The present crisis of foundations in Fundamental Science is manifested as a comprehensive conceptual crisis, crisis of understanding, crisis of interpretation and representation, crisis of methodology, loss of certainty. Fundamental Science "rested" on the understanding of matter, space, nature of the "laws of nature", fundamental constants, number, time, information, consciousness. The question "What is fundametal?" pushes the mind to other questions → Is Fundamental Science fundamental? → What is the most fundamental in the Universum?.. Physics, do not be afraid of (...) Metaphysics! Levels of fundamentality. The problem №1 of Fundamental Science is the ontological justification (basification) of mathematics. To understand is to "grasp" Structure ("La Structure mère"). Key ontological ideas for emerging from the crisis of understanding: total unification of matter across all levels of the Universum, one ontological superaxiom, one ontological superprinciple. The ontological construction method of the knowledge basis (framework, carcass, foundation). The triune (absolute, ontological) space of eternal generation of new structures and meanings. Super concept of the scientific world picture of the Information era - Ontological (structural, cosmic) memory as "soul of matter", measure of the Universum being as the holistic generating process. The result of the ontological construction of the knowledge basis: primordial (absolute) generating structure is the most fundamental in the Universum. (shrink)

In this dissertation I examine the ontological and systematic basis of Hegel’s social and political philosophy. I argue that the structures of the will, discussed in paragraphs five through seven of the Philosophy of Right, present the key for understanding the goal and the argumentative structure of that work. Hegel characterizes the will in terms of the oppositions between the universal and the particular, the infinite and the finite, and the indeterminate and the determinate. Ultimately, he argues that (...) we must grasp the will as the unity of these oppositional moments. The Philosophy of Right presents an extended attempt to grasp this unity. -/- In order to central problem presented by the structure of the will, I argue that we must first recognize the will as the highest instantiation of the more general structures that constitute the notion. On my interpretation, the term ‘notion’ designates Hegel’s doctrine of substance. More specifically, this term presents his conception of substance in terms of categories normally associated with human subjectivity, in terms of representation and purposive action. -/- The will presents the highest or truest instantiation of the notion. Various notions can be ranked along a spectrum in accordance with their degree of success at resolving the basic problem facing all objects – namely the problem of integrating or essentially relating identity and difference through self-constituting activity. The unification of identity and difference presents the central problem or paradox of Hegel’s philosophy. It is a paradox that takes many forms. In this dissertation, I show how change, the structure of judgment, and the nature of the object all exhibit this paradox. I also show how Hegel’s doctrine of the notion develops as a direct response to this paradox. Additionally, I argue that Hegel’s account of the structure of the will – as the unity of the universal and the particular, the unity of the infinite and the finite, and the unity of the indeterminate and the determinate – presents the highest manifestation of the paradox that arises when we seek to explain the unity of identity and difference. (shrink)

Düşünce tarihi insan ve insanla ilgili problemlerin tarihidir. Çünkü her bilim ve felsefe anlayışı az ya da çok insanla ilişkilidir. Bununla birlikte insan ve insana ait problemlerin özel ve bağımsız bir disiplinin konusu olması felsefi antropolojinin kurulmasıyla mümkün olmuştur. Bu çalışma, felsefi antropolojide ortaya konulan kimi yaklaşımları eleştiren ve ontolojik temellere dayalı yeni bir antropoloji anlayışı geliştiren Takiyettin Mengüşoğlu’nun görüşlerini ele almaktadır. Bu antropolojik anlayış insanı herhangi bir kavramdan değil, somut biyopisişik bütünlüğünden hareketle incelediğinden, onu varlık koşullarının bütünlüğünde değerlendirme imkânı (...) sağlamaktadır. *** History of thought is history of the human and human’s problems. Because all field of sciences and philosophy have relation greater or less to human. However human and human’s problems are with established of philosophical anthropology has been the subject of a special and independent discipline. This essay deals with Takiyettin Mengüşoğlu’s views who criticizes some approaches asserted in philosophical anthropology and develops a new anthropology based on ontological grounds. This anthropology approach enables to evaluate human in totality of human’s being contestations as not analyzing any conception but his concrete biopsychic wholeness. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

The aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species, race, memory, intelligence, depression, or obesity are true or false relative to the choice of a biological, psychological, or medical ontology. Second, I show that ontological choices often depend on non-epistemic values. On (...) the basis of these premises, I argue that it is often neither possible nor desirable to evaluate scientific statements independently of non-epistemic values. Finally, I suggest that considerations of ontological choices do not only challenge the value-free ideal but also help to specify positive roles of non-epistemic values in an often neglected area of scientific practice. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds (...) of situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

