Ontology Concepts Research Articles

PheNormGPT: a framework for extraction and normalization of key medical findings.

This manuscript presents PheNormGPT, a framework for extraction and normalization of key findings in clinical text. PheNormGPT relies on an innovative approach, leveraging large language models to extract key findings and phenotypic data in unstructured clinical text and map them to Human Phenotype Ontology concepts. It utilizes OpenAI's GPT-3.5 Turbo and GPT-4 models with fine-tuning and few-shot learning strategies, including a novel few-shot learning strategy for custom-tailored few-shot example selection per request. PheNormGPT was evaluated in the BioCreative VIII Track 3: Genetic Phenotype Extraction from Dysmorphology Physical Examination Entries shared task. PheNormGPT achieved an F1 score of 0.82 for standard matching and 0.72 for exact matching, securing first place for this shared task.

CINEMA, ARTE E VIRADAS ONTOLÓGICAS

In this essay, we will explore the interrelationship between cinema, art and ontological turns, going through the concept of ontology, ontological turns, the importance of cinema and art as language builders and influence in relation to the fundamental understanding of existence, as we also seek illustrate the complexity and interdependence of these elements in the human experience. The methodology used is based on bibliographical research, bringing together information gathering through books and articles. In view of this, putting on the agenda the importance of the relationship between cinema, art and the ontological turn as a reflection on the nature of being and reality.

CINEMA, ARTE E VIRADAS ONTOLÓGICAS CINEMA, ART AND ONTOLOGICAL TURNINGS

In this essay, we will explore the interrelationship between cinema, art and ontological turns, going through the concept of ontology, ontological turns, the importance of cinema and art as language builders and influence in relation to the fundamental understanding of existence, as we also seek illustrate the complexity and interdependence of these elements in the human experience. The methodology used is based on bibliographical research, bringing together information gathering through books and articles. In view of this, putting on the agenda the importance of the relationship between cinema, art and the ontological turn as a reflection on the nature of being and reality.

Intelligent Fault Diagnosis for Aero-Engine Lubrication Systems Using Knowledge Graph and Deep Learning Techniques

Due to the complex structure and function of aero-engine lubrication system, fault diagnosis based on the existing health management system is not explicable and highly dependent on experts' experience. A method for constructing aeroengine lubrication system fault knowledge graph was proposed in this paper. Based on the experts' knowledge, the concept of lubrication system fault knowledge graph ontology was designed. With the help of deep learning techniques such as BiLSTM and CRF, we achieved the automatic extraction of unstructured knowledge. Next, based on the Cosine Distance and Jaccard coefficient, multi-source heterogeneous fault knowledge fusion was realized. In the end, intelligent fault knowledge question answering and fault attribution analysis are realized based on the building of areo-engine lubrication system fault knowledge graph. The application results show that the knowledge graph technology can realize the utilization of prior knowledge of lubrication system faults and the explanation of fault causes. And the knowledge graph technology has a good application prospect in the field of intelligent fault diagnosis.

An ontology-based text mining dataset for extraction of process-structure-property entities

While large language models learn sound statistical representations of the language and information therein, ontologies are symbolic knowledge representations that can complement the former ideally. Research at this critical intersection relies on datasets that intertwine ontologies and text corpora to enable training and comprehensive benchmarking of neurosymbolic models. We present the MaterioMiner dataset and the linked materials mechanics ontology where ontological concepts from the mechanics of materials domain are associated with textual entities within the literature corpus. Another distinctive feature of the dataset is its eminently fine-grained annotation. Specifically, 179 distinct classes are manually annotated by three raters within four publications, amounting to 2191 entities that were annotated and curated. Conceptual work is presented for the symbolic representation of causal composition-process-microstructure-property relationships. We explore the annotation consistency between the three raters and perform fine-tuning of pre-trained language models to showcase the feasibility of training named entity recognition models. Reusing the dataset can foster training and benchmarking of materials language models, automated ontology construction, and knowledge graph generation from textual data.

The relational modeling of hierarchical data in biodiversity databases.

