Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and (...) describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Samuel Butler is usually remembered for Erewhon, widely considered among the best English satires. He also contributed to philosophical biology in works that collectively compose the nineteenth century's finest statement of the evolutionary argument associated with the name of Lamarck. In writing on evolution, Butler was not presenting science for a popular audience but deliberately intervening in the scientific argument about Darwinism. Surprised by the success of his first venture in philosophical biology, Life and Habit, Butler committed himself to the (...) project of developing an alternative to Darwinism, which he did in three additional volumes, and these are the works canvassed in this “delayed book review.”. (shrink)

This paper is a study of Brentano’s ontology, and more specifically of his theory of substance and accident as put forward toward the end of his life in the materials collected together as the Kategorienlehre or Theory of Categories. Here Brentano presents an auditious (re-)interpretation of Aristotle’s theory of substance and accidence. We show that on the Brentano initially defends, it is space which serves as the single substance upon which all other entities depend as accidents of space. In an (...) appendix, however, Brentano puts forward an even more radical suggestion, inspired by the physics of Kelvin. According to this final view, space itself is an accident of a deeper substance: the present time. (shrink)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

Independently of whether an object of experience becomes a candidate for being a part of the self or a part of the external world, it is always given to us as just an object of experience. The observer-observed relation can be seen as a type of relation with many instances, both between the self and different objects of experience and between any given object of experience and different selves. The self is situated in a spatial grid, where the latter can (...) be characterised as an array of relations, of which the relata include both observers and observed. The world, understood as independent existence, including the self, is empty. However, Paolo Bozzi’s method for identifying the self and delimiting its independent existence from the external world has taught us just the opposite lesson. Bozzi’s project is to teach us how to use them, and to recognise that they allow a self to be situated in a world of objects. (shrink)

This paper is a contribution to the historical roots of the analytical tradition. As Michael Dummett points out in his Origins of Analytic Philosophy, many tendencies in Central European thought contributed to the early development of analytic philosophy. Dummett himself concentrates on just one aspect of this historical complex, namely on the relationship between the theories of meaning and reference developed by Frege and by Husserl in the years around the turn of the century. It is to this specific issue (...) that the present essay is devoted, though we attempt a more sympathetic reading of Husserl's views on these matters than is to be found in Dummett’s work. Topics covered include Husserl’s theory of intentionality, his view of meanings as types or essences of mental acts, of the relation between meaning and expression, of states of affairs, and of indexicality. (shrink)

We rely on language to know the minds of others, but does language have a role to play in knowing our own minds? To suppose it does is to look for a connection between mastery of a language and the epistemic relation we bear to our inner lives. What could such a connection consist in? To explore this, I shall examine strategies for explaining self-knowledge in terms of the use we make of language to express and report our mental states. (...) Success in these strategies will depend on the view we take of speakers' understanding of the words they use to speak their minds. The key is to avoid circularity in the account of how they know what they mean; for if knowing what one is saying in speaking a language provides a means of knowing one's own mind, it cannot simply be a part of it. I shall look at ways in which we might proceed here, and examine whether the strategy can make room for a genuinely first-person point of view. But first let me try to motivate the problem of self-knowledge. (shrink)

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

Autobiography of Barry Smith; emphasizes the role of Dummett and Husserl, Austrian philosophy and economics, and the Munich-Göttingen-Kraków school of realist phenomenology.

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

Can there be a theory-free experience? And what would be the object of such an experience. Drawing on ideas set out by Husserl in the “Crisis” and in the second book of his “Ideas”, the paper presents answers to these questions in such a way as to provide a systematic survey of the content and ontology of common sense. In the second part of the paper Husserl’s ideas on the relationship between the common-sense world (what he called the ‘life-world’) and (...) the world of physical theory are subjected to a critical evaluation. The relation of Husserl’s ideas to current work in folk psychology and naive physics and to the direct realism of J. J. Gibson are also treated. (shrink)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of (...) projection, which holds between a judgment p and an object x when the truth of p entails the existence of x. A truthmaker for a judgment p is then a necessitator for p which satisfies the further constraint that it is part of p’s projection. We offer a formal theory of the truthmaker relation thus defined, exploiting ontological tools of basic mereology and the theory of dependence. We then apply the theory to a range of problems connected with generic expressions, ellipsis, vagueness, and indexical and perceptual judgments. (shrink)

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (shrink)

We outline Brentano’s theory of boundaries, for instance between two neighboring subregions within a larger region of space. Does every such pair of regions contain points in common where they meet? Or is the boundary at which they meet somehow pointless? On Brentano’s view, two such subregions do not overlap; rather, along the line where they meet there are two sets of points which are not identical but rather spatially coincident. We outline Brentano’s theory of coincidence, and show how he (...) uses it to resolve a number of Zeno-like paradoxes. (shrink)

A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.