Actualism is the doctrine that the only things there are, that have being in any sense, are the things that actually exist. In particular, actualism eschews possibilism, the doctrine that there are merely possible objects. It is widely held that one cannot both be an actualist and at the same time take possible world semantics seriously — that is, take it as the basis for a genuine theory of truth for modal languages, or look to it for insight into (...) the modal structure of reality. For possible world semantics, it is supposed, commits one to possibilism. In this paper I take issue with this view. To the contrary, I argue that one can take possible world semantics seriously without any commitment to possible worlds or possibilism and hence remain in full compliance with actualist scruples. Moreover, one can do so without without invoking either "ersatz" worlds or haecceities. (shrink)

I shall attempt in what follows to show how mereology, taken together with certain topological notions, can yield the basis for future investigations in formal ontology. I shall attempt to show also how the mereological framework here advanced can allow the direct and natural formulation of a series of theses – for example pertaining to the concept of boundary – which can be formulated only indirectly (if at all) in set-theoretic terms.

Fundamental Science is undergoing an acute conceptual-paradigmatic crisis of philosophical foundations, manifested as a crisis of understanding, crisis of interpretation and representation, “loss of certainty”, “trouble with physics”, and a methodological crisis. Fundamental Science rested in the "first-beginning", "first-structure", in "cogito ergo sum". The modern crisis is not only a crisis of the philosophical foundations of Fundamental Science, but there is a comprehensive crisis of knowledge, transforming by the beginning of the 21st century into a planetary existential crisis, which has (...) exacerbated the question of the existence of Humanity and life on Earth. Due to the unsolved problem of justification of Mathematics, paradigm problems in Computational mathematics have arisen. It's time to return ↔ Into Dialectics. The solution to the problem of the foundations of Mathematics, and therefore knowledge in general, is the solution to the problem of modeling (constructing) the ontological basis of knowledge - the ontological model of the primordial generating process. The idea and model of the primordial generating process, its ontological structure directs thinking to the need for the introduction of superconcept → ontological (cosmic, structural) memory, concept-attractor, supercategory, substantial semantic core of the scientific picture of the world of the nuclear-ecological-information age. Model of basic Ideality→ “Space-MatterMemory-Time” [S-MM-T]. (shrink)

There have been attempts to get some logic out of belief dynamics, i.e. attempts to define the constants of propositional logic in terms of functions from sets of beliefs to sets of beliefs. It is interesting to see whether something similar can be done for ontological categories, i.e. ontological constants. The theory presented here will be a (modest) expansion of belief dynamics: it will not only incorporate beliefs, but also parts of beliefs, so called belief fragments. On the (...) basis of this we will give a belief-dynamical account of the ontological categories of states of affairs, individuals, properties of arbitrary adicities and properties of arbitrary orders. (shrink)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through (...) which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

In this paper, I develop a criticism to a method for metaontology, namely, the idea that a discourse’s or theory’s ontological commitments can be read off its sentences’ truth- conditions. Firstly, I will put forward this idea’s basis and, secondly, I will present the way Quine subscribed to it. However, I distinguish between two readings of Quine’s famous ontological criterion, and I center the focus on the one currently dubbed “ontological minimalism”, a kind of modern Ockhamism (...) applied to the mentioned metaontological view. I show that this view has a certain application via Quinean thesis of reference inscrutability but that it is not possible to press that application any further and, in particular, not for the ambitious metaontological task some authors try to employ. The conclusion may sound promising: having shown the impossibility of a semantic ontological criterion, intentionalist or subjectivist ones should be explored. (shrink)

Ingarden’s puzzle is: how can we come to know what is essentially involved in an act of knowing? As starting point he takes what he holds to be a particular good candidate example of such an act, namely an act of perceiving an apple. Here we have act and object standing in a certain first-level relation to each other. We now in a second level act of reflection, make this first-level relation into an object, and strive to apprehend this object (...) as an instantiation of the essence knowledge. But how, on this basis, could we ever establish that we had indeed grasped this essence, and that this is indeed the appropriate essence? Surely, through some third-level act of reflection on this second-level act. We expound from an ontological point of view Ingarden's idea as to how this regress can be avoided. (shrink)

