A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

We take up the challenge of developing an international network with capacity to survey the world’s scientists on an ongoing basis, providing rich datasets regarding the opinions of scientists and scientific sub-communities, both at a time and also over time. The novel methodology employed sees local coordinators, at each institution in the network, sending survey invitation emails internally to scientists at their home institution. The emails link to a ‘10 second survey’, where the participant is presented with a single statement (...) to consider, and a standard five-point Likert scale. In June 2023, a group of 30 philosophers and social scientists invited 20,085 scientists across 30 institutions in 12 countries to participate, gathering 6,807 responses to the statement Science has put it beyond reasonable doubt that COVID-19 is caused by a virus. The study demonstrates that it is possible to establish a global network to quickly ascertain scientific opinion on a large international scale, with high response rate, low opt-out rate, and in a way that allows for significant (perhaps indefinite) repeatability. Measuring scientific opinion in this new way would be a valuable complement to currently available approaches, potentially informing policy decisions and public understanding across diverse fields. (shrink)

With the widespread use of vaccines in research and clinical settings, there is an urgent need to standardize vaccine representation, integrate information across diverse vaccine types, and support computer-assisted reasoning. Accordingly, we have since 2007 developed the community-based Vaccine Ontology (VO), which aligns with the Basic Formal Ontology and adheres to OBO Foundry principles. VO models ontologically vaccines, vaccine components, vaccine immune responses, vaccine investigation studies and other vaccine-related topics. VO represents more than 10,000 vaccines targeting 289 infectious pathogens and (...) cancers in humans and over 30 nonhuman animal species. VO provides mappings to external resources such as RxNorm, CVX, FDA, and USDA. Various VO use cases exist. VO facilitates vaccine standardization in resources such as the VIOLIN vaccine database, ImmPort, and the Vaccine Adjuvant Compendium (VAC). Semantic queries can be made to query VO. VO has been shown to enhance experimental and clinical vaccine data analysis and vaccine literature mining. Overall, VO standardizes vaccine modeling and representation and greatly supports vaccine AI research in the Semantic Web era. (shrink)

This book researches the thought of Jin Yuelin’s epistemology with some notions and methods of contemporary epistemology as the frame of reference. There are two kinds of academical significance in this book, one is that author has accurately comprehended the specific content, inadequacies and contradictions in Jin’ s epistemology, recognized the methods by which Jin Yuelin built his theory of knowledge. The other is that author has known about the differences in research objects and methods between Jin’s theory and contemporary (...) epistemology, and showed the position of Jin’s epistemology in the whole theory of knowledge through the comparative study. On the one hand, the book focuses on the core problem of Jin Yuelin’ epistemology that is how objective knowledge is produced. On the other hand, it is made up of seven chapters in accordance with the structure of Jin’s Theory of Knowledge. The first chapter introduces and comparatively analyzes the comprehensions about the concepts of “knowledge” and “epistemology” between Jin Yuelin and contemporary epistemologists. This chapter supplies the means and methods for following chapters. The second chapter describes Jin’s standpoint and criticism to idealism starting mode, analyzes the objective starting mode that belongs to Jin’s theory and reveals his negative attitude to skepticism. This chapter shows the essential characteristics of the Jin Yuelin’s epistemology. The given is the content of sensation, which is the most basic part of cognitive activity. Moreover Jin Yuelin regards sensation as foundation of knowledge, so the research on theory of the given is separated from the whole study of cognitive activity and treated as the third chapter, which presents Jin’s theory of the given and analyzes the problems of Jin’s theory, then introduces some kinds of theory of the given and theory of perception in the contemporary epistemology, finally comparatively investigates theories of the given between Jin Yuelin and contemporary epistemologists. From the perspective of cognitive activity, the fourth chapter describes the perceptual activity, the activity of knowing, the activity of thinking, means and outlines of reception in Jin’s epistemology, then exposes its contradictions and inadequacies; Induction is the important research object of the Western epistemologists, similarly Jin Yuelin paid more attention to induction and regards the principle of induction as outline of reception. In fact, his standpoint about the principle of induction is vital and creative, so the study of induction separately belongs to the fifth chapter. This chapter presents the Jin’s comprehension about the principle of induction and some answers to the problem of induction in contemporary epistemology, then comparatively analyzes two kinds of the thought about induction. The sixth chapter successively introduces being, nature and fact which all are objects of cognitive activity, then analyzes the problems within them. From the perspective of cognitive results, the last chapter presents the Jin’s standpoint about verification and demonstration of proposition, definition and criteria of truth, then simply describes the point views of contemporary epistemologists about verification and truth of proposition, finally comparatively investigates two kinds of thought. From the vertical, the thesis analyzes the fundamental sections of objective knowledge one by one, such as the given, experience, idea, proposition and truth. From the horizontal, the book focuses on the three main parts of knowledge event, for example, cognitive activity, objects of knowledge and the true proposition treated as knowledge. In a word, the whole book is coherent and organic unity. Through the comparative study, it can be concluded that it is reasonable for Jin Yuelin to enjoy a high academic status, because he is the first philosopher who specializes in the study of epistemology. At the same times, he improves transmission of logic, metaphysics and epistemology from the Western to China. So, his hard work enriches and expands the realm of Chinese philosophy. With the development of the study of epistemology, descriptive content of it, such as, perceptual activity and rational activity, will be regarded as the objects of psychology and cognitive science. Meanwhile, normative content will be retained. For example, analysis of conditions of knowledge, justification for belief claims, comprehension about the proofs of justification, as well as reactions to challenges of skepticism. The latter will continue to be objects of epistemology, of course, they must establish close relationships with psychology and cognitive science. According to this prospect, we should split Jin Yuelin’s theory of knowledge, of which the descriptive content would be allocated to psychology and cognitive science. On the contrary, the normative content would be kept as important resource for deeply studying epistemology. Key words: Knowledge; Contemporary epistemology; Compare; The given; Idea; The principle of induction; Fact. (shrink)