The unifying element of all biodiversity data is the issue of taxon hierarchy modeling. We compared 25 existing databases in terms of handling taxa hierarchy and presentation of this data. We used documentation or demo installations of databases as a source of information and next in line was the analysis of structures using R packages provided by inspected platforms. If neither of these was available, we used the public interface of individual databases. For almost half (12) of the databases analyzed, we did not find any formalized taxa hierarchy data structure, providing only biological information about taxon membership in higher ranks, which is not fully formalizable and thus not generally usable. The least effective Adjacency List model (storing parentId of a taxon) dominates among the remaining providers. This study demonstrates the lack of attention paid by current biodiversity databases to modeling taxon hierarchy, particularly to making it available to researchers in the form of a hierarchical data structure within the data provided. For biodiversity relational databases, the Closure Table type is the most suitable of the known data models, which also corresponds to the ontology concept. However, its use is rather sporadic within the biodiversity databases ecosystem.

Concepts of justice beyond suum cuique

The concept of justice is fundamental in many spheres of human life and in academic disciplines such as law, philosophy, and theology. This article surveys a range of concepts of justice from these disciplines, threading a path from the idea of justice as fairness or proportionality in the works of Hart, Kelsen, and Rawls, to the notion of justice applied in a legal system (juridical justice) as understood by Gunther Teubner, then to concepts of justice beyond equivalence in the work of Ágnes Heller, either seeing justice as a step toward the good or understanding justice as righteousness. The article ends up discussing the idea of love as justice with the help of Paul Tillich. This paves the way for the possibility of critiquing worldly law and juridical justice from the perspective of an ontological concept of justice. The aim of the article is to put the understanding of justice which dominates the conceptual apparatus of the legal discipline in a new and critical light.

A world of Palantir – ontological politics in the Danish police’s POL-INTEL

ABSTRACT When Palantir Technologies customized the Gotham platform into POL-INTEL, a data integration and analysis platform purchased and used by the Danish police, it also enforced a new ontology that simultaneously shaped the police organization and policing practices. In this context, the concept of ontology should be understood in a twofold, albeit interconnected, way: it stands for its usual philosophical burden, but also refers to a centralized concept repository. In Computer Science, ontology refers to the basic concepts for how data is structured. Based on a series of interviews with Palantir engineers and police-officer users of POL-INTEL, this paper investigates what kind of politics, concepts, and bias in the form of data are inserted, processed and materialized in and by POL-INTEL’s ontology. We argue that POL-INTEL’s ontology is inherently political, as it is articulated by an assemblage of data, ideological positions, and economic concerns that are translated into the Danish context. POL-INTEL as a vector of platformization of police work also implies ideological choices with important consequences for the organizational life and accountability of law enforcement, establishing new distributions of skills between the platform and police officers.

Ontologies and Research Data

This study examines the relationship between ontologies and open research data within the framework of the Semantic Web. The objective is to investigate the interconnectivity of both subjects through scholarly works that offer enhancements to the Web ecosystem and scientific research processes. The paper reviews critical theoretical frameworks related to the Semantic Web and the significance of metadata within this model. It also delves into the function that ontologies can fulfill in the Semantic Web landscape. The paper provides a historical overview of the emergence of ontologies and definitions in both Computer Science and Information Science. It chronicles how theorists in Information Science have progressively embraced the concept of ontologies since the late 20th century and assesses the current scholarly consensus on the subject. The study also addresses the importance of open research data in modern science by doing a systematic literature review; this study sources relevant publications from the Web of Science and Scopus databases, with a temporal focus from 2000 to 2023. The findings offer a comprehensive analysis of existing literature that bridges the two domains above, aiding in the theoretical and methodological systematization of the subject matter. The discussion section elaborates on the findings, offering insights into the evolutionary trajectory of the subject matter. Emphasis is placed on the utility of ontologies as tools for the sustainable and effective utilization of research data, accentuating the value of such data as a basis for future scholarly work. In conclusion, we advocate for information science to take a leading role in initiatives that leverage ontological frameworks to manage specialized knowledge in research data sets effectively, ensuring that such data remains an asset for advancing scientific understanding.