What is a number? Answering this will answer questions about its philosophical foundations - rational numbers, the complex numbers, imaginary numbers. If we are to write or talk about something, it is helpful to know whether it exists, how it exists, and why it exists, just from a common-sense point of view [Quine, 1948, p. 6]. Generally, there does not seem to be any disagreement among mathematicians, scientists, and logicians about numbers existing in some way, but currently, in the mainstream (...) arena only definitions, descriptions of properties, and effects are presented as evidence. Enough historical description of numbers in history provides an empirical basis of number, although a case can be made that numbers do not exist by themselves empirically. Correspondingly, numbers exist as abstractions. All the while, though, these "descriptions" beg the question of what numbers are ontologically. Advocates for numbers being the ultimate reality have the problem of wrestling with the nature of reality. I start on the road to discovering the ontology of number by looking at where people have talked about numbers as already existing: history. Of course, we need to know not only what ontology is but the problems of identifying one, leading to the selection between metaphysics and provisional approaches. While we seem to be dimensionally limited, at least we can identify a more suitable bootstrapping ontology than mere definitions, leading us to the unity of opposites. The rest of the paper details how this is done and modifies Peano's Postulates. (shrink)

The goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within a given domain and the (...) relations between them. The construction of an ontology begins when a Community of Interest (COI) identifies its authoritative data sources (ADS), which are usually manifest in relevant doctrinal publications, glossaries, data dictionaries, and logical data models. The identified terms are then defined in relation to a common logical framework that has been designed to ensure interoperability with other ontologies created on the basis of the same strategy. As will be described, the Command and Control (C2) Ontology will include representations of a substantial number of entities within the Command and Control (C2) domain. If domain ontologies (e.g. Strike and Counterinsurgency) semantically align with the C2 Ontology, then a substantial barrier to systems interoperability is thereby crossed. (shrink)

In Ontological Catastrophe, Joseph Carew takes up the central question guiding Slavoj Žižek’s philosophy: How could something like phenomenal reality emerge out of the meaninglessness of the Real? Carefully reconstructing and expanding upon his controversial reactualization of German Idealism, Carew argues that Žižek offers us an original, but perhaps terrifying, response: experience is possible only if we presuppose a prior moment of breakdown as the ontogenetic basis of subjectivity. Drawing upon resources found in Žižek, Lacanian psychoanalysis, and post-Kantian (...) philosophy, Carew thus develops a new critical metaphysics—a metaphysics which is a variation upon the late German Idealist theme of balancing system and freedom, realism and idealism, in a single, self-reflexive theoretical construct—that challenges our understanding of nature, culture, and the ultimate structure of reality. (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

Fundamental Science is undergoing an acute conceptual-paradigmatic crisis of philosophical foundations, manifested as a crisis of understanding, crisis of interpretation and representation, “loss of certainty”, “trouble with physics”, and a methodological crisis. Fundamental Science rested in the "first-beginning", "first-structure", in "cogito ergo sum". The modern crisis is not only a crisis of the philosophical foundations of Fundamental Science, but there is a comprehensive crisis of knowledge, transforming by the beginning of the 21st century into a planetary existential crisis, which has (...) exacerbated the question of the existence of Humanity and life on Earth. Due to the unsolved problem of justification of Mathematics, paradigm problems in Computational mathematics have arisen. It's time to return ↔ Into Dialectics. The solution to the problem of the foundations of Mathematics, and therefore knowledge in general, is the solution to the problem of modeling (constructing) the ontological basis of knowledge - the ontological model of the primordial generating process. The idea and model of the primordial generating process, its ontological structure directs thinking to the need for the introduction of superconcept → ontological (cosmic, structural) memory, concept-attractor, supercategory, substantial semantic core of the scientific picture of the world of the nuclear-ecological-information age. Model of basic Ideality→ “Space-MatterMemory-Time” [S-MM-T]. (shrink)

Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communication to happen, (...) the conceptual systems of the originators and users of the information must be sufficiently similar. A formal conceptual framework that can provide the basis for exchange of information is termed an ontology. In its most fundamental form, ontology studies the most basic constituents of reality. Traditionally, ontology seeks to reflects structures that are independent of thought and cognition. The term ontology is used more broadly in artificial intelligence and software engineering, to refer to the conceptual basis for an information system. (shrink)

