the most important heuristic and ontological component – the search for personal identity, as the correlation of the ever-forming civilizational mass of existence with the process of self-reflection of an individual.