Within the Hypha: The Deconstruction of the Anthropocentric Perspective in László Sepsi’s Novel Fruiting Bodies

In my study, I interpret one of the most outstanding stories of Hungarian fiction, László Sepsi’s weird, body- and biohorror novel, Fruiting Bodies [Termőtestek]. The narrative depicts the rivalry between gangster families who fight for the hallucinogenic mushrooms, an important commodity in their town Höksring. As the novel progresses, the rivalry of the crime families fades into the background against the disease spread by the mushrooms, and thus the story presents the beginning of an eco-dystopia and apocalypse. As the title suggests, one of the central motifs of the text is the mushroom, which is both a drug (essentially food) and the basis of the city and houses (living space). In this paper, I will show how the metaphors and similes in the narrative, through the compared things, represent the blurred boundaries between the human body, nature, disease, food and the city, which are central to the novel’s narrative. In my view, the narrative and the parts of the story that focus on the relationship between humans and environment/nature are themed around the breakdown of binary oppositions. The boundaries between culturally distinct categories, the Great Divide (to use Bruno Latour’s term), are dissolved, and the ecological viewpoint, the circulation of matter and reciprocity predominate. I will show that Fruiting Bodies dismantles hierarchies at the narrative level of both the action and the storytelling, offering a more universal perspective rather than a purely anthropocentric one, by situating humanity in the relationships of natural cycles. I will build on the main terms of plant studies (such as plant blindness and plant will), and through the concepts of phytosemiology, Object-Oriented Ontology, flat ontology, hyperobject and dark ecology, I will show how the fungus as metaphor and motif organizes the narrative, and thus offers a posthuman perspective instead of an anthropocentric one.

Teaching Human Geography Sustainability: The Concept of the Anthropocene as a Didactic Tool for Higher Education

Thesis. This critical reflection outlines the didactical challenge of teaching human geography in higher education, focusing on the concept of the Anthropocene as a tool for highlighting sustainability issues. Concepts. The critical reflection discusses the diverse knowledge production traditions, including modernist, postmodernist, and post-postmodernist approaches. It highlights the importance of understanding the ontological and epistemological assumptions underlying these frameworks, in relation to human geography, the concept of the Anthropocene and sustainability. Results and conclusion. The suggestion is a fourfold strategy for improving human geography education: emphasizing the relevance of knowledge production, understanding its impact on the student-teacher relationship, enriching teaching with epistemological discussions, and presenting the Anthropocene as a contested ontological concept rather than a predefined framework. Originality. This critical reflection offers a novel perspective on human geography higher education in how the concept of the Anthropocene can be used for didactic purposes. The paper argues that the concept of the Anthropocene can function as a didactic tool for higher and human geography education, by drawing out the human element within scientific knowledge production.

Modelling user notification scenarios in privacy policies

The processing of personal data gives a rise to many privacy concerns, and one of them is to ensure the transparency of data processing to end users. Usually this information is communicated to them using privacy policies. In this paper, the problem of user notification in case of data breaches and policy changes is addressed, besides an ontology-based approach to model them is proposed. To specify the ontology concepts and properties, the requirements and recommendations for the legislative regulations as well as existing privacy policies are evaluated. A set of SPARQL queries to validate the correctness and completeness of the proposed ontology are developed. The proposed approach is applied to evaluate the privacy policies designed by cloud computing providers and IoT device manufacturers. The results of the analysis show that the transparency of user notification scenarios presented in the privacy policies is still very low, and the companies should reconsider the notification mechanisms and provide more detailed information in privacy policies.

From Sacred Doctrine to Confucian Moral Practice: Giulio Aleni’s Cross-Cultural Interpretation of “Goodness and Evil of Human Nature”

This paper explores the cross-cultural interpretation of “the goodness and evil of human nature” by Jesuit missionary Giulio Aleni in the late Ming Dynasty, and it examines the intersections and complementarity between Catholicism and Confucianism in moral ethics based on Aleni’s integration. The study finds that Aleni, while basically adhering to the Catholic “original sin”, connected the “spirituality” endowed to humans at the beginning of God’s creation with the Confucian ontological concepts such as “ultimate good” (zhishan 至善); centering on “self-mastery” (zizhuan 自專), “sharpening” (dili 砥礪), and “overcoming nature” (kexing 克性), he actively guided the goodness–evil debate towards a Confucian practical morality, and sacred doctrines are served as an impetus of moral practices. The redemption, together with reward and punishment of God, further intensifies the ultimate concern and the way of transcendence. Aleni’s bridging and synthesizing of the two traditions is highly significant: concerning both sanctity and practicality of ethics can to some extent overcome the risks brought by the instrumentalization of ethics or the illusory issues of existence. This has important implications for the self-development and integration of Christian and Confucian morality.