Applied technological developments are represented by (1) genetic engineering as management tools of biological evolution and (2) socio-economic engineering as management tools of civilizational and socio-cultural development. This binary structure logically follows from the postulated three-module organization of the sustainable evolutionary strategy of the sentient human being. Naturphilosophy once again acquires the status of the basis of the theory of evolution in an explicit way. There is a system of metaphysical postulates and ontological categories derived from the anthropic (...) principle of participation. For modern neoliberal political democracy, bio-power and biopolitics look like the most effective technology for stabilizing the scenarios and trends of the global evolutionary process that are optimal within this ideological system. Conclusions.Transbipolitics in our understanding is a political problematic related to the rationalization of the global evolutionary process. In the coming decades transbipolitics will become the carrier element of the global process of evolution of the noosphere with the consequent complication and increase of cohesion between the individual socio-cultural types that are part of the system of modern globalizing civilization. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: (...) This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

This article presents a formal ontology which accounts for the general nature of artefacts. The objective is to help structure application ontologies in areas where specific artefacts are present - in other words, virtually any area of activity. The conceptualization relies on recent philosophical and psychological research on artefacts, having resulted in a largely consensual theoretical basis. Furthermore, this ontology of artefacts extends the foundational DOLCE ontology and supplements its axiomatization. The conceptual primitives are as follows: artificial entity, intentional (...) production of entities, (state of) capacity, capacity to play a role in actions of a given type, function and functional object. These primitives enable artefacts in general to be characterized as intentionally and successfully produced entities, and isolate an important subclass of “technical” artefacts to which a function is ascribed. Lastly, we emphasize the novelty of this ontology by comparing it with other works with similar objectives. (shrink)

This paper elaborates distinctions between a core and a periphery in the ontological and the conceptual domain associated with natural language. The ontological core-periphery distinction is essential for natural language ontology and is the basis for the central thesis of my 2013 book Abstract Objects and the Semantics of Natural Language, namely that natural language permits reference to abstract objects in its periphery, but not its core.

The work of Gregory Bateson offers a metaphysical basis for a “process psychology,” that is, a view of psychological practice and research guided by an ontology of becoming—identifying change, difference, and relationship as the basic elements of a foundational metaphysics. This article explores the relevance of Bateson's recursive epistemology, his re-conception of the Great Chain of Being, a first-principles approach to defining the nature of mind, and understandings of interaction and difference, pattern and symmetry, interpretation and context. Bateson's philosophical (...) contributions will be drawn into relationship with Wittgenstein's philosophy of language as use, Melnyk's theory of causal levels of explanation, Korzybski's account of map and territory, the rejection of the heuristic rigidity of substantialist ontologies, and a cybernetics communication science-informed approach to contextual bi-directionality of causality. We thereby arrive at an understanding of Bateson's process psychology that, given its ecological-systemic nature, is explanatorily applicable across the mind sciences. This process psychology equips us to answer the question: What is mind? Not by explanatory appeal to substantial entities contained within mind, but instead by recourse to the contextually relevant patterns for understanding mind to a particular purpose. We have thereby attended to the gulf between heuristics and fundamentals, between psychological models and an onto-epistemic account of reality. Insufficient attention has been given to characterising the vital nature of Bateson's philosophical oeuvre to psychological practice. This article draws out Bateson's relevance to establishing foundational principles for a process psychology capable of reinvigorating psychological thought. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical (...) power and great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in (...) the form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

The article will expose the problem of the nature of reality stablished in the first sections of Wittgenstein"s “Tractatus Logico-Philosophicus”, especially the aphorisms 1 to 2.063 seeking to show points of contact between the Aristotelian-Thomistic and Suarezian thought. Initially, (I) a distinction is made between metaphysics and ontology in order to understand why Wittgenstein, notorious for his anti-metaphysical thought, actually ends up producing a theory of reality. Subsequently, (II) the relationship between reality and language will be drawn from the characteristic (...) isomorphism of the Tractatus in which a structural similarity will appear with the Aristotelian-Thomistic thought. This relationship will be the basis for (III) the construction of an ontological image of reality as the condition of possibility for a meaningful language. With this outlook, the (IV) hypothesis of the influence of Francisco Suárez"s thought as the content behind this Wittgensteinian description of reality will be advanced. (shrink)

As Augustine himself testifies, he did not know Origen’s work so well. However, this does not mean that he was not acquainted with his key soteriological hypotheses, especially his teachings on apocatastasis. Although Augustine’s doctrine of predestination has completely opposite consequences in comparison to Origen’s teaching about apocatastasis, we believe that these teachings share the common ontological basis, which is the subject of this study. While Origen’s Christology is often called into question, Augustine’s Christology is considered correct. However, (...) with both authors we find a certain marginalisation of Christology in the field of ontologically understood soteriology. Theological insights of these two authors influenced to a significant extent the development of theology of both the East and West, making their works significant up until today, both from the aspect of Christian self-understanding and from the aspect of ecumenical dialogue. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

