The Ontology of Knowledge (OK) states: The laws of the world cannot be distinguished from the laws by which representation emerges from intensional thought. The laws of a physical world in vis-à-vis are not necessary. The forms of the world resulting from these laws cannot be distinguished from the laws of thought. They have no object. (see appendix I) OK seems to make of Knowledge, the substance from which the subject gives rise for himself to a representation (...) of the world and himself. The OK is realistic in that it states that there is a reality, but it also states clearly that the Reality is informal and that there is no being in reality, no other beings than those created by the subject in representation. That justifies the title of this article: Would the knowing subject be, in fact, the only being in the world, all other beings being only representation? While the Cogito guarantees the Existence of the "I" that enunciates it, is there no other Me than this "I"? As much as our mind can consent to the idea that objects and material facts are only representations, including the atoms of our own body, as much as it seems absurd to us, paradoxical, contrary to the evidence of every moment, the idea that "I" would be the one and only knowing subject. The first part of this article proposes, by a clarification of concepts and terms, to answer specifically to the question of the existence of other “I's” The second part will try to widen the spectrum of our reflection to study, within the conceptual framework of the OK, the possibility of a supra-human thought/knowledge. Of a “Us” . (shrink)

In this article, we would like to clarify the concept of transcendental Subject according to the Ontology of Knowledge (OK), not with the idea of contradicting but with that of completing the Kantian vision. We would nevertheless like to show how Kant's lack of a true transcendence of the subject limits and disorients the development of his thought. We would finally like to trace some tracks towards new ontological (and scientific) options that the OK makes possible beyond those (...) which the Kantian critique entailed. (shrink)

Despite the efforts undertaken to separate scientific reasoning and metaphysical considerations, despite the rigor of construction of mathematics, these are not, in their very foundations, independent of the modalities, of the laws of representation of the world. The OdC shows that the logical Facts Exist neither more nor less than the Facts of the world which are Facts of Knowledge. Mathematical facts are representation facts. The primary objective of this article is to integrate the subject into mathematics as a (...) mode of emergence of meaning and then to evaluate its consequences. (shrink)

The deterministic or probabilistic laws of our representations and our science do not link what “is” to what “will be” but what “I know” to what “I could know”. Consistency is not a predicate on the physical laws of the world but on the logical laws of Meaning. If you cannot convince yourself of that. If you want to believe that the Softmatter of the Meaning cannot be more consistent than the Hardmatter of the physical world. Think again ... ...and (...) try to answer this question : Why would it be less unlikely for a physical world to evolve from the big bang to individuated knowing persons than for an amorphous interdependence to assemble (logically) individuated representations of the world ? (shrink)

From 1) the main ideas of the Kantian CRP - 2) a reinterpretation of the concept of transcendental subject and - 3) the logical principle of Individuation, we propose a new ontology in which subject and object are of the same reality. We describe the dynamic principle by which the Existence of the subject emerges from formless meta-substance and separates into an animated representation of the world.

The Ontology of Knowledge (OK) does not claim to expose the truth of reality but only to propose a coherent model of representation according to which: -Reality is not subject to form or time. -The Knowing Subject is a wave of meaning running through the immobile reality.

[issue 20211210] Qbism (quantum bayesism) is a philosophical interpretation of quantum mechanics (QM) that places the agent and its expectations at the heart of theory. The QBists advocate a "subjectivist" interpretation of probabilities that allows to understand the quantum laws of Born and to eliminate certain enigmas of interpretation of the QM going "beyond" the interpretation of Copenhagen. The Ontology of Knowledge (OK) is in agreement with the main ideas of the Qbism. For the OdC indeed: -The agent (...) is the focal point of the representation -Representation is specific to the agent -There are no "states of the world" but only "states of knowledge" -There is no probability of evolution of the "state of the world" but only probabilities, for the subject, of evolution of his Knowledge. -These probabilities lead to the future actions and experiences of the agent. The aim of this article is to propose, according to the OdC, ways for an extension of the explanatory power of the QBism. (shrink)