The paper investigates the role played by ethical deliberation and ethical judgment in Wittgenstein's early thought in the light of twentieth?century German legal philosophy. In particular the theories of the phenomenologists Adolf Reinach, Wilhelm Schapp, and Gerhart Husserl are singled out, as resting on ontologies which are structurally similar to that of the Tractatus: in each case it is actual and possible Sachverhalte which constitute the prime ontological category. The study of the relationship between the states of affairs depicted, e.g., (...) in the sentences of a legal trial and prior fact?complexes to which these may correspond suggests one possible connecting link between the logical and ontological sections of the Tractatus and the ethical reflections appearing at the end. It is argued that the latter can best be understood in terms of the idea of a ?last judgment? (with its associated ethical rewards and punishments) which would relate to the world as a whole as a penal trial relates to individual complexes of facts. (shrink)

The theory of document acts is an extension of the more traditional theory of speech acts advanced by Austin and Searle. It is designed to do justice to the ways in which documents can be used to bring about a variety of effects in virtue of the fact that, where speech is evanescent, documents are continuant entities. This means that documents can be preserved in such a way that they can be inspected and modified at successive points in time and (...) grouped together into enduring document complexes. We outline some components of a theory of document acts, and show how it can throw light on certain problems in Searle’s ontology of social reality. (shrink)

Some defenders of so-called `artificial intelligence' believe that machines can understand language. In particular, Søgaard has argued in his "Understanding models understanding language" (2022) for a thesis of this sort. His idea is that (1) where there is semantics there is also understanding and (2) machines are not only capable of what he calls `inferential semantics', but even that they can (with the help of inputs from sensors) `learn' referential semantics. We show that he goes wrong because he pays insufficient (...) attention to the difference between language as used by humans and the sequences of inert symbols which arise when language is stored on hard drives or in books in libraries. (shrink)

Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is an (...) essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

Of Chisholm’s many signal contributions to analytic metaphysics, perhaps the most important is his treatment of boundaries, a category of entity that has been neglected, to say the least, in the history of ontology. We can gain some preliminary idea of the sorts of problems which the Chisholmian ontology of boundaries is designed to solve, if we consider the following Zeno-inspired thought-experiment.

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)

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

This essay is a contribution to social ontology, drawing on the work of John Searle and of Hernando de Soto. At the center of the argument is the proposition advanced by de Soto in his Mystery of Capital to the effect that many of the entities which structure our contemporary social reality are entities which exist in virtue of the fact that there are (paper or digital) documents which support their existence. I here develop de Soto’s argument further, focusing specifically (...) on the ontological problems raised by a family of new types of social phenomena – exemplified most dramatically in the domain of finance for example in the form of what are called ‘structured investment vehicles’ – made possible as a result of the employment of computer technology in entity creation. I address also Searle’s most recent work on social ontology, and conclude with an appendix on the theory of documentality advanced by Maurizio Ferraris. (shrink)

It will be the thesis of this paper that there are among our mental acts some which fall into the category of real material relations. That is: some acts are necessarily such as to involve a plurality of objects as their relata or fundamenta. Suppose Bruno walks into his study and sees a cat. To describe the seeing, here, as a relation, is to affirm that it serves somehow to tie Bruno to the cat. Bruno's act of seeing, unlike his (...) feeling depressed, his putative thinking-about-Santa-Claus or his musing, abstractedly, about the tallest spy, has at least two fundamenta: it is, as a matter of necessity, dependent for its existence upon both Bruno himself and the cat that he sees. This idea will naturally raise echoes of Russell's doctrine of knowledge by acquaintance. 'I am acquainted with an object', Russell tells us, 'when I have a direct cognitive relation to that object, i. e. when I am directly aware of the object itself' (1918, p. 209). And indeed a distinction in many ways like that between acquaintance and description will find a place within the theory here projected, but there are crucial differences. (shrink)

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a bank's computers, however, the formula fails, because these (...) are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (shrink)

In his The Meaning of Disgust, Colin McGinn employs elements of the phenomenological theory of disgust advanced by Aurel Kolnai in 1929. Kolnai’s treatment of what he calls “material” disgust and of its primary elicitors—putrefying organic matter, bodily wastes and secretions, sticky contaminants, vermin—anticipates more recent scientific treatments of this emotion as a mode of protective recoil. While Nina Strohminger charges McGinn with neglecting such scientific studies, we here attempt to show how Kolnai goes beyond experimental findings in his careful (...) description of the phenomenological differences between disgust and other emotions of forceful disapproval. (shrink)

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)