The Industrial Ontologies Foundry (IOF) was formed to create a suite of interoperable ontologies. Ontologies that would serve as a foundation for data and information interoperability in all areas of manufacturing. To ensure that each ontology is developed in a structured and mutually coherent manner, the IOF has committed to the tiered architecture of ontology building based on the Basic Formal Ontology (BFO) as top level. One of the critical elements of a successful tiered architecture build is the domain mid-level (...) ontologies. However, thus far there has been no mid-level manufacturing ontology that is based on BFO. The IOF has recently released the IOF Core version 1 beta to fill this gap. This paper documents the development process and gives an overview of the current content of the IOF Core. Finally, the paper describes how the IOF Core can be used as the basis for a more domain-specific Supply Chain Ontology. (shrink)

The concept of fields available in physics will be considered for application to unravel the mysteries of form, structure and function of human consciousness and mind. The sameness of functions of human consciousness and mind in language acquisition and communication and also acquiring knowledge of various kinds and its will be discussed. In the light of this the limitations of concepts of pure physics and modern physics probes will be discussed. -/- The information and ideas available in the Upanishads in (...) the form of Brahmajnaana will be applied to understand the physical nature of human consciousness and mind and their functions. This information and translation into modern and cognitive scientific terms would be correlated with brainwaves concept of modern physiology. The physiochemical, physical and chemical natures of experiences, purport, meanings, ideas, thoughts and expressions will be presented based on Upanishadic insight thus acquired. The advantage of this alternative probe, method and model to understand the functions of human consciousness and mind will be demonstrated. -/- This model of human consciousness and mental functions is also correlated to brain wave EEG frequency changes. -/- . (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop (...) a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm in (...) ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research. (shrink)

This article presents an ontological proof that God is impossible.I define an ‘impossibility’ as a condition which is inconceivable due to its a priori characteristics (e.g. a ‘square circle’). Accordingly, said conditions will not ever become conceivable, as they could in instances of a posteriori inconceivability (e.g. the notion that someone could touch a star without being burned). As the basis of this argument, I refer to an a priori observation (Primus, 2019) regarding our inability to imagine inconsistency (...) (difference) within any point of space. This observation renders the notion of absolute power to be inconceivable, a priori.I briefly discuss the moral implications of religious faith in the context of Purism: a moral rationalist paradigm. I conclude that whilst belief in God can be aesthetically expressed it should not be possessed as a material purpose, due to the illogicality of the latter category of belief and/or expression. With this article I provide conceptual delineation between harmless religious belief and expression—which, I argue, should be protected from persecution, as per any other artistic expression— and religious belief and expression which is materially harmful to society. Whilst I aim to protect religious freedom of expression on one hand, I duly aim to reduce instances of material faith in God(s) on the other. Finally, I aim to bring hope in the possibility for human salvation via technology—such that they should exist indefinitely as ‘demigods,’ defined by conditional, relative power over their environment. (shrink)

The essay presents the main ideas of the philosophical system «OntoTopoLogia», developed and promoted since 1990 at the I-IV, VIII Russian Philosophical Congresses, the XX World Philosophical Congress (Boston, 1998), Conference «Problems of Consciousness in Philosophy and Science» (Institute of Philosophy RAS, 1996), Conference «Philosophy of Physics: Current Problems» (MSU, 2010), seven International contests The Foundational Questions Institute (USA, FQXi Essay 2012-2020), International scientific conference «Modern Ontology» (St. Petersburg , 2013, 2017, 2019, 2023), Third All-Russian Scientific Conference «Philosophy of Mathematics: (...) Current Problems» (MSU, 2013), International Congress «Fundamental Problems of Natural Science» (St. Petersburg, 2013, 2016, 2022), Conference «Foundations of Fundamental Physics and Mathematics» (RUDN University, 2023). The ideas of the «OntoTopoLogia» system are aimed at overcoming the conceptual-paradigmatic crisis in the metaphysical/ontological basis of fundamental science (mathematics, physics, cosmology) on the basis of a holistic paradigm («paradigm of understanding»), a comprehensive conceptual-figurative synthesis, a method of dialectical-ontological construction, MetaCategory, MetaAxiom, SuperPrinciple and Metasymbol, a new holistic understanding of matter, its ontological unification across all levels of existence of the Universe as eternal holistic process of generating more and more new meanings, forms and structures. A model of the Primordial (absolute) generating structure is being built - a single ontological basis of knowledge: ontological frameworc, carcass, foundation as an all-encompassing Ideality, a single basis for the «sciences of nature» and «sciences of the spirit». (shrink)