The thesis that Dennett argues for in Breaking the Spell: Religion as a Natural Phenomenon has a double aspect. First, religion being but one natural phenomenon among many should be subject to scientific investigation. Resistance to this notion constitutes the first spell or taboo and is in complicity with the second “master” spell, that of the phenomenon of religion itself. Dennett’s tentative naturalistic recommendation is two-pronged: he primarily deploys an evolutionary biology perspective, and derivatively a highly suggestive appeal to memetics. (...) To acknowledge that religion is natural “is only the beginning of the answer, not the end”. Religion as a natural phenomenon has to answer to Dennett’s Darwinist refrain — cui bono? (to whose advantage?). And derivatively, how or why highly exotic and implausible supernatural religious ideas (or memes) are transmitted and sustained? Humankind, naturally disposed cause-seeking creatures, are inclined to hypostasize all manner of beliefs (virtual agents free to evolve to amplify our yearnings or our dreads — when explanation of some phenomenon is not forthcoming — this constitutes the “master” spell. (shrink)

Although it is well known that Gestalt theory had an important impact on Merleau-Ponty’s philosophy throughout his career, there is still no detailed study either of its influence on his ideas or of his own understanding of the notoriously polysemic notion of Gestalt. Yet, this notion is a key to Merleau-Ponty’s fundamental project of overcoming “objective thought” and its inherent dichotomies. By indicating how signification or ideality can be immanent in, rather than opposed to, matter, it compels us to redefine (...) both consciousness and the world it is bound up with. The aim of this article is to clarify Merleau-Ponty’s notion of Gestalt against the historical background that he refers to, including Kurt Goldstein’s theory of the organism that was crucial for his interpretation of it. -/- On sait que la théorie de la Gestalt a eu un impact majeur sur la philosophie merleaupontienne. Il n’existe pourtant pas d’étude extensive de l’influence de cette théorie sur les thèses de Merleau-Ponty ou sur sa compréhension propre de la notion fort polysémique de Gestalt. Or cette notion s’avère être l’une des meilleures clés pour comprendre le projet fondamental du dépassement merleau-pontien de la « pensée objective » et de ses dichotomies. En effet, en montrant comment le sens ou l’idéalité sont immanents, plutôt qu’opposés, à la matière, la Gestalt conduit à définir à nouveaux frais la conscience et le monde auquel elle est liée. L’article vise à clarifier la conception de la Gestalt chez Merleau-Ponty à partir de son fond historique. On étudie en particulier la théorie de l’organisme de Kurt Goldstein, qui a été essentielle pour l’interprétation merleaupontienne de la notion de Gestalt. -/- Benché sia noto che la Gestalttheorie abbia avuto un impatto rilevante sull’intero tragitto della filosofia di Merleau-Ponty, non esiste ancora uno studio dettagliato dell’influenza del gestaltismo sulle sue idee né sulla sua comprensione di un concetto notoriamente sfaccettato come quello di Gestalt. Tuttavia proprio questa nozione costituisce una chiave d’accesso fondamentale al grande progetto merleaupontyano di oltrepassare il “pensiero oggettivo” insieme alle dicotomie che lo accompagnano. Indicando come il significato o l’idealità possano essere immanenti, anziché opposti, alla materia, tale nozione ci obbliga a ridefinire tanto la coscienza quanto il mondo a cui essa è legata. L’obiettivo di questo articolo è quello di chiarire la nozione merleaupontyana di Gestalt nel suo contesto storico, con particolare riferimento alla teoria dell’organismo elaborata da Kurt Goldstein, determinante per l’interpretazione merleaupontyana della nozione di Gestalt. (shrink)

