Relational Ontology Research Articles

BiotXplorer: Navigating Evidence-Based Biotic Interactions

BiotXplorer is an exploration tool to navigate biotic interactions in BiodiversityPMC (Pasche et al. 2023, Gobeill et al. 2020), a digitally native research library of articles for biomedical, biodiversity and environmental sciences stored in Journal Article Tag Suite (JATS)/BioC formats (Comeau et al. 2019). BiotXplorer pre-processes all documents and supplementary data thanks to the Swiss Institute of Bioinformatics (SIB) Literature Services (SIBiLS) to build pairs of species co-occurring in the same sentence together with a biotic interaction concept as defined in the Relation Ontology. A search service is built on top of this database, which aggregates all triplets matching the query and using taxonomic hierarchies to expand the search. Researchers can thus discover new biotic interactions and understand how they are supported by published evidence. We manually evaluated the precision of BiotXplorer with two benchmarks: 100 randomly selected biotic interactions from BiotXplorer and GLOBI (Global Biotic Interactions), a database of biotic interactions based on tabular datasets. Out of the 100 random triples generated by BiotXplorer, we achieved a precision of 31% when identifying the interacting species. For 74% of the correct interacting species, we accurately identified the type of interaction between the two species. The main causes of error were instances where passages listed multiple species, which can be automatically filtered out. For the second benchmark, we focused on a set of validated biotic interactions—instead of using potential ones—with 85% of the returned passages confirming an interaction between the two species. Our primary goal is to support the detection of biotic interactions across all species. While the precision is dependent on many factors, the vast amount of data it processes can reveal new insights and patterns. The inclusion of evidence for each triplet can support a wide range of One Health/Biosecurity (Hulme 2020) applications (e.g., eDNA characterization, virus spillover prediction). Furthermore, we are working on refining the system using different post-processing methods, such as reducing the volumes of triples by retaining only top-ranked, and therefore most reliable, triples.

The Holy Spirit as “the Gift” in Charles Nyamiti's Trinitarian Theology: A Pentecostal-Lutheran Dialogical Perspective

This article starts from the theology of the Tanzanian-born Charles Nyamiti (1931–2020), as one of the most creative in his generation of African theologians. Nyamiti proposed that ancestral veneration is a foundational human relationship which reflects divine realities. Thus, he proposed an understanding of the Trinity where the Father is the Ancestor, the Son is the Descendant, and the Holy Spirit is the mutual Oblation connecting the two. Because an ancestor does not exist as an ancestor without sacred ritual communication, the Holy Spirit becomes thus absolutely necessary for the Godhead. We maintain that Nyamiti's ancestral approach describes an African logic of gift-giving. Translating his theological contribution into gift-language preserves the theological insights while solving some of the logical problems with the ancestral imaginary, such as how the Father who never died is supposed to be the Ancestor. Through gift-language, Nyamiti's theological insights, which are based on African relational ontologies, become more readily applicable in World Christianity and have potential to transform ecumenism into a vibrant and inclusive embodied pneumatic action for abundant life. In other words, Nyamiti's theological heritage invites theologians to envision Christian faith beyond the confines of Hellenistic-based philosophy.

ICDXML: enhancing ICD coding with probabilistic label trees and dynamic semantic representations

Accurately assigning standardized diagnosis and procedure codes from clinical text is crucial for healthcare applications. However, this remains challenging due to the complexity of medical language. This paper proposes a novel model that incorporates extreme multi-label classification tasks to enhance International Classification of Diseases (ICD) coding. The model utilizes deformable convolutional neural networks to fuse representations from hidden layer outputs of pre-trained language models and external medical knowledge embeddings fused using a multimodal approach to provide rich semantic encodings for each code. A probabilistic label tree is constructed based on the hierarchical structure existing in ICD labels to incorporate ontological relationships between ICD codes and enable structured output prediction. Experiments on medical code prediction on the MIMIC-III database demonstrate competitive performance, highlighting the benefits of this technique for robust clinical code assignment.

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.