The moot point of the Western philosophical rhetoric about free will consists in examining whether the claim of authorship to intentional, deliberative actions fits into or is undermined by a one-way causal framework of determinism. Philosophers who think that reconciliation between the two is possible are known as metaphysical compatibilists. However, there are philosophers populating the other end of the spectrum, known as the metaphysical libertarians, who maintain that claim to intentional agency cannot be sustained unless it is assumed that (...) indeterministic causal processes pervade the action-implementation apparatus employed by the agent. The metaphysical libertarians differ among themselves on the question of whether the indeterministic causal relation exists between the series of intentional states and processes, both conscious and unconscious, and the action, making claim for what has come to be known as the event-causal view, or between the agent and the action, arguing that a sort of agent causation is at work. In this paper, I have tried to propose that certain features of both event-causal and agent-causal libertarian views need to be combined in order to provide a more defendable compatibilist account accommodating deliberative actions with deterministic causation. The ‘‘agent-executed-eventcausal libertarianism’’, the account of agency I have tried to develop here, integrates certain plausible features of the two competing accounts of libertarianism turning them into a consistent whole. I hope to show in the process that the integration of these two variants of libertarianism does not challenge what some accounts of metaphysical compatibilism propose—that there exists a broader deterministic relation between the web of mental and extra-mental components constituting the agent’s dispositional system—the agent’s beliefs, desires, short-term and long-term goals based on them, the acquired social, cultural and religious beliefs, the general and immediate and situational environment in which the agent is placed, etc. on the one hand and the decisions she makes over her lifetime on the basis of these factors. While in the ‘‘Introduction’’ the philosophically assumed anomaly between deterministic causation and the intentional act of deciding has been briefly surveyed, the second section is devoted to the task of bridging the gap between compatibilism and libertarianism. The next section of the paper turns to an analysis of folk-psychological concepts and intuitions about the effects of neurochemical processes and prior mental events on the freedom of making choices. How philosophical insights can be beneficially informed by taking into consideration folk-psychological intuitions has also been discussed, thus setting up the background for such analysis. It has been suggested in the end that support for the proposed theory of intentional agency can be found in the folk-psychological intuitions, when they are taken in the right perspective. (shrink)

The question of what ontological insights can be gained from the knowledge of physics (keyword: ontic structural realism) cannot obviously be separated from the view of physics as a science from an epistemological perspective. This is also visible in the debate about 'scientific realism'. This debate makes it evident, in the form of the importance of perception as a criterion for the assertion of existence in relation to the 'theoretical entities' of physics, that epistemology itself is 'ontologically laden'. This (...) is in the form of the assumption that things (or entities) in themselves exist as such and such determined ones (independent of cognition, autonomously). This ontological assumption is not only the basis of our naïve understanding of cognition, but also its indispensable premise, insofar as this understanding is a fundamentally passive, 'receptive' one. Accordingly, just as 'perception' is the foundation, ('objective') description is the aim of cognition, that which cognition is about. In this sense, our idea of cognition and our idea of the things are inseparably linked. Without the ontological premise mentioned we just would not know what cognition is, but it is basically just a kind of image that we have in our minds (an assumption that helps us understand 'cognition'). Epistemology not only shares this basic assumption (which it also shares with metaphysics), but it revolves (unlike metaphysics) entirely around it by making the idea and demand of 'certainty' a condition of 'real' knowledge. As 'certainty' is a subjective criterion this entails the 'remodelling' of the real, holistic cognitive situation (to which metaphysics adheres) into a linear subject-object-relation (which results in the strict 'transcendence' of the objects). And it also establishes, due to its 'expertise' in matters of cognition, the 'primacy of epistemology' over all other sciences. Now, on closer inspection, however, the expertise of epistemology seems not all that dependable, because it basically consists only of paradigms which, from the point of view of the holism of the real cognitive situation itself, are nothing more than relatively simplistic interpretations of this situation. However, we do not yet know what another conception of cognition might look like (which is not surprising given the high rank of the phenomenon of cognition in the hierarchy of phenomena according to their complexity). 'Certainty' as a criterion of cognition is thus excluded from the outset, and thus the linear relational model of cognition appears as what it is, a gross distortion of the real, holistic cognitive situation. The significance of this argumentation with regard to physics is that the linear epistemological model of cognition itself is a major obstacle to an adequate epistemological understanding of physics. This is because it is fixed 'a priori' to an object-related concept of cognition, and to 'description' as the only mode of ('real') cognition. But physics (without questioning our naïve notion of cognition on the level of epistemology) simply works past it and its basic assumptions. Its cognitive concept (alias heuristic) is fundamentally different from that of metaphysics. The acceptance of the real, holistic cognitive situation is, in my opinion, the condition for an adequate understanding of physics' heuristic access to objects, its transcendental, generalizing cognitive concept, as well as its ontological relevance and dimension of its own. (shrink)