We can only know what determines us as being and by the fact that it determines us as being. Our knowledge is therefore logically limited to what determines us as being. Since representation is defined as the act that makes knowledge dicible, our representation is logically limited to what dynamically determines us as being. Our representation is included in our becoming. Nothing that we represent, no infinite, can exceed the mere necessity of our becoming. The world, my physical (...) being and my consciousness are subsumed by the necessity of my becoming. We know nothing but “we become” To the question "Is there anything else to know?" we can give no logical answer -/- Summary: Reality is pure logical interdependence, immanent, formless, unspeakable. Logos is a principle of order in this interdependence. Individuation is the necessary asymptote of any instance of the Logos. Each knowing subject is Individuation, a mode of order among infinites of infinites of possible modes of order. Everything that appears to the subject as Existing participates in his Individuation. This convergence into Individuation defines a perspective that gives meaning. The subject is representation. It is in this representation that exist the subject, objects and laws of the world. Without subject there are no objects, no laws, no framework. The representation is not isomorphism but morphogenesis. The physical world and the Spirit have the same logical nature: they are categories of representation. The representation is animated because meaning is an Act. Representation is limited by a horizon of meaning. Below this horizon the subject represents the universe and itself. Beyond this horizon there is no prevailing space, time or form. The predicate expresses, below the horizon of meaning, a necessity whose source is beyond this horizon, unfathomable. The OK is neither materialism nor idealism and frees itself from any psychological preconceptions. The OK does not propose an "other reality" than that described by common sense or science, but another mode of representation. The OK is compatible with the current state of science, while offering new interpretive avenues. The OK differs from ontic structural realism (OSR) in various ways: Just like being, the relationship is representation, The knowing subject is present in any representation, the real is non-founded. (shrink)

The following article will attempt to highlight four questions which, in my opinion, are left unanswered (or overlooked) by QBism and to show the answers that the Ontology of Knowledge (OK) can provide. ● How does the subject come to exist for itself, individuated and persistent? ● From what common reality do world, mind, and meaning emerge? ● How does meaning emerge from the mathematical fact of probabilistic expectation? ● Is meaning animated by its own nature?

Objective The relations between thought and reality are studied in many fields of philosophy and science. Examples include ontology and metaphysics in general, linguistics, neuroscience and even mathematics. Each one has its postulates, its language, its methods and its own constraints. It would be unreasonable, however, for them to ignore each other. In the pages that follow we will try to identify areas of proximity between the ideas of contemporary philosophers of language and those issued mainly by Ontology (...) of Knowledge but also by mathematics and neuroscience. We will try to take advantage of the clarity and the perfect structuring of the lecture « La philosophie contemporaine du langage » (the contemporary philosophy of language) given by Professor Denis Vernant . We will make use of this lecture, both for the ideas presented and as a reference process. The goal of this article is to bring out, through a benevolent confrontation, new ideas for the benefit of knowledge in general. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

This article investigates the challenges posed by the reliability of knowledge in neurophenomenology and its connection to reality. Neurophenomenological research seeks to understand the intricate relationship between human consciousness, cognition, and the underlying neural processes. However, the subjective nature of conscious experiences presents unique epistemic challenges in determining the reliability of the knowledge generated in this research. Personal factors such as beliefs, emotions, and cultural backgrounds influence subjective experiences, which vary from individual to individual. On the other hand, (...) scientific knowledge aims to uncover universal truths based on empirical observations and objective principles. Reconciling the subjective and objective realms presents a significant challenge in determining the reliability of knowledge generated through neurophenomenological research. This article aims to examine the inherent limitations and challenges of neurophenomenological research to shed light on the complexities involved in understanding the nature of knowledge itself. This article highlights that the ontological implications of the reliability of knowledge in neurophenomenology arise from the question of how subjective experiences relate to objective reality. Understanding the neural correlates and mechanisms behind subjective experiences can provide insight into the underlying ontological nature of consciousness. (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)

The view of nature we adopt in the natural attitude is determined by common sense, without which we could not survive. Classical physics is modelled on this common-sense view of nature, and uses mathematics to formalise our natural understanding of the causes and effects we observe in time and space when we select subsystems of nature for modelling. But in modern physics, we do not go beyond the realm of common sense by augmenting our knowledge of what is going (...) on in nature. Rather, we have measurements that we do not understand, so we know nothing about the ontology of what we measure. We help ourselves by using entities from mathematics, which we fully understand ontologically. But we have no ontology of the reality of modern physics; we have only what we can assert mathematically. In this paper, we describe the ontology of classical and modern physics against this background and show how it relates to the ontology of common sense and of mathematics. (shrink)

In order to develop the ontology of tendencies for use in the representation of medical knowledge, tendencies are compared with other kinds of entities possessing the realizable-realization-structure, specifically: dispositions, propensities, abilities and virtues. The peculiarities of tendencies are discussed and a standard schema of tendency ascription is developed in order to represent the relations between the ascriptions of tendency tokens to particulars and the ascriptions of tendency types to universals. Two non-standard cases and their epistemic variants are discussed.