An Enhanced Technology for Ontology Mapping

The process of defining content from different ontologies is time-consuming, tedious and error-prone. To solve these problems, new methods for ontology comparison have been developed. This process focuses on the integration of ontologies for various applications, but also requires maintaining the integrity of the integrated ontologies. The concept ontology associated with integration is designed to be more efficient, accurate and useful. You can combine these two and compete together to increase accuracy. Comparing this approach with existing methods should provide greater accuracy and efficiency in ontology comparison.

Identification of molecular targets and small drug candidates for Huntington's disease via bioinformatics and a network-based screening approach.

Huntington's disease (HD) is a gradually severe neurodegenerative ailment characterised by an increase of a specific trinucleotide repeat sequence (cytosine-adenine-guanine, CAG). It is passed down as a dominant characteristic that worsens over time, creating a significant risk. Despite being monogenetic, the underlying mechanisms as well as biomarkers remain poorly understood. Furthermore, early detection of HD is challenging, and the available diagnostic procedures have low precision and accuracy. The research was conducted to provide knowledge of the biomarkers, pathways and therapeutic targets involved in the molecular processes of HD using informatic based analysis and applying network-based systems biology approaches. The gene expression profile datasets GSE97100 and GSE74201 relevant to HD were studied. As a consequence, 46 differentially expressed genes (DEGs) were identified. 10 hub genes (TPM1, EIF2S3, CCN2, ACTN1, ACTG2, CCN1, CSRP1, EIF1AX, BEX2 and TCEAL5) were further differentiated in the protein-protein interaction (PPI) network. These hub genes were typically down-regulated. Additionally, DEGs-transcription factors (TFs) connections (e.g. GATA2, YY1 and FOXC1), DEG-microRNA (miRNA) interactions (e.g. hsa-miR-124-3p and has-miR-26b-5p) were also comprehensively forecast. Additionally, related gene ontology concepts (e.g. sequence-specific DNA binding and TF activity) connected to DEGs in HD were identified using gene set enrichment analysis (GSEA). Finally, in silico drug design was employed to find candidate drugs for the treatment HD, and while the possible modest therapeutic compounds (e.g. cortistatin A, 13,16-Epoxy-25-hydroxy-17-cheilanthen-19,25-olide, Hecogenin) against HD were expected. Consequently, the results from this study may give researchers useful resources for the experimental validation of Huntington's diagnosis and therapeutic approaches.

Critical Posthumanist Literacy: Building Theory for Reading, Writing, and Living Ethically with Everyday Artificial Intelligence

AbstractLiteracy has become inextricably bound with machine processes, especially in the age of ubiquitous, consequential artificial intelligence (AI). Despite a relatively long history of AI involvement in our everyday reading and writing practices, the public availability of generative AI tools has set off a wave of heated debate—and concern—about AI's role in our lives. We argue that critical literacy theory and tools can serve as a foundation, when combined with posthumanist ideas and some technical knowledge, for understanding, teaching, and participating in our AI‐infused world. In this paper, we outline our theory of critical posthumanist literacy, which draws on posthumanist scholarship to re‐imagine critical literacy with respect to concepts of ontology, agency, ethics and justice, and pedagogy. For each concept, we build on humanist, critical perspectives to show how posthumanist scholarship can help theorize for literacy in the age of AI, especially as AI presents both lingering and new challenges to conceptions of human text production and consumption. Posthumanism provides us with alternative modes of thinking about the nature of “things” (and ourselves); with an understanding of agency as not a human possession but an accomplishment among/within many human and non‐human actors; with an expanded ethics that accounts more deeply for non‐humans; and with pedagogy that embraces ambiguity, movement, and speculation. Using these ideas to expand critical literacy practices, we offer concepts and questions for guiding literacy practice and research, with the understanding that these are no longer separable from complex computational systems.