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that (...) will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications. (shrink)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (...) (b) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

There are two types of theories regarding many worlds: one is modal, while the other is temporal. The former regards reality as consisting of many possible worlds, while the latter holds that reality consists of many momentary worlds, which are usually called moments. I compare these two theories, paying close attention to the concept of transworld identity and compare trans-possible world identity with trans-momentary world identity (or transmoment identity). I characterize time from the point of many-worlds view, believing this to (...) be one of the best ways of grasping the reality of time. First, I show that there is reason to adopt the many-worlds view because transworld identity is meaningful for both of them, while it is not for space. Second, I argue that transmoment identity is different from transpossible world identity concerning reality. The former is a realistic relation, while the latter is not. Thus, I find that the reality of time is in the relation of transmoment identity. Such a view, I contend, has merit on the basis that it recognizes the reality of time in a sense that is not true of space. (shrink)

Intelligent defence support systems are confronted with the need to manage ever-increasing floods of data in a way that raises significant challenges because the data are described and presented using different terminologies and formats. How, on this basis, is it possible to reach a common understanding of the information content of these data among people and software agents? How is it possible to ensure that domain knowledge is reused in consistent fashion in a way that makes this information available (...) for integration and analysis? How can we support the identification, selection, composition, and orchestration of services based on such diverse data providing homogeneous support by a service-oriented architecture? This collection is devoted to the use of ontologies to answer questions such as these. (shrink)

The paper argues that the reconciliation of the Causal Theory of Perception with Disjunctivism requires the rejection of causal particularism – the idea that the ontology of causation is always and everywhere an ontology of particulars (e.g., events). The so-called ‘Humean Principle’ that causes must be distinct from their effects is argued to be a genuine barrier to any purported reconciliation, provided causal particularism is retained; but extensive arguments are provided for the rejection of causal particularism. It is then explained (...) how the reconciliation of the causal theory with disjunctivism can proceed on the basis of an ontology of facts. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate (...) representation of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

In this paper we begin categorizing a plurality of possible worlds on the basis of permitting or not permitting ontologically different things to be causally connected. We build the work on the dual principle that all universes are causally closed either because no universe causes anything outside itself or because no universe has anything in it that is caused by another universe.

Philosophers of dispositionalism deny the Humean account of causality in terms of constant conjunction, contiguity, temporal priority and contingency. And some of them go further to explain the causal relation not between events or objects, but between properties, in terms of reciprocity, simultaneity, ubiquity, intentionality and holism. But their exposition seems to remain fragmented even though they try to make use of the notions of intentionality and holim. I would inquire reasons why it is piecemeal, by analysing that they employ (...) these notions of intentionality and holism which has been constructed within the dualistic tradition. If one wants to make the dispositional project to be powerful, she should look for the notions of intentionality and holism which are free of the dualistic traits and which have been constructed in the tradition of naturalism. The concept of integrationality may be a candidate for such a task. This conception was coined in Zhongyong under the name of cheng in that there is nothing without cheng, and was developed in one of Sok-hon Ham's thesis that any entity in the world contains "seed" within it to realize objectives shared by all involved. Humans are privileged and distinct from other natures, but there is continuity between them. An example of the integrationality applied to the case of humans would be that realization of myself and realizations of all others are one and not two. I would summarize notions of "cheng" and "seed" by offering the integrationality thesis, that is, that there is integrationality in any entity like dispositions such that the integrationality is a power to realize the embedded objective of it in the context where it interacts with all others. I would claim that integrationality is a metaphysical basis for a way of human thinking, by arguing that it is a necessary part of presupposition for our understanding of the world without which the world is not intelligible. The notion of integrationality is involved empirically as well as conceptually. Empirically, there are numerous reports from physics, biology and information science, which provide with a clue which may well be taken to show the ubiquitous integrationality. But some conceptual considerations would also indicate necessarily toward the same direction. These would include various theses of ontology, epistemology, disposition, modality, naturalized intentionality, fitting and topics like these. I will investigate some of them in order to justify my claim of this paper. (shrink)