Mechanical property and damage mechanism of ultrasonic vibration assisted tensile Cf/SiC composites

Ceramic matrix composites (CMCs) have a wide range of applications in key areas, such as aerospace and defense, and to study the mechanical properties and damage mechanisms of fiber-reinforced CMCs under different tensile conditions. Firstly, an ultrasonic vibration tensile device was designed, based on stress superposition and softening effect, the ontological relationship of materials under ultrasonic vibration-assisted stretching was established to study the damage mechanism of materials under different vibration conditions. The results show that tensile damage has multiple damage mechanisms occurring, i.e., matrix multiple cracking, interfacial debonding, and fiber fracture, and is also the main cause of nonlinear characteristics. Under high-frequency alternating load, the tensile strength decreased by up to 32 MPa, and the strain at break increased by up to 0.24 %; the tensile damage mechanism changed, the interfacial strength of the fiber and matrix decreased, the fiber toughness increased significantly, and the fracture morphology became flatter.

The Theory of Projection

Abstract Whitehead’s process philosophy offers a wide range of speculatively generalized concepts that allow for an application in transdisciplinary research. The notion of projection is an often-overlooked detail of his philosophy that not only appears in his far-reaching theory of perception, but also constitutes an integral part of his theory of extension as the formal foundation of his metaphysical project. His perceptive theory relies on the idea of projection as the fundamental ontological relationship that lifts the past into the present. Projections of sensa describe one side of the ‘double-barreled’ theory of perception and the spatial relations of the contemporary world. The microscopic projection is just as fundamental for perception and for the integrity of a relational theory of becoming, as the perceptual projection is necessary ingredient for symbolic modes of experience. The simple projection in the mode of presentational immediacy is the basis of temporary stability of events and of any perceptual situation in the biological realm. Whitehead was aware of the possible misconceptions that this term might lead to. Discussing his remarks on the hierarchical variety of different modes of projection can resolve those misconceptions and throw a new light on the importance of projection for interdisciplinary inquiries.

Cinema, Displayed

Abstract This essay details that which is arguably the essential nature of a ubiquitous kind of visual display prominently involved in a great many phenomena that people have in mind when they think and talk about the cinema. My argument begins with a summary and critique of an important precedent, Noël Carroll’s essentialist definition of the detached moving image display. The remainder of my discussion concentrates on the structure and dynamics of a particular sort of luminescent display. This display is essential to what I call the cinematic display. As I understand it, the cinematic display is neither the or a medium of cinema nor perforce a vehicle for artistic content. It is, rather, a luminescent display in service of someone’s presentational intentions. I conclude with thoughts about the ontological relation between cinematic displays and works, the latter tentatively defined as a display of expressive or artistic agency.

Centering Africa as context and driver for Global Health Ethics: incompleteness, conviviality and the limits of Ubuntu

Silences exist in global health ethics scholarship because of the particular caricatures of Africa that abound in the world, and these silences profoundly impact scholarship in this field. In this paper, I outline three such silences. The first concerns the consequences of representations of Africa as a place of theoretical scarcity, where the only theory seemingly worth mentioning is relational ontology. The second issue I highlight is the impact of dehumanization on global health and ethics. The third concerns the expectation that African science should serve the goal of development, which limits not only the scientific imagination but also the range of ethical questions that are engaged with. Finally, I turn to Francis Nyamnjoh’s theory of incompleteness and conviviality to propose a shift in bioethics scholarship towards increased focus on the interconnections, encounters and mutual dependency of people and places elsewhere. Incompleteness requires epistemic humility and a curiosity about the views and experiences of others; conviviality is the predisposition required to allow for meaningful exchanges and mutual learning in global health ethics. As a theoretical framework, incompleteness and conviviality are part of a rich African intellectual tradition to help articulate opportunities for a transformative research agenda that helps us understand our world, and its crises, better.

Tomorrow let’s all be pangolins! Western affirmation of a relational ontology in thinking and acting for a multi-species future

How should we envision the future of environmental justice in a context where the imbalances between part of humanity and other living beings seem irreversible and could compromise the survival of the majority? The scientific world and activist movements, both in the West and among indigenous peoples, are making their voices heard to denounce an industrial, productivist and extractivisit lifestyle that is predatory and incompatible with ensuring the well-being and intentionalities of all living beings. The ontological framework of the Anthropocene era seems to support this type of social relationship of domination. Indeed, naturalism puts humans as distinct from the rest of the animal kingdom and as having the right to use the different components of the environment as material resources. Due to the succession of environmental and social crises, whether worldwide or local, these power relationships need to be re-examined. The study of scientific results and observations from the last forty years, listening to people’s accounts of their attachments to their living environment, and the observation of new social and environmental movements all point to the emergence of hybrid ontologies that question naturalism, opening the door to the possibility of multi-species justice as an alternative to inequality.