Husserl’s philosophy, by the usual account, evolved through three stages: 1. development of an anti-psychologistic, objective foundation of logic and mathematics, rooted in Brentanian descriptive psychology; 2. development of a new discipline of "phenomenology" founded on a metaphysical position dubbed "transcendental idealism"; transformation of phenomenology from a form of methodological solipsism into a phenomenology of intersubjectivity and ultimately (in his Crisis of 1936) into an ontology of the life-world, embracing the social worlds of culture and history. We show that this (...) story of three revolutions can provide at best a preliminary orientation, and that Husserl was constantly expanding and revising his philosophical system, integrating views in phenomenology, ontology, epistemology and logic with views on the nature and tasks of philosophy and science as well as on the nature of culture and the world in ways that reveal more common elements than violent shifts of direction. We argue further that Husserl is a seminal figure in the evolution from traditional philosophy to the characteristic philosophical concerns of the late twentieth century: concerns with representation and intentionality and with problems at the borderlines of the philosophy of mind, ontology, and cognitive science. (shrink)

This paper examines Spinoza’s view on the consistency of mental representation. First, I argue that he departs from Scholastic tradition by arguing that all mental states—whether desires, intentions, beliefs, perceptions, entertainings, etc.—must be logically consistent. Second, I argue that his endorsement of this view is motivated by key Spinozistic doctrines, most importantly the doctrine that all acts of thought represent what could follow from God’s nature. Finally, I argue that Spinoza’s view that all mental representation is consistent pushes him to (...) a linguistic account of contradiction. (shrink)

We argue that a modified version of Mill’s method of agreement can strongly confirm causal generalizations. This mode of causal inference implicates the explanatory virtues of mechanism, analogy, consilience, and simplicity, and we identify it as a species of Inference to the Best Explanation (IBE). Since rational causal inference provides normative guidance, IBE is not a heuristic for Bayesian rationality. We give it an objective Bayesian formalization, one that has no need of principles of indifference and yields responses to the (...) Voltaire objection, van Fraassen’s Bad Lot objection, and John Norton’s recent objection to IBE. (shrink)

In this essay we argue that an agent’s failure to assist someone in need at one time can change the cost she can be morally required to take on to assist that same person at a later time. In particular, we show that the cost the agent can subsequently be required to take on to help the person in need can increase quite significantly, and can be enforced through the proportionate use of force. We explore the implications of this argument (...) for the duties of the affluent to address global poverty. (shrink)

Frank Cabrera argues that informational explanatory virtues—specifically, mechanism, precision, and explanatory scope—cannot be confirmational virtues, since hypotheses that possess them must have a lower probability than less virtuous, entailed hypotheses. We argue against Cabrera’s characterization of confirmational virtue and for an alternative on which the informational virtues clearly are confirmational virtues. Our illustration of their confirmational virtuousness appeals to aspects of causal inference, suggesting that causal inference has a role for the explanatory virtues. We briefly explore this possibility, delineating a (...) path from Mill’s method of agreement to Inference to the Best Explanation (IBE). (shrink)

The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in people’s minds – and we argue that (...) they serve still as the basis for a series of influential confusions. We argue further that an ontology based unambiguously, not on concepts, but on the classification of entities in reality can, by removing these confusions, make a vital contribution to ensuring the interoperability of coding systems and healthcare records in the future. (shrink)

Relevance logic has become ontologically fertile. No longer is the idea of relevance restricted in its application to purely logical relations among propositions, for as Dunn has shown in his (1987), it is possible to extend the idea in such a way that we can distinguish also between relevant and irrelevant predications, as for example between “Reagan is tall” and “Reagan is such that Socrates is wise”. Dunn shows that we can exploit certain special properties of identity within the context (...) of standard relevance logic in a way which allows us to discriminate further between relevant and irrelevant properties, as also between relevant and irrelevant relations. The idea yields a family of ontologically interesting results concerning the different ways in which attributes and objects may hang together. Because of certain notorious peculiarities of relevance logic, however,1 Dunn’s idea breaks down where the attempt is made to have it bear fruit in application to relations among entities which are of homogeneous type. (shrink)

We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political affairs. Crucially, the X and the Y terms are here identical. A (...) problem arises for this theory for cases involving 'free-standing Y terms', as for example in the case of money in a computerized bank account. Here there is no physical X to which a status function might be attached. We conclude by arguing that Searle's response to this problem creates difficulties for his naturalistic framework. (shrink)

ABSTRACT We have previously argued that there are forms of greenhouse gas offsetting for which, when one emits and offsets, one imposes no risk. Orri Stefansson objects that our argument fails to distinguish properly between the people who stand to be harmed by one’s emissions and the people who stand to be benefited by one’s offsetting. We reply by emphasizing the difference between acting with a probability of making a difference to the distribution of harm and acting in a way (...) that worsen’s someone’s prospect. (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)