Thinking the Visual, Visualizing the Thought.A perceptual and Political Model of VisionMerleau-Ponty’s program of perceptivizing thought has depoliticizing effects that, though he does not recognize them, undermine his understanding of politics. These anti-political consequences, moreover, bring out the internal difficulties of his anti-intellectualist starting point. There are three areas in which Merleau-Ponty gave a thorough application, though with unequal success, of his perception-based model: the presentation of his own thought, in which his program of picturalization had a striking success; the (...) explanation of the historical process, in which his visualization model was only partly effective; and access to other people’s thought, in which his perceptivist views encountered an undeniable failure. Merleau-Ponty’s successive approaches to other people’s thought show, by two distinct paths, and beyond his own intentions, an unforeseen political defect. His perceptive model proves incompatible with his political ideas when it is applied in depth, and it thus breaks apart the cohesion of his thought. From a larger perspective, it disrupts reflective approaches to politics since it damages their conceptual bases. This article shows successively that Merleau-Ponty laid out a perceptive model of universal scope; that he applied it to several areas, including politics; that this model proves politically deficient when it serves to remove the autochthonous sources of sense; that these depoliticizing effects become more acute when Merleau-Ponty employs the perceptive model to elucidate other people’s thought; and that its frustration in this area not only devalues his political reflections, but also signals that the perceptive model simply prevents a “thinking of the political.”Pensare il visuale, visualizzare il pensiero.Un modello percettivo e politico della visioneIl programma di percettivizzazione del pensiero intrapreso da Merleau-Ponty comporta effetti spoliticizzanti che sconfessano nascostamente la sua comprensione della politica. Tali conseguenze antipolitiche mettono altresì in rilievo le difficoltà intrinseche alla sua posizione anti-intellettualista. Vi sono tre ambiti nei quali Merleau-Ponty, con diverso successo, ha applicato il suo modello percettivo : la presentazione del suo stesso pensiero, nella quale questo programma di pittoricizzazione incontra un successo trionfale; la chiarificazione del processo storico, dove tale modello “visualeˮ non è efficace che in parte; infine l’accesso al pensiero di altri autori, terreno sul quale questa prospettiva percettivista subisce uno scacco innegabile. Molti tentativi merleaupontiani di approcciare il pensiero di altri autori attestano in vario modo un imprevisto deficit politico. Il modello percettivo di Merleau-Ponty si rivela in altri termini incompatibile con le sue idee politiche, nel momento in cui viene applicato in profondità, e in ultima analisi mette a dura prova la coerenza del suo pensiero. In una prospettiva più ampia, esso ostacola un approccio riflessivo alla politica poiché ne degrada le stesse basi concettuali. Il nostro articolo mostra quindi che Merleau-Ponty ha articolato un modello percettivo di portata universale; che l’ha applicato a svariati ambiti d’indagine, tra cui la politica; che quel modello si rivela deficitario quando viene utilizzato per attingere a specifiche fonti di senso; che tali effetti spoliticizzanti si acuiscono nel momento in cui Merleau-Ponty adotta il modello percettivo per illuminare il pensiero di altri autori; che, per concludere, la sua incongruenza con questo peculiare ambito di riflessione non solo impoverisce le sue riflessioni politiche, ma attesta che in linea generale il modello percettivo sbarra la strada a un qualsiasi «pensiero del politico». (shrink)

This essay offers a reading of Guido Cornia’s Angeli ingenui dalle ali di mosca, aiming to highlight its main thematic cores: the nature of the epiphanic experience, the temporal, cultural, and psychological distances between artist and audience, the different roles played by the writer and the narrative voice, and the importance of audience “recognition,” which allows the artwork’s destiny to be fully realized. After a theoretical survey of the concept of epiphany, traced in its literary genealogy from Shelley to Joyce (...) and in Cornia’s own statements, the analysis focuses on the text itself, examining its intertextual references (van Gogh and Melville) and the expectations, illusions, and anxieties that often accompany the artist as he awaits the reception, recognition, and evaluation of his work by the audience. In this context, the narrative voice becomes the space where the artist’s fragility is revealed, suspended between hope and frustration. Finally, the figures of the “naive angels with fly wings”—extremely fragile and vulnerable creatures with pure hearts—are read as metaphors for those people who, by authentically recognizing the value of the work, make its destiny possible, as illustrated by references to Johanna van Gogh-Bonger, Vincent van Gogh’s sister-in-law who succeeded in promoting and valuing his work, and David Herbert Lawrence, who played a crucial role in the rediscovery of Moby-Dick. Cornia’s text thus emerges as a penetrating reflection on the structural fragility of art and the relational nature of its fulfillment. -/- Questo mio saggio propone una lettura dell’epifania Angeli ingenui dalle ali di mosca di Guido Cornia volta a metterne in luce i principali nuclei tematici: la natura dell’esperienza epifanica, le distanze temporali, culturali e psicologiche tra artista e pubblico, i diversi ruoli che rivestono lo scrittore e voce narrante, e l’importanza del “riconoscimento” da parte del pubblico che permette al destino dell’opera d’arte di compiersi adeguatamente. Dopo una ricognizione teorica sul concetto di epifania, ricostruita nella sua genealogia letteraria da Shelley a Joyce e nelle dichiarazioni dello stesso Cornia, l’analisi si concentra sul testo, soffermandosi sui suoi riferimenti intertestuali (van Gogh e Melville) e sulle aspettative, illusioni e ansie che spesso accompagnano l’artista nell’attesa che la sua opera venga recepita, riconosciuta e valutata dal pubblico. In questo contesto, la voce narrante diventa il luogo in cui si manifesta la fragilità dell’artista, sospeso tra speranza e frustrazione. Infine, le figure degli “angeli ingenui dalle ali di mosca”—fragilissime e vulnerabili creature dal cuore puro—vengono lette come metafore di quelle persone che, riconoscendo autenticamente il valore dell’opera, ne rendono possibile il destino, come mostrano i riferimenti a Johanna van Gogh-Bonger, la cognata di Vincent van Gogh che ne seppe promuovere e valorizzare l’opera, e a David Herbert Lawrence, il quale contribuì in modo fondamentale alla riscoperta di Moby-Dick. Il testo di Cornia emerge così come una penetrante riflessione sulla fragilità strutturale dell’arte e sul carattere relazionale del suo compimento. (shrink)

This essay critiques Donald Davidson's thesis in "What Metaphors Mean," which posits that metaphors convey only their literal meanings without hidden or additional layers of cognitive or figurative content. Davidson argues that metaphors function by evoking novel perspectives through the literal meanings of words, without involving any special meanings. This paper challenges Davidson's view by examining the limitations that arise when metaphors are modified or when synonymous terms are substituted, which often results in a loss of metaphorical effectiveness. The proposed (...) theory introduces the concepts of "focus" and "lens" terms, emphasizing the role of cultural resonance in generating secondary meanings in metaphors. The lens term, with its rich cultural and historical associations, interacts with the focus term to produce meanings deeply embedded in cultural understanding. This theory addresses the shortcomings of Davidson's approach, offering a more comprehensive framework for understanding the function of metaphors in language. Future research directions are also suggested, including the exploration of cultural resonance across different cultures, the cognitive processes involved in metaphor interpretation, and the implications for artificial intelligence. This paper underscores the importance of cultural and historical contexts in metaphorical language, providing a robust understanding of the interplay between literal meanings and cultural associations. (shrink)