Unconjugating Community with Fernand Deligny and Jean-Luc Nancy

This article takes as its point of departure unexpected similarities in the ways that the experimental educator, writer and filmmaker Fernand Deligny and Jean-Luc Nancy conceptualize community. Deligny is remembered for his alternative community for non-speaking children with autism, established in the Cévennes in 1967 and founded on the absence of language and relationality as it is commonly understood. This article probes the paradox that in this community we find a rapprochement with Nancy's relational ontology. Drawing on Deligny's theoretical responses to the dynamics he witnessed and the cartographical methods employed to trasce the movements of the children as they roamed, and placing these in dialogue with Nancy's texts on community through the decades, I suggest a kinship between the two thinkers which opens onto broader questions about the relationship between theories and practices of community.

Relational ontologies and epistemologies that are informed by our philosophies: Inaugural Ubuntu Annual Lecture 2022

It’s always a pleasure, a privilege, and an honour to share my thoughts with other African scholars. So, today I chose to talk about decolonising research and evaluation methodologies. I’ll start off with my understanding of what social workers do, then talk about the challenges that are there for social workers and others as evaluators and researchers. And then I introduce the decolonising paradigms and present the opportunities that are there for us as African scholars to work together to further our vision of an Africa that is liberated from only hearing from the global north. I understand that as social worker, you provide help and support to children and others in need, and that in doing so, you are informed by research. I understand that social workers are also evaluators, and they evaluate interventions to inform policy revisions and even modification of their interventions. I understand that social workers, they do research on social problems to inform design and evaluation of the interventions they design for efficacy. According to the SDGs, social workers have a responsibility, and this responsibility includes making sure that the interventions that they design are sustainable, that they provide long-term solutions for the wellbeing of the entire ecosystem that includes human beings and nature. I understand that social workers are also guided by the principles of social justice, human rights, and holistic and sustainable development to reach freedom and wellbeing. And I understand that social workers are expected to use various theories that take into account historical, cultural, and environmental underpinnings of society. Now, there are challenges with evaluation if you are a social worker. And the biggest challenge that we have today is that the paradigms that we use, the world views that we use that inform how we do evaluation have been informed by the ways of knowing of the West, the ways of seeing reality of the West, and the value systems of the West, and are also driven by Euro-Western methodologies. This has resulted in stagnation of thinking about other ways of doing evaluation and other ways of doing research. The biggest problem is that Western researchers and evaluators and the funders and donors from the West are reluctant also, because remember, most of our development interventions are funded from the West. These people are reluctant to engage with philosophies that see a connection between the living and the non-living. And these are called relational ontologies and epistemologies that are basically informed by our philosophies, especially the philosophy of Ubuntu. HOW TO REFERENCE USING ASWDNET STYLE Chilisa, B. (2024). Relational ontologies and epistemologies that are informed by our philosophies: Inaugural Ubuntu Annual Lecture 2022. Ubuntu Lecture delivered on 25 November 2022. African Journal of Social Work, 14(3), 158-165. https://dx.doi.org/10.4314/ajsw.v14i3.8 Visit journal website: https://ajsw.africasocialwork.net

Ethnic, national, and African consciousness: lessons learned from Ghanaian teachers about decolonising citizenship(s)

ABSTRACT Redefining Ghanaian citizenship has been the impetus for the new 2019 educational reform. For President Akufo-Addo, fostering a more located historic expression of citizenship in learners is central for renewing pride and innovation to move Ghana out of poverty. Teachers are seen as central to this change. Based on 26 interviews, this qualitative study explores lessons learned from government primary schoolteachers about citizenship, in relation to their learners. Primarily, their Ghanaian citizenship(s) was an interdependent definition covering their ethnic, national, and (Black) African consciousness. Inspired by the Pan-African theorist, Kwame Nkrumah, the definition was articulated as ‘Oneness;’ an African relational ontology for seeking unity in difference to disinherit colonialism. This was grounded in ‘Rootedness,’ symbiotic with how teachers located their learners’ ethnic identities and differences through indigeneity. A conceptual model for decolonising citizenship(s) is presented, offering praxis within and beyond the African classroom, highlighting Ghana’s role in the decolonial project.