Artificial intelligence is man's attempt to use software to emulate the intelligence of human beings. But the complexity of the human neurological system formed in the course of evolution is impossible to replicate: "Human languages and societies are complex systems, indeed complex systems of many complex systems," so much so that their mathematical modeling is impossible. Barry Smith, philosopher and professor at the University at Buffalo. shows no uncertainty about this. His latest book written with Jobst Landgrebe, a mathematician (...) and entrepreneur in the AI field, leaves no doubt – starting with the title: Why machines will never rule the world (Routledge 2023). The book was presented in Turin during an evening organized by the Fondazione CRT and the Bruno Leoni Institute, in which Smith was interviewed based on questions developed by generative Ai. We have accepted the challenge to conduct an interview parallel to the one done with GPT4. (shrink)

For Meinong, familiarly, fictional entities are not created, but rather merely discovered (or picked out) from the inexhaustible realm of Aussersein (beyond being and non-being). The phenomenologist Roman Ingarden, in contrast, offers in his Literary Work of Art of 1931 a constructive ontology of fiction, which views fictional objects as entities which are created by the acts of an author (as laws, for example, are created by acts of parliament). We outline the logic of fiction which is implied by Ingarden’s (...) approach, showing how it distinguishes the properties possessed by fictional objects (for instance of having been created by such and such an author in such and such a work) from characteristics (for instance of smoking a pipe, of living in Baker Street) which are merely associated with such objects. (shrink)

The aim of this volume is to present Kafka not as a writer, or not only as a writer, but as a philosopher. However, even after narrowing the scope of our interest down, there will still be several Kafka’s left on the table. Themes treated in the volume include: the so-called Brentano School in Prague, Kafka’s affiliation to the Louvre Circle, Kafka and existentialist philosophy, Kafka’s Jewish heritage, his love of Nietzsche and Meister Eckhart and—last but not least, since he (...) was such an exceptional writer—his aesthetics. (shrink)

What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas were (...) developed prior to the scientific discoveries of the modern era, he approached the objects and relations of everyday reality with the same ontological seriousness with which scientists today approach the objects of physics. We shall seek to show that what Aristotle has to say about these commonsensical objects and relations can, when translated into more formal terms, be of use also to contemporary ontologists. More precisely, we shall argue that his ideas can contribute to the development of a rigorous theory of those social and institutional components of everyday reality – the settings of human behavior – which are the subject of this volume. When modern-day philosophers turn their attentions to ontology they begin not with Aristotle but rather, in almost every case, with a set-theoretic ontology of the sort which is employed in standard model-theoretic semantics. Set-theoretic ontology sees the world in atomistic terms: it postulates a lowest level of atoms or urelements, from out of which successively higher levels of set-theoretic objects are then constructed. The approach to ontology to be defended here, in contrast, starts not with atoms but with the mesoscopic objects by which we are surrounded in our normal day-to-day.. (shrink)

It is argued, on the basis of ideas derived from Wittgenstein's Tractatus and Husserl's Logical Investigations, that the formal comprehends more than the logical. More specifically: that there exist certain formal-ontological constants (part, whole, overlapping, etc.) which do not fall within the province of logic. A two-dimensional directly depicting language is developed for the representation of the constants of formal ontology, and means are provided for the extension of this language to enable the representation of certain materially necessary relations. The (...) paper concludes with a discussion of the relationship between formal logic, formal ontology, and mathematics. (shrink)

The magisterial analyses of logic and meaning advanced in Husserl's Logical Investigations of 1900/01 have for a number of reasons been neglected by analytical philosophers in subsequent decades. This state of affairs has to do, in part, with the history of the editions and translations of Husserl's writings. Findlay's readable but imperfect translation appeared seventy years after the work itself was first published, and the editors and translators and expositors of Husserl's works have reflected the prevailing philosophical atmosphere on the (...) Continent by concentration their energies on Husserl's later writings. Now, however, over eighty years after the appearance of Husserl's one true masterpiece, a critical edition of the work is at last available in completed form. We here analyze the structure and content of this new edition, published as part of the Husserliana series by the Husserl Archive in Louvain. (shrink)

Despite the prevalence of human rights discourse, the very idea or concept of a human right remains obscure. In particular, it is unclear what is supposed to be special or distinctive about human rights. In this paper, we consider two recent attempts to answer this challenge, James Griffin’s “personhood account” and Charles Beitz’s “practice-based account”, and argue that neither is entirely satisfactory. We then conclude with a suggestion for what a more adequate account might look like – what we call (...) the “structural pluralist account” of human rights. (shrink)