This paper investigates Newton’s ontology of space in order to determine its commitment, if any, to both Cambridge neo-Platonism, which posits an incorporeal basis for space, and substantivalism, which regards space as a form of substance or entity. A non-substantivalist interpretation of Newton’s theory has been famously championed by Howard Stein and Robert DiSalle, among others, while both Stein and the early work of J. E. McGuire have downplayed the influence of Cambridge neo-Platonism on various aspects of Newton’s own (...) spatial hypotheses. Both of these assertions will be shown to be problematic on various grounds, with special emphasis placed on Stein’s influential case for a non-substantivalist reading. Our analysis will strive, nonetheless, to reveal the unique or forward-looking aspects of Newton’s approach, most notably, his critical assessment of substance ontologies, that help to distinguish his theory of space from his neo-Platonic contemporaries and predecessors. (shrink)

[In Czech] Merleau-Ponty holds that Husserl’s descriptions of the body go beyond the conceptual framework of subject-object ontology to which his philosophy is usually thought to conform. Merleau-Ponty says of his own philosophy that it is founded on the circularity in the body; that is, on the fact that from the ontological point of view, perception and availability to be perceived, are one and the same in the body. The inseparability of these two aspects of the body he calls (...) "flesh" (chair). According to Husserl, I perceive my body such that in a certain perceived object I also co-perceive sensations roused by the perception of that object – I observe the “consequential parallel” between two series of objective and subjective phenomena. Husserl argues that the unity of the body should be descrived as a double unity, and the body as a subject-object. In this article I analyse Husserl’s example of two hands of the same body touching mutually and, following Merleau-Ponty, I attempt to show that the body can appear to itself as an object only on the basis of a differentiation of the body as a particular field of perceiving. The body as a double unity of subject and object is therefore grounded in the body as a pre-objective and pre-subjective field; that is, in flesh as Merleau-Ponty understands it. This is also the point of departure for an original conception of ontology as we find it in his later philosophy. [In Czech language.]. (shrink)

Contemporary theoretical physics is divided into diversified theories of different phenomena. These are characteristically frameworks for giving mathematical descriptions of perceptions, in the absence of understandable explanations or a unified worldview. This is not an optimal state of affairs, for people by nature desire to understand; this sets a major obstacle for an optimal progress rate of physics, for understandable explanations are more prolific of new predictions and applications than non-understandable explanations. Disunification in physics can be remedied only by discovering (...) an understandable ontology and applying it as the basis of unifying explanations of phenomena that were earlier explained by different theories. Due to disunified physics and the nature of traditional analysis in philosophy, there is no consensus about central concepts such as time, possibility and truth. It is suggested that philosophical analysis would be more prolific of understandable and applicable concepts, were it complemented by a method of unification. (shrink)

According to the accepted translation-failure interpretation, the problem of incommensurability involves the nature of the meaning-referential relation between scientific languages. The incommensurability thesis is that some competing scientific languages are mutually untranslatable due to the radical variance of meaning or/and reference of the terms they employ. I argue that this interpretation faces many difficulties and cannot give us a tenable, coherent, and integrated notion of incommensurability. It has to be rejected. ;On the basis of two case studies, I find (...) that the confrontations between many classical incommensurable languages are not confrontations between two untranslatable languages with different distribution of truth values, but rather the confrontations between incompatible fundamental presuppositions at the ontological level. We can always identify a truth-value gap between two incommensurable languages. Such a truth-value gap indicates a communication breakdown between the two language communities on the one hand, and is caused by the incompatible fundamental presuppositions underlying them on the other. ;I thereby identify the truth-value functional relationship between sentences, instead of the meaning-referential relationship between terms, as the dominant semantic relation between two incommensurable languages. According to my presuppositional interpretation of incommensurability, the real secret of incommensurability lies in the ontological setup of two competing presuppositional languages. When two presuppositional languages with incompatible factual commitments encounter with each other, the confrontation leads to a truth-value gap, and consequently a communication breakdown between them. Formally put, two scientific languages are incommensurable when core sentences of one language, which have truth values when considered within its own context, lack truth values when considered within the context of the other due to an ontological gap between them. ;The presuppositional interpretation makes many significant contributions to the discussion of the issue of incommensurability and the related metaphysical and epistemological issues: It confirms the existence of the phenomenon of incommensurability and makes it metaphysically and epistemologically significant. It establishes the tenability and integrity of the notion of incommensurability. It avoids many alleged unattractive epistemological and metaphysical consequences of the translation-failure interpretation. (shrink)