Place, empire, environmental education, and the Community of Inquiry

Place-based education is founded on the idea that the student’s local community is one of their primary learning resources. Place-based education’s underlying educational principle is that students need to first have an experiential understanding of the history, culture, and ecology of the environment in which they are situated before tackling broader national and global issues. Such attempts are a step in the right direction in dealing with controversial issues in a democracy by providing resources for synthesising curriculum though theory (curriculum content, including traditional subjects) and practice (practical learning as experiential education). Nevertheless, many place-based accounts discount Indigenous conceptions of place, which are integral to Indigenous ways of knowing, being and doing, especially in relation to the ontological relationship to Land and Country. Indigenous philosophy has the potential to inform what place-based education means by students developing a ‘sense of place’ when engaging with local communities as their ‘own’ place. In this article we re-imagine the community of inquiry as a place-responsive pedagogy by learning from Indigenous philosophy, and recentring Indigenous notions of place in experiential learning. In addition to exploring the pedagogical potential of a place-responsive account of the community of inquiry, we look to the implications for teacher preparation.

Hospitality and Ontology

Open to the arrival of the other, ready to receive the other unconditionally, the responsibility is born as a response to the eventful arrival of the other. Hospitality, understood in this way, is thus an unconditional condition of possibility for meeting the other, even before any legal institution. In this sense, ethics is more original than law, and the hospitality relationship is more fundamental than any social, political, or legal relationship. This primordiality also means that Derrida reinterprets hospitality as an ontological relation, which now becomes an openness to the arrival of the arrivant, and a readiness to encounter the other. In coexistence, the absolute presence always poses a question to all beings and expects an answer from all beings. Still, in a certain sense, our ontological relation to all beings is also a responsive and responsiblerelationship.

Experience without essentialism: on ‘posting’ phenomenology

ABSTRACT In contemporary qualitative research, phenomenology is often dismissed by postqualitative inquiry (PQI) for clinging to a view of reality as fixed, self-evident, and containing inherent essences. The purpose of this article is to ask how committed phenomenologists might respond to these charges. Employing a somewhat paradoxical defense strategy, the article jumps to phenomenology’s defense by conceding most of PQI’s criticism, but arguing that these deficiencies are contingent theoretical assumptions that can (and should) be developed through dialogue with poststructuralist traditions like PQI. The article then delves into the process of ‘posting’ phenomenology. More specifically, it introduces postphenomenology, a contemporary approach that seeks to reconcile phenomenological insights with poststructuralist concerns and is explicitly anchored in an antiessentialist, relational ontology. Finally, the article argues that the inclusion of postphenomenological insights in PQI would enable a deeper comprehension of the intricate dynamics between humans, technologies, and the worlds that they inhabit.

Introduction to Hiromatsu Wataru's "relational ontology"

Introduction to Hiromatsu Wataru's "relational ontology"

Ethnic Minority Inclusion in Well-Being Research: Beyond Widening Participation

AbstractThis commentary paper welcomes calls for widening participation amongst ethnic minorities in research that aims to understand well-being. However, we demonstrate how a history of exclusion in the daily routines of communities render such calls limited in their ability to address inclusion fully. The absence of ethnic minorities from spaces and dialogues that define what constitutes good well-being is highlighted. We use life-courses that align with Western norms as an example to develop our arguments. Overall, exclusion is rooted in colonial histories and the discrimination experienced by ethnic minorities during day-to-day, routine living. Additionally, relational ontologies of well-being are overwhelmed by individualised constructs. We outline how the suppression of marginalised values in everyday spaces and activities has limited meaning-making in relation to well-being amongst ethnic minority individuals and groups. We characterise this marginalisation as an epistemic injustice in defining well-being. In our conclusions, we call for dialogues and developments in critical race theory (CRT) to be considered in research commissioning processes. Spaces and dialogues that are owned and shaped by ethnic minorities should be supported before we can widen participation in well-being research meaningfully. Values that are practised and developed in such spaces can then contribute to how communities define well-being and the appropriate ways in which it can be studied. It should be acknowledged that we use the term ethnic minority throughout this paper for brevity. The diverse experiences and perspectives that this term covers should be engaged with when considering the recommendations that we make.