_(MA thesis)_ Immunity to error through misidentification (IEM) describes a sort of immunity against such a situation that the thinker wrongly identifies something as other things. Philosophers consider it as being especially relevant to first-person or de se judgments. Many philosophers seem to advance IEM as an alternative to a Cartesian method of defining first-person privilege and of circumscribing the first-person perspective. However, as more and more representative instances are substantiated as being vulnerable to error through misidentification, it is thus (...) necessary to offer an account sufficient to explain IEM. Then, there are roughly two approaches in the literature: the identification-freedom approach and the metasemantic approach. The former is characterised by the claim that the presence of IEM is always explained by the absence of an identificatory-component in the thought's grounds. The latter is more heterogeneous than the former. Nevertheless, it can be roughly described by their focus on explaining the IEM of de se thoughts based on an account of how the reference of de se thoughts is fixed, rather than just on the grounds of particular de se thoughts. However, there are still some problems with the existing accounts. More specifically, some problems from the indexical thoughts put at risk Recanati's appeal, which is viewed as a representative of the metasematic approach. Nonetheless, I think these problems can be resolved competently by pointing out the fact that there are three levels of reflection in introspection. Thoughts produced by the first level of reflection (first-level thoughts, hereafter) correspond to Recanati's implicit thoughts; Third-level thoughts are Recanati's explicit thoughts (whether it is made explicit by an extra reflective act, as Recanati puts it). However, second-level thoughts, which include a sort of aboutness in their content, could explain the subject appearing in indexical statements with IEM, guaranteeing IEM of these thoughts in the meanwhile. (shrink)

In order to use the framework of general system theory (GST) to unify the three mechanics subjects of classical mechanics, quantum mechanics, and relativistic mechanics, a new general system theory (NGST) is developed based on a new ontology of ether and minds as the fundamental existences in the world. Based on this new ontology, many fundamental concepts have been detected to be ambiguously defined nowadays and particularly lack of ontological support. In our previous work, some of the fundamental concepts such (...) as universe, world, time, space, matter, ether, mind, life, field, force have been redefined. The purpose of this paper is to clarify the concepts of energy, heat, work, entropy, and information in our NGST. This is an important and necessary step in the development of the NGST. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Contemporary scholarships on various accounts of the concept of harmony in Chinese philosophy have produced fruitful outcomes by examining the term he. A standard use of he to account for harmony comes from the Analects, and this account sets up disjunctions not just between he and tong but also between harmony and tong. Such disjunctions are even more conspicuous in the political discourses from the Zuozhuan and Guoyu, and hence, has led scholars to overlook the more nuanced resonances between tong, (...) he, and harmony that can be identified from other canonical texts, such as in shangtong of the Mozi, in hetong of the Guanzi, and in datong of the Liji. This article aims to present nuanced relations between harmony, he, and tong, and proposes tong as another viable option to express harmony, thereby correcting the imbalance that the predominant scholarships recognize he and neglect tong. (shrink)

This paper introduces Jin He's Tips Engineering (JHTE), a novel framework for zero-shot text evaluation using large language models. By designing precise textual instructions called ''Tips'', JHTE elicits inherent model capabilities to perform specific NLP tasks without task-specific training. We demonstrate its rational foundation through a case study on aspect-based sentiment analysis, where JHTE achieves exceptional output consistency across multiple independent runs. The framework represents a paradigm shift from traditional model engineering to capability elicitation, offering unprecedented flexibility and development efficiency (...) across various text evaluation tasks. Its operational principle-treating LLMs as programmable computers-ensures that potential variances remain within safe bounds of granularity rather than critical misunderstandings, underscoring its reliability and practical viability. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Thomas Raleigh’s Meta-Belief Account and Verena Wagner’s Endorsement Account are two competing higher-order accounts of agnosticism. In this paper, I do two tasks. Firstly, I defend the Meta-Belief account from two challenges: the Transition Challenge, which says that the Meta-Belief Account cannot explain how a rational agent can transition between mere indecision and agnosticism, and the Settledness Challenge, which says that the Meta-Belief Account cannot guarantee the incompatibility between agnosticism and inquiry. Secondly, I argue that there exist two cases against (...) the Endorsement Account. On the basis of these discussions, I conclude that the Meta-Belief Account is better than the Endorsement Account. (shrink)

A popular version of epistemic Permissivism says that, given the total evidence, sometimes there is a permissible credence range towards a proposition. Ginger Schultheis (2018) offers a Dominance Argument against it. Schultheis argues that it is irrational to hold a credence at the edge of any permissible range because the edge credence takes higher risks of being irrational than the credence in the middle. In this paper, I propose two new responses. Firstly, I argue that after the risk assessment in (...) irrationality, a new stable range may emerge such that each credence from it does not take more risks than others. Schultheis’s Dominance Argument can only shrink the original credence range to this new stable range. Second, I argue that sometimes it is rational for us to hold a more risky credence when a safer alternative is available. If rationality aims at truth-conduciveness and informativeness, a credence’s higher risks of being irrational do not render it irrational when one risks being less truth-conducive in exchange for informativeness. (shrink)