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)

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 International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.

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)

This work aims to make tense logic a more robust tool for ontologists, philosophers, knowledge engineers and programmers by outlining a fusion of tense logic and ontology of time. In order to make tense logic better understandable, the central formal primitives of standard tense logic are derived as theorems from an informal and intuitive ontology of time. In order to make formulation of temporal propositions easier, temporal operators that were introduced by Georg Henrik von Wright are developed, (...) and mapped to the ontology of time. (shrink)

William Oliver Martin published "The Order and Integration of Knowledge" in 1957 to address the problem of the nature and the order of various kinds of knowledge; in particular, the theoretical problem of how one kind of knowledge is related to another kind. Martin characterizes kinds of knowledge as being either autonomous or synthetic. The latter are reducible to two or more of the autonomous (or irreducible) kinds of knowledge, viz., history (H), metaphysics (Meta), theology (...) (T), formal logic (FL), mathematics (Math), and generalizations of experimental science (G). Metaphysics and theology constitute the two domains of the ontological context while history and experimental science are the two domains of the phenomenological context. The relation of one kind of knowledge to another may be instrumental, constitutive, and/or regulative. For instance, historical propositions are constitutive of G, metaphysical propositions are regulative of G, and propositions in formal logic and mathematics are instrumental to G. Theological propositions are not related to G and so there is no conflict between science and theology. Martin's work sheds light on the possible areas of incompatibility between science and religion. (shrink)

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

We can locate the problematic of time within three philosophical questions, which respectively designate three central areas of philosophical reflection and contemplation. These are: 1) The ontological question, i.e. 'what is being?' 2) The epistemological question, i.e. 'what can we know with certainty?' 3) The existential question, i.e. 'what is the meaning of existence?' These three questions, which are philosophical, but also scientific and political, as they underline the political and moral question of truth and justice, arise from the phenomenon (...) of time, the irreversible constant flow of phenomena that undermines every claim to absolute knowledge. The purpose of this essay is to illuminate the importance of time for philosophical thought and, more generally, for human social and psychical life, in the context of the ontology of Cornelius Castoriadis. Castoriadis, who asserted that " being is time – and not in the horizon of time " , correlated history to society and being to temporality within the social-historical stratum, the ontological plane created by human existence, where " existence is signification ". Time is interpreted as the creation and destruction of forms in a magmatic, layered with a non-regular stratification, reality, where the social-historical manifests as the creation of collective human activity, in the manner of social imaginary significations. This notion of temporality is accompanied by a profound criticism of traditional rationalistic philosophy, to which Castoriadis assigns the name 'ensemblistic/identitary', that highlights the necessity of a new, magmatic ontology, based on the primacy of time. (shrink)

Intellectual property law tends to be viewed as the only (or most significant) mechanism for achieving policy goals relating to innovation assets. Yet more creative and effective solutions are often available. When analysed from a transdisciplinary perspective, relying on the cooperative efforts of researchers from fields other than law, innovation governance is characterized not simply as the product of legal rules, but as a function of the interaction of legal rules, practices and institutions. When policy-makers seek to identify conditions under (...) which the creation, use and exchange of innovation assets flourishes, care should be taken to focus on this combination of factors. This article describes the development of an ontology—a computerized method of representing knowledge as concepts and relations between concepts—to convey such understanding. Policy makers (and researchers) are provided with an organized, accessible representation of innovation governance that enriches their understanding and improves their decision-making. (shrink)

The suggestion of Logical Quanta (LQ) is a bidirectional synthesis of the theory of logos of Maximus the Confessor and the philosophical interpretation of quantum mechanics. The result of such a synthesis is enrichment to the ontology of classical mechanics that enable us to have a unified view and an explanatory frame of the whole cosmos. It also enables us to overcome the Cartesian duality both on biology and the interaction of body and mind. Finally, one can reconstruct a (...) new understanding of religion. (shrink)