Developing a computational representation of human physical activity and exercise using open ontology-based approach: a Tai Chi use case.

Many studies have examined the impact of exercise and other physical activities in influencing the health outcomes of individuals. These physical activities entail an intricate sequence and series of physical anatomy, physiological movement, movement of the anatomy, etc. To better understand how these components interact with one another and their downstream impact on health outcomes, there needs to be an information model that conceptualizes all entities involved. In this study, we introduced our early development of an ontology model to computationally describe human physical activities and the various entities that compose each activity. We developed an open-sourced biomedical ontology called the Kinetic Human Movement Ontology that reused OBO Foundry terminologies and encoded in OWL2. We applied this ontology in modeling and linking a specific Tai Chi movement. The contribution of this work could enable modeling of information relating to human physical activity, like exercise, and lead towards information standardization of human movement for analysis. Future work will include expanding our ontology to include more expressive information and completely modeling entire sets of movement from human physical activity.

Enhanced agency and the visual thinking of design

Abstract Visual thinking is a systematic way to produce knowledge in design by means of mental imagery, spatial reasoning, and the use of an array of visual representations. Pictorial representations such as sketches are crucial for the activity of designing at the early stage of the creative process. Designers see more information in sketches than was actually drawn. The ability to see more information than is sketched out can be seen as an enhanced visual capacity of human agency. Enhanced agency is the prosthetic incorporation of artifacts to improve the original agentive capacities. The incorporation of artifacts to draw raises some fundamental questions: Is the pencil an extension of the mind? Can we think with our hands? What agentive capacities are increased with the use of the pencil? What is the representational status of sketching? The chapter is structured around these key questions to suggest some answers inspired by the work of Göran Sonesson. Using the notion of enhanced agency and the layered model of agency, I explore the way in which the pencil improves the visual thinking of design. In doing so I found that it is important to maintain the principle of asymmetry in cognitive systems to reconsider relational ontology in favor of ecological relationships.

Knowledge-based query system for the critical minerals

Critical minerals are increasingly used in advanced, modern technologies. Exploration for these minerals require efficient mechanisms to search for the latest geological knowledge about the petrogenesis and spatial distribution of these essential resources. Although the current text-based deposit classification schemes help geoscientists to understand how and where these critical minerals form, they cannot easily be queried by software without extensive natural language processing and knowledge modeling. Ontologies can explicitly specify the knowledge scattered in the texts and tables of these schemes and the Critical Minerals Mapping Initiative (CMMI) database by way of logical structures whose results can automatically be processed and queried. They can also draw new knowledge by inference from the ones that are explicitly specified in them. These qualities make ontologies a perfect choice for digital knowledge storage, search, and extraction. The Critical Minerals Ontology (CMO) is described herein by reusing the logical class and property structures of the top-level Basic Formal Ontology (BFO) and mid-level Common Core Ontologies (CCO) and Relation Ontology (RO). The CMO formally models the knowledge about the critical mineral systems using the latest deposit classification scheme and the CMMI database schema. The ontology specifies the geochemical and geological processes that operate in various geotectonic environments of mineral systems to form the critical minerals in different deposit types. It models the properties of both the host minerals that contain the rare-earth elements and those that bear other types of elements. The CMO also represents uses of specific critical minerals in the manufacturing of industrial products, their alternate substitutes, and countries that produce, import, and export them. A query system, applying the Python programming language, accesses the knowledge modeled in the CMO and allows users through interactive web pages to query the ontology and extract different types of information from it. The ontology and the query system are useful for research in ore mineralogy and critical mineral prospecting. The information modeled by the ontology and served by the query system allows users to classify their ore specimen data into specific deposit types.