Having established "difference" as the fundamental ontological cost, a deeper question arises: how can we transcend this limitation? In response, this paper proposes a core thesis: the sameness of the indistinguishable. This principle establishes a fundamental philosophical contrast to Leibniz's "identity of indiscernibles": whereas his principle is a metaphysical decree about the world, our framework is an epistemological protocol for constituting the world. We develop a mathematized formal framework to demonstrate that the deep logic underlying both the Ship of Theseus (...) and Einstein's elevator can be unified under this principle—existence is defined by operation, and what manifests within operation is the sole reality of the world in the process of cognition. By systematically elaborating the Principle of Operational Indiscernibility, this work completes a decisive shift from analyzing ontological costs to constructing an epistemological methodology, thereby establishing a new theoretical foundation for systematically addressing fundamental controversies from quantum foundations to artificial intelligence. (shrink)

The graph tong同and its associated concepts, such as da-tong (Great tong大同) and xuan-tong (mystic or dark tong玄同), have played important roles in the development of Chinese philosophy. Yet tong has received scant attention from either western or eastern scholarships. This paper is a first attempt to remedy such regret. Unlike usual understandings of tong as sameness or unity, this paper presents a nuanced account from early China, that is, ‘difference to one,’ a definition from the Mozi墨子. This definition can be (...) supported from etymological, textual, and lexical evidence. ‘Difference to one’ should not be solely attributed to a Mohist understanding; it in fact represents a common understanding of tong across philosophical streams in early China. This nuanced account provides new insights into the concept of tong in early philosophical texts, and furthermore breaks solid grounds for further studies of tong and its associated concepts. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

In the development of humanity, it seems that everything is in a state of balance, and this vague feeling may have always accompanied humanity. The pervasiveness of trade-offs is conventionally attributed to physical limitations. This paper demonstrates that the necessity for trade-offs is not a contingent limitation of our universe, but an ontological cost inherent to existence itself. Wherever there is discernible difference, computation and balance inevitably arise.

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

In a 2019 paper, Hausmann raised a new and interesting problem for Kripke’s account of negative existentials. He argued that Kripke’s account leads to the absurd consequence that anybody who has good reasons to believe that there are no propositions also has good reasons to believe that he or she does not exist. In this paper I propose a modified Kripkean theory, which is invulnerable to a Hausmann-like argument. As will be seen, the modified theory can be squarely justified in (...) light of the key observations behind Kripke’s original proposal. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This paper employs a method of contextual-relational interpretation, integrating perspectives from structuralism and philosophical hermeneutics, to conduct a systematic philosophical reconstruction of The Analects: The Bayi Chapter. The research breaks through the fragmented expository model of traditional commentaries, revealing that the chapter is, in fact, a complete philosophical outline on governance centered on "institutional construction." It begins by presenting the crisis of a "discrepancy between name and substance"—the collapse of the ritual system—through the examples of the Ji clan's "eight rows (...) of dancers in their courtyard" and "sacrificing at Mount Tai." It then systematically unfolds the path to rebuilding civilizational order, successively arguing for a paradigm of benign competition, the emotional foundation of institutions, and the living transmission of civilization. The analysis deeply examines the reconstruction of the value of "reverence" (敬) and the vitality and universality that institutions should possess. Finally, through a new interpretation of Guan Ju (The Osprey's Cry), historical reflection, and the metaphor of musical education, it constructs an institutional "generation-operation-feedback" model. This reconstruction elevates The Bayi Chapter from a critique of rituals to a philosophy of systemic civilizational governance, providing a methodological paradigm for the construction of China's discourse on governance. (shrink)

The standard Lewis–Stalnaker semantics of counterfactuals, given the Strong Centering Thesis, implies that all true–true counterfactuals are trivially true. McGlynn developed a theory, based on Penczek, to rehabilitate the non-triviality of true–true counterfactuals. I show here that counterfactuals with true but irrelevant components are counterexamples to McGlynn’s account. I argue that an extended version of the connection hypothesis is sustainable, and grounds a full theory of counterfactuals explicable in a broadly standard way, if an indispensable asymmetry between semifacuals and other (...) counterfactuals is acknowledged. (shrink)

A century after its inception, the counterintuitive nature of quantum mechanics challenges the role of intuition in science. Grounded in the framework of “the theory of unknown”, which is itself built upon the Principle of Operational Indiscernibility—asserting that cognition arises from operations rather than presupposed essences—this paper re-examines the most contentious property of quantum theory: randomness. By rigorously conditioning “randomness” on sets of operations, we establish a spectral definition: pseudo-randomness (algorithmically determined), relative true randomness (indiscernible under all current operations), absolute (...) true randomness (indiscernible under all possible operations), and the epistemologically fundamental “Unknown-Theoretic Randomness” (indiscernible under all defined operations). Our analysis demonstrates that the historic Einstein-Bohr debate on “whether God plays dice” was essentially a misaligned dialogue between the belief-based notion of absolute true randomness and the empirical evidence for relative true randomness. Within the operational framework, regardless of the underlying ontology, the stable statistical patterns of quantum phenomena (as governed by the law of large numbers) constitute the only valid starting point for scientific cognition and practice. We therefore argue that once randomness is operationally clarified within the context of the theory of unknown, the associated philosophical disputes dissolve. (shrink)

Xuantong 玄同 (tentatively translated as dark oneness) is a unique Daoist idea that represents an ideally mental and physical state as a result of cultivation. However, owing to limited context in the Laozi, there is no consensus on the interpretation of xuantong. Contemporary studies have also neglected xuantong’s evolution in early texts and assumed a homogeneous understanding, and hence, failed to provide a nuanced account. In this article, I investigate how xuantong evolves from the Guodian Laozi to the Huainanzi and (...) Wenzi. I argue that although xuantong may originate from the Laozi, it is in the Wenzi that a coherent theory of xuantong is accomplished. This theory advocates an orderly process of cultivation that covers internal mental states, external acts, and integration with the whole universe. The cultivation would eventually lead people to adopt an undifferentiated perspective on, and reach oneness with, all things in the universe. (shrink)