This study conducts an epistemological and contextual discourse analysis of the idea of knowledge in the philosophy of the 20th century. The main key stones of this work are as follows: the identification of the essential characteristics indicating the ontological genesis of the existing crisis of epistemological and ethical foundations; consideration of the main distinctive features of knowledge interpretation in epistemology and contextualism as a possible knowledge production instrument; study of the possibility of restoring an integral picture (...) of the world based on phenomenological ontologies; study of possibilities in the language domain from a hermeneutical point of view in the light of the resolution of epistemological contradictions. For all people interested in modern philosophy. (shrink)

The main objective of the paper is to provide a conceptual apparatus of a general logical theory of language communication. The aim of the paper is to outline a formal-logical theory of language in which the concepts of the phenomenon of language communication and language communication in general are defined and some conditions for their adequacy are formulated. The theory explicates the key notions of contemporary syntax, semantics, and pragmatics. The theory is formalized on two levels: token-level and type-level. As (...) such, it takes into account the dual – token and type – ontological character of linguistic entities. The basic notions of the theory: language communication, meaning and interpretation are introduced on the second, type-level of formalization, and their required prior formalization of some of the notions introduced on the first, token-level; among others, the notion of an act of communication. Owing to the theory, it is possible to address the problems of adequacy of both empirical acts of communication and of language communication in general. All the conditions of adequacy of communication discussed in the presented paper, are valid for one-way communication (sender-recipient); nevertheless, they can also apply to the reverse direction of language communication (recipient-sender). Therefore, they concern the problem of two-way understanding in language communication. (shrink)

Current controversies about knowledge integration reflect conflicting ideas of what it means to “take Indigenous knowledge seriously”. While there is increased interest in integrating Indigenous and Western scientific knowledge in various disciplines such as anthropology and ethnobiology, integration projects are often accused of recognizing Indigenous knowledge only insofar as it is useful for Western scientists. The aim of this article is to use tools from philosophy of science to develop a model of both successful integration and (...) integration failures. On the one hand, I argue that cross-cultural recognition of property clusters leads to an ontological overlap that makes knowledge integration often epistemically productive and socially useful. On the other hand, I argue that knowledge integration is limited by ontological divergence. Adequate models of Indigenous knowledge will therefore have to take integration failures seriously and I argue that integration efforts need to be complemented by a political notion of ontological self-determination. (shrink)

We will argue here, that one of the salient messages of standard quantum formalism implies a failure of Classical Theory of Knowledge (hereafter CTK) which is primarily based on the presumption that, our knowledge is predetermined by Nature. This failure provides pointers against the classically held ontological definiteness of future. Quantum formalism admits interpretation , that suggests, that there is no such thing as ‘universal global present’ in the sense of being able to confirm a complete set of (...) facts of matter about it, unless this is coupled with a specific observation recipe. (shrink)

Researchers of different calibres from phenomenology to posthumanism and beyond have outlined the processuality of the body and the environment (Alaimo 2010; Gendlin 2017), stressing the importance of changing the ontological presuppositions of the body-environment bond (Schoeller and Duanetz 2018: 131), since the existing models facilitate the alienation and intangibility of the environment, thus, leading to reduced societal awareness of the importance of environmental issues (Neimanis, Åsberg, Hedrén 2015: 73–74). In this article, I argue that in questions relating to food, (...) product-oriented ideologies dominate over process-oriented ethicality, in part, due to an embodied and lived ideology that can be best described via the concept of reactive nihilism and substance ontology. The article aims to demonstrate a necessity to rethink and recontextualize situated practices as alternatives to the prevalent ontogenealogies of the Global North. By problematizing the complimentary axis of reactive nihilism in food contexts and the genealogy of contemporary pop food “ethics”, I argue for a shift away from product-oriented ideologies and supplementation of the ontologies-we-live-by with situated alternative models. In the first part of the article, I use a genealogical approach, tracing the predominant meaning cluster encapsulated in Feuerbach’s famous expression “Man is what he eats” (Feuerbach 1846-1866, X: 5) in today’s contexts. To illustrate the leading discourses, I follow a Deleuzian understanding of the concept of “reactive nihilism” and contextualize food choices with the dominant understanding of the body in the Global North. With this discussion, I hope to provide context for the need to reconsider local ontologies as knowledge resources for the future. In the second part of the article, the framework present in the Global North is then complemented by a discussion of some local factors, to suggest ways in which global food philosophy and, particularly, lifestyle choices of food consumption could benefit from acknowledging the knowledge embedded in food consumption trends in Latvia. (shrink)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations (...) dedicated to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (...) (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led to (...) a proliferation of ontologies of varying scope and quality. We define one strategy for achieving quality assurance of ontologies—a plan of action already adopted by a large community of collaborating ontologists—which consists in subjecting ontologies to a process of peer review analogous to that which is applied to scientific journal articles. (shrink)