Cross-Mapping the Portuguese Nursing Ontology with ICNP, SNOMED CT and NANDA-I.

EHR Interoperability is crucial to obtain a set of benefits. This can be achieved by using data standards, like ontologies. The Portuguese Nursing Ontology (NursingOntos) is a reference model describing a set of nursing concepts and their relationships, to represent nursing knowledge in the Electronic Health Records (EHR). The purpose of this work was to define a set of correspondences between Nursing Ontology concepts of NursingOntos and other terminologies, which have the same or similar meaning. In this project, we are using the ISO/TR12300:2016 standard on the principles of mapping between terminological systems. Regarding the domain of "airway clearance", we can say that Portuguese Nursing Ontology has a good level of mapping with other terminologies. In conclusion, we can say that Portuguese Nursing Ontology can be used in EHR with the purpose of a global digitalization of health.

PROBLEM-BASED LEARNING TASKS FOR INTERPRETING A MULTIMODAL TEXT WHEN DELIVERING UNIVERSITY FL EDUCATION DEGREE PROGRAMMES

We discuss theoretical issues connected with methodological construction of problem-solving tasks for development of polycode competence in the system of language tertiary education. As one of the salient genres of polycode texts we take British and American political cartoon and the process of its interpretation. Yet another object of discussion is formed by particular difficulties when we try to include this format into text analysis. It gives us grounds to single out key features of polycode texts, which make them different from traditional text format. Here we include lack of precise genre typology, combination of various semiotic codes, lacunas presence, clip character, specific nature of intertextual chains. We single out several stages in the process of polycode competence formation and development. In particular, problem-solving tasks aimed at identification and primary decoding of certain elements typical for any polycode text; problem-solving tasks aimed at interpretation of verbal and visual components; carrying out group project/group projects of scientific educational or scientific research, of cultural and discourse character; participation in culturally-oriented discussions; assessment of the level of student’s polycode competence formation when interpreting a certain genre of polycode text. In this article, we focus upon possible problem-solving tasks of the first two stages. As one of possible solutions, we suggest conceptual cognitive metaphor modelling and oppositions. The oppositions in this case are built on basic sociocultural values while metaphor modelling includes structural, orientational and ontological concepts, which can be further found out in various types of polycode texts. As possible advantages of this approach, we consider it giving ground for interdisciplinary connections in the course of professional foreign language training. It also enables to widen the scope of questions and topics discussed with students as well as introduce certain linguocultural and sociocultural phenomena. All this assists in building professional competence of a would-be specialist as far as foreign media and multimodal environment is concerned, including its destructive practices. We also describe results of the experimental work. As part of the experiment, we assessed student’s ability to recognise images, symbols, archetypes, linguocultural subjects and meanings, precedent phenomena, continuity of forms and structures, conceptual metaphors and models, conceptual oppositions, basic and transferred meanings, connotations.

How to classify domain entities into top-level ontology concepts using large language models

How to classify domain entities into top-level ontology concepts using large language models

Force of the Postmodern: The Deconstructive Drive in Jack Amariglio’s Writings

This essay traces the genealogy of the concept of the postmodern in Jack Amariglio’s body of work. It recognizes the collaborative accent of Amariglio’s writing practice and renders visible a field of discourse that has materialized through the network of collaborations that Amariglio, through the concept of the postmodern, has thereby activated. According to Amariglio, the postmodern, as an epistemological rather than ontological concept, is a discursive byproduct of modernist discourses that emerge endogenously from within the latter but always in a relation of heterogeneity toward their native discourses. A key characteristic of Amariglio’s writing has been to highlight these extimate tendencies and trace their consequences on economics as a postmodern discourse. In the spirit of his deconstructive drive, this essay extends his thinking on the postmodern through a number of postmodern moments he has identified, especially in his work with David Ruccio, through the psychoanalytical concept of the uncanny.