The ‘Wu xing’ belongs to Guodian bamboo slips texts, which were buried around 300 BCE and excavated in 1993. Its relation with Mengzi is widely investigated. Yet how it is philosophically related to Xunzi receives little attention. In this article, I illustrate a neglected relation between ‘Wu xing’ and Xunzi, by elucidating how shan 善 (goodness) is first raised in ‘Wu xing’ and developed by Xunzi into a concrete idea. Both ‘Wu xing’ and Xunzi propose that shan exists in action, (...) which boils down to the harmonious unity of the mind and body, and to secure the ideal relation between the mind and body requires constant learning and practicing, particularly, of rituals. Learning and practicing not only lead one to realize shan, but eventually to become a consummate practitioner of rituals, to use Xunzi’s words, to become a sage. (shrink)

The Philosophical Forum, Volume 53, Issue 1, Page 47-61, Spring 2022.

Divers argued that there are modal truths that are inconvenient for the canonical Lewisian theory of modality. Noonan and Jago proposed an answer to the challenge, by invoking a duplicate interpretation of the modal truths. Here, I present a slightly different kind of modal truth that would prove inconvenient even for a Lewisian who accepts Noonan and Jago's proposal.

This article investigates a central yet perplexing term yiming in the ‘Qiwulun’ chapter of the Zhuangzi. Yiming describes a crucial way to detach from epistemic distinctions and debates. This term is often explained as ‘using ming’ or contradictorily as ‘stopping ming’. Yet neither of the two explanations can provide a full understanding of how yiming is adopted. I take three steps to explain yiming. First, taking an etymological approach, I argue that ming can be formulated as ‘X shining on Y’. (...) Second, I use the formula of ‘X shining on Y’ to account for yiming and argue that this term refers specifically to ‘using tian to shine on everything’. Third, I unpack a cluster of tian-associated metaphors, which provides a deep understanding of yiming as an ideal way to mental tranquility. (shrink)

A well-documented “beauty is good” stereotype is expressed in the expectation that physically attractive people have more positive characteristics. Recent evidence has also found that unattractive faces are associated with negative character inferences. Is what is good (bad) also beautiful (ugly)? Whether this conflation of aesthetic and moral values is bidirectional is not known. This study tested the hypothesis that complementary “good is beautiful” and “bad is ugly” stereotypes bias aesthetic judgments. Using highly controlled face stimuli, this preregistered study examined (...) whether moral character influences perceptions of attractiveness for different ages and sexes of faces. Compared to faces paired with nonmoral vignettes, those paired with prosocial vignettes were rated significantly more attractive, confident, and friendlier. The opposite pattern characterized faces paired with antisocial vignettes. A significant interaction between vignette type and the age of the face was detected for attractiveness. Moral transgressions affected attractiveness more negatively for younger than older faces. Sex-related differences were not detected. These results suggest information about moral character affects our judgments about facial attractiveness. Better (worse) people are considered more (less) attractive. These findings suggest that beliefs about moral goodness and physical beauty influence each other bidirectionally. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

How does aging affect facial attractiveness? We tested the hypothesis that people find older faces less attractive than younger faces, and furthermore, that these aging effects are modulated by the age and sex of the perceiver and by the specific kind of attractiveness judgment being made. Using empirical and computational network science methods, we confirmed that with increasing age, faces are perceived as less attractive. This effect was less pronounced in judgments made by older than younger and middle-aged perceivers, and (...) more pronounced by men (especially for female faces) than women. Attractive older faces were perceived as elegant more than beautiful or gorgeous. Furthermore, network analyses revealed that older faces were more similar in attractiveness and were segregated from younger faces. These results indicate that perceivers tend to process older faces categorically when making attractiveness judgments. Attractiveness is not a monolithic construct. It varies by age, sex, and the dimensions of attractiveness being judged. (shrink)

The concept of tong played an important role in early Chinese political thought, as in the “Shangtong” chapter of the Mozi and the “Liyun” chapter of the Liji. Nevertheless, tong as a political thought has received little scholarly attention. In this article, I diverge from the common understandings of tong as sameness or unity and call on etymological and textual evidence to suggest that tong fundamentally refers to “difference to one.” In light of this understanding of tong as “difference to (...) one,” I focus on the “Shangtong” and the “Liyun” and compare the two visions of political tong that the two chapters present. With this research, I argue that the “Shangtong” and “Liyun” represent two different political streams as to how to unite a society with early China’s differences and divisions. (shrink)

Abstract -/- Drawing upon a contextual and correlative interpretive method and integrating perspectives from structuralism and philosophical hermeneutics, this paper conducts a systematic philosophical reconstruction of the "On Governance" chapter of the Analects of Confucius. This study moves beyond traditional, fragmented interpretations to integrate the entire chapter into a cohesive ideological system centered on the cultivation of the Junzi (exemplary person) personality and the practice of virtuous governance. We argue that the "On Governance" chapter is not merely a collection of (...) aphorisms but rather a structurally complete and practical manual for character cultivation. It establishes "governing by virtue" (为政以德) as its foundational principle, lays the mental and emotional groundwork with "thoughts without deviation" (思无邪), and constructs a governance philosophy where ethical sentiment and institutional structures coexist through the "Four Questions on Filial Piety." From this foundation, it systematically elaborates on the methods and paths for cultivating the Junzi personality, ultimately elevating the discourse to an insight into the patterns of history and the affirmation of the mission to be a guardian of civilization. This interpretation offers a methodologically significant exploration for the modern transformation of classical culture and the construction of a philosophical discourse system with Chinese characteristics. (shrink)