Argument that Marx has a realist ontology and a correspondence theory of truth. His views are compared to both Hegel's and Kant's. This interpretation departs from more Hegelian, 'idealist' interpretations that often rely on misunderstanding some of the work of the early Marx. There is also a discussion and partial defence of Lenin's Materialism and Empirio-Criticism.

Bernard Lonergan has argued for a theory of cognition that is transcendentally secure, that is, one such that any plausible attempt to refute it must presuppose its correctness, and one that also grounds a correct metaphysics and ontology. His proposal combines an identity theory of knowledge with an intentional relation between knower and known. It depends in a crucial way upon an appropriation of one’s own cognitional motives and acts, that is, upon “knowing one’s own knowing.” I argue (...) that because of conflicts between the identity and intentionality components of the theory, rational self-appropriation cannot, as Lonergan claims, be an iteration of just the same acts by which we acquire other sorts of knowledge. I propose an amended theory in which the relation between intending-subject and intended-object of first-level cognition becomes, in RSA, a numerical identity of knower and known and of the epistemic and the ontological. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

We present a preliminary high-level formal theory, grounded on knowledge representation techniques and foundational ontologies, for the uniform and integrated representation of the different kinds of (quali- tative and quantitative) knowledge involved in the designing process. We discuss the conceptual nature of engineering design by individuating and analyzing the involved notions. These notions are then formally charac- terized by extending the DOLCE foundational ontology. Our ultimate purpose is twofold: (i) to contribute to foundational issues of design; and (...) (ii) to support the development of advanced modelling systems for (qualitative and quantitative) representation of design knowledge. (shrink)

All eyes are turned towards genomic data and models as the source of knowledge about whether human races exist or not. Will genomic science make the final decision about whether racial realism (e.g., racial population naturalism) or anti-realism (e.g., racial skepticism) is correct? We think not. We believe that the results of even our best and most impressive genomic technologies underdetermine whether bio-genomic races exist, or not. First, different sub-disciplines of biology interested in population structure employ distinct concepts, aims, (...) measures, and models, producing cross-cutting categorizations of population subdivisions rather than a single, universal bio-genomic concept of "race." Second, within each sub-discipline (e.g., conservation biology, phylogenetics), genomic results are consistent with, and map multiply to, racial realism and anti-realism. Indeed, racial ontologies are constructed conventionally, rather than discovered. We thus defend a /constructivist conventionalism/ about bio-genomic racial ontology. Choices and conventions must always be made in identifying particular kinds of groups. Political agendas, social programs, and moral questions premised on the existence of naturalistic race must accept that no scientifically grounded racial ontology is forthcoming, and adjust presumptions, practices, and projects accordingly. (shrink)

This is an exploration of the importance of the collocation approach in investigating language. It underpins a new conception of grammar that is: (i) intrinsically connected with lexis; (ii) investigates the language as it is naturally used in life; (iii) can be developed as a corpus-driven grammar. The collocation approach in language exploration is also examined from the perspective of some recent developments in the philosophy of language. In conclusion, I defend the identity between philosophical ontology, linguistic ontology (...) and computational ontology. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to (...) move beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

A condensed summary of the adventures of ideas (1990-2020). Methodology of evolutionary-phenomenological constitution of Consciousness. Vector (BeVector) of Consciousness. Consciousness is a qualitative vector quantity. Vector of Consciousness as a synthesizing category, eidos-prototecton, intentional meta-observer. The development of the ideas of Pierre Teilhard de Chardin, Brentano, Husserl, Bergson, Florensky, Losev, Mamardashvili, Nalimov. Dialectic of Eidos and Logos. "Curve line" of the Consciousness Vector from space and time. The lower and upper sides of the "abyss of being". The existential tension of (...) being. Five reference “points” (existential-extremum) - world events in the evolution of Consciousness from “homo habilis” to “homo sapiens sapiens”. “Prometheus Effect". Inversion and reversion of Сonsciousness. "Open" and "closed" Сonsciousness. Consciousness and Self-Consciousness. Protogeometer: fall in the future, in the "EgoLand". The problem of justification/substantiation of mathematics (knowledge) is an ontological problem. The crisis of ontology and ontological limits of cognition. Ontological structure of space. The project of constructive dialectic ontology. The methodology of dialectical-ontological construction (modeling): conceptual-figure synthesis, total unification of matter, coincidence of ontological opposites, primordial Meta-Axioma and Superprinciple, vector (bivector) of the absolute state (states) of matter (absolute forms of existence). The ontological "celestial triangle" (Plato). Ontological invariants of the Universum and their ontological paths. Ontological and gnoseological dimensions of space. Triune (ontological) space of nine gnoseological dimensions: absolute rest (linear state, "Continuum")+ absolute motion (absolute vortex, "Discretuum") + absolute becoming (absolute wave, "Dis-Continuum"). Primordial generating structure: ontological framework, ontological carcass and ontological foundation. Ontological (structural, cosmic) memory - the semantic core of the conceptual construction of the Universum being as an eternal process of generation of new meanings and structures. Consciousness is an absolute (unconditional) attractor of meanings, a univalent phenomenon of ontological memory, which manifests itself at a certain level of the Universum being. Ontological space-MatterMemory-Ontological time (S-MM-T). Ontological Rhythm and Cycle. The nature and structure of ontological time. Natural (absolute) determinism. (shrink)

Discussions of group knowledge typically focus on whether a group’s knowledge that p reduces to group members’ knowledge that p. Drawing on the cumulative reading of collective knowledge ascriptions and considerations about the importance of the division of epistemic labour, I argue what I call the Fragmented Knowledge account, which allows for more complex relations between individual and collective knowledge. According to this account, a group can know an answer to a question in virtue (...) of members of the group knowing parts of that answer, when the whole answer is available to group-level action. I argue that this account explains a swathe of central cases of group knowledge, as well as explaining some central features of group knowledge. (shrink)

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

Ontologies are some of the most central constructs in today's large plethora of knowledge technologies, namely in the context of the semantic web. As their coinage indicates, they are direct heirs to the ontological investigations in the long Western philosophical tradition, but it is not easy to make bridges between them. Contemporary ontological commitments often take causality as a central aspect for the ur-segregation of entities, especially in scientific upper ontologies; theories of causality and philosophical ontological investigations often go (...) hand-in-hand, and were essentially inseparable in medieval thought. This constitutes the foundation for a bridge, and this article analyzes the causality-based ontology of the late medieval philosopher Dietrich of Freiberg from the viewpoint of today's upper-ontology engineering. In this bridging attempt, it offers a translation into English of the first part of Dietrich's De origine (abbreviated title) that is a compromise between traditional scholarly translations of medieval Latin philosophical texts and contemporary ontology. (shrink)

The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable strategy for (...) the alignment, reconciliation and integration of diverse and disparate data. The scope of OE includes: consistent capture of knowledge pertaining to the types of entities involved; facilitation of cooperation among diverse group of experts; more effective ongoing curation, and update of manufacturing data; collaborative design and knowledge reuse. As an illustrative case study we propose an ontology focused on the representation of composite materials focusing in particular on the class of Functionally Graded Materials (FGM) in particular. The scope of the ontology is to provide information about the components of such materials, the manufacturing processes involved in creation, and diversity of application ranging from additive manufacturing to restorative dentistry. The ontology is developed using Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). (shrink)