The Xue Er Chapter has long been regarded as the gateway to understanding the thought of Confucius and the spirit of Confucianism. However, we often interpret it merely as a manual on learning, friendship, and navigating the world. Such an interpretation, perhaps, fails to touch the very core of Confucius's philosophy. -/- Throughout his life, what Confucius sought to teach was how to become a person of virtue—someone whose words and actions are one, whose knowledge and conduct are unified—not a (...) calculating person who simply caters to worldly conventions. Therefore, let us try to explore Confucius's inner world from the perspective of one's inner character and disposition. Let us connect our reading of The Analects to a central theme: how to become a person who is internally strong, independent in character, with their own judgment and convictions, and who has established a fundamental understanding of life and society. -/- Following this line of thought, we discover that the Xue Er Chapter is, in fact, a coherent and interconnected whole. In the very first chapter, Confucius points out the path to becoming a truly authentic person. The key to cultivating this character lies not in book knowledge, but in learning from other people. The most fundamental arena for this learning is the family. From our parents and siblings, we learn care, sincerity, warmth, and kindness, thereby perfecting our own character. This learning must take place in authentic scenarios, which is why we must be wary of "clever words and an insincere demeanor." Once it becomes superficial, what is learned is nothing but falsehood. -/- The cultivation and perfection of this character begins with the disciple and is ultimately applied to the governance of a state, that is, "to govern a state of a thousand chariots." So, how specifically does one learn from others? Confucius next points out that one must first understand friendship, learning to discern who is a worthy teacher and a true friend, which is the meaning of "valuing the worthy." At the same time, one must also become a person of substance and reliability, as "a person of virtue who lacks gravitas will not command respect." If such role models cannot be found in reality, we can also learn from historical tradition, connecting with the spirit of our ancestors through "being mindful of the end and pursuing the distant." We can even learn through books, studying people like Confucius, who embodied the virtues of "gentleness, kindness, courtesy, modesty, and forbearance." -/- This highlights the deeper meaning of filial piety. The essence of xiao is a form of cultural and spiritual inheritance. Through reverence, we establish a connection of both bloodline and spirit with our ancestors, receiving this precious legacy. But after receiving this inheritance, one must also know how to apply it flexibly, just as "in the application of ritual, harmony is prized One must both integrate the principles and hold firm to one's own convictions. -/- As your learning deepens, your realm of understanding elevates, and your character becomes more refined, you may find that when you speak of ideals and principles, some people will not understand and may even mock you. But you will not get angry, because life is like a journey of cultivation, and everyone is at a different stage. When you have climbed higher and look back on the path you've traveled, you will naturally understand those still at the starting point. Their misunderstanding and ridicule are, to you, merely part of the scenery along the way. -/- What you truly need to be concerned about is not whether others understand you, but whether you can understand those who walk ahead of you. As Confucius said: "I am not concerned that others do not know me; I am concerned that I do not know others." -/- What you must do is, in your own place, become a bright lamp, illuminating the path for those who come after. (shrink)

Abstract -/- From the perspective of human nature, this paper philosophically reconstructs the Li Ren chapter of The Analects. Addressing the spiritual dilemmas of modern individuals, this paper posits that the philosophy of the Li Ren chapter is not a collection of fragmented moral injunctions, but rather a systematic psychology and practical philosophy concerning the "shaping of the mind-nature." -/- At its core, the paper restructures the 26 chapters of the Li Ren into a-tier progressive framework: "Cognition—Attributes—Practice—Realm." Within this framework, (...) "Ren" (Benevolence) is defined as "a life state of abundance and self-consistency," which forms the axiological foundation for self-cultivation. It further identifies "Righteousness (Yi), Virtue (De), Propriety (Li), Frugality (Jian), and Wisdom (Zhi)" as the five fundamental attributes of "Ren," which together constitute the core architecture of a wholesome personality. -/- Building on this foundation, the paper proposes the "Nine-Step Method for Shaping the Mind-Nature" (Awakening, Learning, Respectful Nurturing, Commitment, Trustworthiness, Caring, Reflecting on Shame, Self-Discipline, Action), offering a clear and actionable path for personal cultivation. Finally, through the "theory of personal magnetism," derived from "De bu gu, bi you lin" (Virtue is not orphaned; it will surely attract neighbors), and the "theory of boundary wisdom," from "Shi jun shu, si shu yi" (To serve a ruler too frequently is to become distant), the paper elucidates the ultimate social realm and life wisdom achieved through cultivation. -/- This paper is not merely a modern interpretation of a classic text but also a theoretical endeavor to construct a "Chinese indigenous psychology." It aims to provide an Eastern psychological framework—rooted in Chinese culture and characterized by its systematic and practical nature—for achieving spiritual tranquility and personal fulfillment in the digital age. (shrink)

To obtain effective fusion results of multi source evidences with different importance, an evidence fusion method with importance discounting factors based on neutrosopic probability analysis in DSmT framework is proposed. First, the reasonable evidence sources are selected out based on the statistical analysis of the pignistic probability functions of single focal elements. Secondly, the neutrosophic probability analysis is conducted based on the similarities of the pignistic probability functions from the prior evidence knowledge of the reasonable evidence sources. Thirdly, the importance (...) discounting factors of the reasonable evidence sources are obtained based on the neutrosophic probability analysis and the reliability discounting factors of the real-time evidences are calculated based on probabilistic-based distances. Fourthly, the real-time evidences are discounted by the importance discounting factors and then the evidences with the mass assignments of neutrosophic empty sets are discounted by the reliability discounting factors. Finally, DSmT+PCR5 of importance discounted evidences is applied. Experimental examples show that the decision results based on the proposed fusion method are different from the results based on the existed fusion methods. Simulation experiments of recognition fusion are performed and the superiority of proposed method is testified well by the simulation results. (shrink)