My topic is the materialist appropriation of empiricism – as conveyed in the ‘minimal credo’ nihil est in intellectu quod non fuerit in sensu (which interestingly is not just a phrase repeated from Hobbes and Locke to Diderot, but is also a medical phrase, used by Harvey, Mandeville and others). That is, canonical empiricists like Locke go out of their way to state that their project to investigate and articulate the ‘logic of ideas’ is not a scientific project: “I shall (...) not at present meddle with the Physical consideration of the Mind” (Essay, I.i.2, in Locke 1975; which Kant gets exactly wrong in his reading of Locke, in the Preface to the A edition of the first Critique). Indeed, I have suggested elsewhere, contrary to a prevalent reading of Locke, that the Essay is not the extension to the study of the mind of the methods of natural philosophy; that he is actually not the “underlabourer” of Newton and Boyle he claims politely to be in the Epistle to the Reader (Wolfe and Salter 2009, Wolfe 2010). Rather, Locke says quite directly if we pay heed to such passages, “Our Business here is not to know all things, but those which concern our Conduct” (Essay, I.i.6). There would be more to say here about what this implies for our understanding of empiricism (see Norton 1981 and Gaukroger 2005), but instead I shall focus on a different aspect of this episode: how a non-naturalistic claim which falls under what we now call epistemology (a claim about the senses as the source of knowledge) becomes an ontology – materialism. That is, how an empiricist claim could shift from being about the sources of knowledge to being about the nature of reality (and/or the mind, in which case it needs, as David Hartley saw and Denis Diderot proclaimed more overtly, an account of the relation between mental processes and the brain). (David Armstrong, for one, denied that there could be an identification between empiricism and materialism on this point: eighteenth-century history of science seems to prove him wrong: see Armstrong 1968 and 1978.) Put differently, I want to examine the shift from the logic of ideas in the seventeenth century (Locke) to an eighteenth-century focus on what kind of ‘world’ the senses give us (Condillac), to an assertion that there is only one substance in the universe (Diderot, giving a materialist cast to Spinozism), and that we need an account of the material substrate of mental life. This is neither a ‘scientific empiricism’ nor a linear developmental process from philosophical empiricism to natural science, but something else again: the unpredictable emergence of an ontology on empiricist grounds. (shrink)

The problem addressed in this article is the relationship between law and morality. It is asked (1) to what extent law and morality are connected and separated and (2) since when has it been so. To the extent that law and morality are distinct normative orders, it is asked (3) whether they rule exactly the same behaviors or whether each order rules dierent kinds of behaviors. If they rule at least some of the same behaviors, it is asked (4) whether (...) there can be antinomies (contradictions) between them. If there are an- tinomies, it is asked (5) whether the antinomies are only apparent (prima facie) and are therefore mistakes of human reason, or are definite and real. If the antinomies are apparent or real, it is asked (6) whether law or morality prevails (or should prevail) in the case of an antinomy. If one of these prevails, it is asked (7) whether this is always so, or whether law sometimes prevails (and should prevail) over morality and vice versa. In the case of existing coherence or at least solvable antinomies between law and morality, it is asked (8) whether the consequent achieved unity of practical reason is a specifically moral unity and whether it is a matter of cognition, of institutionalization, of individual or collective construction, or of consensus. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing (...) in abstract fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (shrink)

How does Quine fare in the first decades of the twenty-first century? In this paper I examine a cluster of Quinean theses that, I believe, are especially fruitful in meeting some of the current challenges of epistemology and ontology. These theses offer an alternative to the traditional bifurcations of truth and knowledge into factual and conceptual-pragmatic-conventional, the traditional conception of a foundation for knowledge, and traditional realism. To make the most of Quine’s ideas, however, we have to (...) take an active stance: accept some of his ideas and reject others, sort different versions of the relevant ideas, sharpen or revise some of the ideas, connect them with new, non-Quinean ideas, and so on. As a result the paper pits Quine against Quine, in an attempt to identify those Quinean ideas that have a lasting value and sketch potential developments. (shrink)

Renaissance philosopher, mathematician, and theologian Nicholas of Cusa (1401-1464) said that there is no proportion between the finite mind and the infinite. He is fond of saying reason cannot fully comprehend the infinite. That our best hope for attaining a vision and understanding of infinite things is by mathematics and by the use of contemplating symbols, which help us grasp "the absolute infinite". By the late 19th century, there is a decisive intervention in mathematics and its philosophy: the philosophical mathematician (...) Georg Cantor (1845-1918) says that between the realm of the finite and the absolute infinite, there is an intermediate realm partaking in properties in a certain sense of both the finite and the infinite: the transfinite realm. Like the finite, the transfinite realm is a realm of mathematical objects, numbers, and knowledge. Like the absolute infinite, the transfinite is a form of infinity insofar as transfinite sets and numbers transcend any finite number. Echoing Cusanus and neo-Platonism, Cantor says that the transfinite sequence of all ordinals is a symbol of the absolutely infinite, that is, God. This paper considers how the doctrine of symbolism and the philosophers' different commitments to the laws of logic, especially the Law of Non-Contradiction (LNC), enables these thinkers to articulate a transcendental apophatic approach to divinity. (shrink)