Abstract: Women under-representation in senior management post inside academic organizations remains to be an issue which needs a serious concern at national and international levels. Thus, women leaders are not in place to champion the change process. Societies, organizations and people themselves have determined that, only the males make good leaders. The gender status in the senior management positions in HE in Tanzania is virtually non-existent. Data was sourced through administered questionnaire, FGD and interview where’s senior academic and non-academic staff, (...) together with senior university management officials were involved. Results in all seven studied universities that is SUA, MU, UDSM, JUCO, MuM and UDOM, show the positions of VC, DVCA and DVCAF to be headed by men except OUT which has a female DVCAA. Basing on the findings of this study, the researcher recommended on the transparency of procedures for recruitment and promotion, empowering women to meet employment criteria, developing a gender management system as well as mentoring and establishment of the networks for women in order to close the prevailing gender leadership gap. (shrink)

Considerable evidence proves that causal learning and causal understanding greatly enhance our ability to manipulate the physical world and are major factors that distinguish humans from other primates. How do we enable unintelligent robots to think causally, answer the questions raised with "why" and even understand the meaning of such questions? The solution is one of the keys to realizing artificial intelligence. Judea Pearl believes that to achieve human-like intelligence, researchers must start by imitating the intelligence of children, so he (...) proposed a "causal inference engine" to help future artificial intelligence make causal inference, pass the Minimal Turing Test, and even become a moral subject who can discern good from evil. This study attempts to provide some insights into the development of children's education from basic assumptions and construction goals of artificial intelligence, and to reflect on the causal model of artificial intelligence through children's education. (shrink)

Abstract: This article mainly intends to identify barriers that cause the under-representation of women in top leadership positions in higher education in Tanzania. The study comprises the sample of 250 respondents with the use of a case study research design constructed on the application of mixed methods (qualitative and quantitative). Thus, non-probability sampling was applied to qualitative data collection while probability sampling was used in quantitative data. The findings show the fundamental relationship between individual, administrative and societal factors that block (...) women to reach the top leadership position in universities. Besides, the study has demonstrated the gender mainstreaming as the system which can be connected to adjust the hierarchical structures, methods and culture and bring the positive condition which advance gender equality. Nevertheless, as the well-known saying "Fix the holes in the pipe" goes, the variety of actions and activities are needed. Thus, in accordance with the proof from the study and individual encounters, the researcher, marked on Focused Gender Research, Capacity Development Programs, Parliamentary Charter, Setting Targets as well as Regular Monitoring and Reporting as interventions sustainable for bridging the prevailing gender leadership gap in higher education in Tanzania. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

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. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. 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 virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

Classic change blindness is the phenomenon where seemingly obvious changes which coincide with visual disruptions (such as blinks or brief blanks) go unnoticed by an attentive observer. Some early work into the causes of classic change blindness suggested that any pre-change stimulus representation is overwritten by a representation of the altered post-change stimulus, preventing change detection. However, recent work revealed that even when observers do maintain memory representations of both the pre- and post-change stimulus states, they can still miss the (...) change, suggesting that change blindness can also arise from a failure to compare the stored representations. Here we study slow change blindness, a different but related phenomenon that occurs even in the absence of visual disruptions when the change occurs sufficiently slowly, to determine whether it could be explained by conclusions from classic change blindness. Across three different slow change blindness experiments we found that observers, who consistently failed to notice the change, had access to at least two memory representations of the changing display. One representation was precise but short-lived: a relatively detailed representation of the more recent states of slow-change display, but fragile. The other representation lasted longer but was fairly general: stable but too coarse to differentiate the various stages of the changing display. These findings suggest that although multiple representations are formed, the failure to compare hypothesis might not explain slow change blindness; even if a comparison were made, the representations formed would be either too sparse (longer term stores) or too fragile (short-lived stores) for such a comparison to be informative about a change. (shrink)

The term “credential” encompasses educational certificates, degrees, certifications, and government-issued licenses. An occupational credential is a verification of an individual’s qualification or competence issued by a third party with relevant authority. Job seekers often leverage such credentials as evidence that desired qualifications are satisfied by their holders. Many U.S. education and workforce development organizations have recognized the importance of credentials for employment and the challenges of understanding the value of credentials. In this study, we identified and ontologically defined credential and (...) credential-related terms at the textual and semantic levels based on the Occupation Ontology (OccO), a BFO-based ontology. Different credential types and their authorization logic are modeled. We additionally defined a high-level hierarchy of credential related terms and relations among many terms, which were initiated in concert with the Alabama Talent Triad (ATT) program, which aims to connect learners, earners, employers and education/training providers through credentials and skills. To our knowledge, our research provides for the first time systematic ontological modeling of the important domain of credentials and related contents, supporting enhanced credential data and knowledge integration in the future. (shrink)

In this position paper, we have used Alan Cooper’s persona technique to illustrate the utility of audio- and video-based AAL technologies. Therefore, two primary examples of potential audio- and video-based AAL users, Anna and Irakli, serve as reference points for describing salient ethical, legal and social challenges related to use of AAL. These challenges are presented on three levels: individual, societal, and regulatory. For each challenge, a set of policy recommendations is suggested.