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 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)

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 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)

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)

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)

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)

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)

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)

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)

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)

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)

[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)

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)

The significance of and the role played by Knowledge Management (KM) is ever increasing in today's business and organizational decision-making environment. This paper attempts to underline the importance of organizing knowledge not for its own sake, but for its efficient use in organizational decision making. The tremendous explosion of knowledge resources, both electronic and conventional, within the last few decades calls for an understanding of how knowledge is organized for management of data and information. This is (...) so for the reason that they can be proficiently employed to create value and utility. This also calls for a search for 'relevance' in KM with regard to its situated nature in different contexts within which knowledge is situated, and that which nevertheless indirectly refers to its ontological scaffolding. We have devised two simple mathematical models of reference with regard to the design of the systems mostly intended for organizing knowledge in knowledge organizations for its most efficient utilization. The model specifies several unique scenarios aided by discovery of arguments related to its ontological framework within which knowledge is situated. Several contexts were drawn to draw inferences from the research study. The results bear relevance to knowledge managers who make important decisions for realization of organizational goals and objectives. (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 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)

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.

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

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

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)

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)

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)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. (...) Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (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)

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)

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)

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.

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and (...) use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (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)

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)

The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world (...) actors and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts. Of particular importance to the Cognitive Process Ontology is the class Representation that is Warranted. Such a representation is descriptive in nature and deserving of trust in its veridicality. The latter is because a Representation that is Warranted is always produced by a process that was vetted (or successfully designed) to reliably produce veridical representations. As such, Representations that are Warranted are what in other contexts we might refer to as ‘items of knowledge’. (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)

Where humans can manipulate and integrate the information they receive in subtle and ever changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, (...) chemistry, mathematics, medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

The orbital debris problem presents an opportunity for inter-agency and international cooperation toward the mutually beneficial goals of debris prevention, mitigation, remediation, and improved space situational awareness (SSA). Achieving these goals requires sharing orbital debris and other SSA data. Toward this, I present an ontological architecture for the orbital debris and broader SSA domain, taking steps in the creation of an orbital debris ontology (ODO). The purpose of this ontological system is to (I) represent general orbital debris and SSA (...) domain knowledge, (II) structure, and standardize where needed, orbital data and terminology, and (III) foster semantic interoperability and data-sharing. In doing so I hope to (IV) contribute to solving the orbital debris problem, improving peaceful global SSA, and ensuring safe space travel for future generations. (shrink)

Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not (...) be comparable if the ontological commitments employed differ. Comparisons between different nomenclatures cannot assume that either the naming practices or the object to which these names are intended to apply identifies some universally agreed upon object of interest. Investigating this suite of philosophical problems, I explore the role grey nomenclatures play in classification. ‘Grey nomenclatures’ are defined as those that employ names that are either intentionally or accidentally non-Linnaean. The classification of the lichen thallus (a symbiont) has been classified outside the Linnaean system by botanists relying on the International Code of Nomenclature for algae, fungi, and plants (ICN). But, I argue, the use of grey names is not isolated and does not occur exclusively within institutionalized naming practices. I suggest, ‘grey names’ also aptly describe nomenclatures employed by indigenous communities such as the Samí of Northern Finmark, the Sherpa of Nepal, and the Okanagan First Nations. I pay particular attention to how naming practices are employed in these communities; what ontological commitments they hold; for what purposes are these names used; and what anchors the community’s nomenclatural practices. Exploring the history of lichen naming and early ethnolichenological research, I then investigate the stakes that must be considered for any attempt to preserve, retain, integrate, or compare the knowledge contained in both academically formalized grey names and indigenous nomenclatures in a way that preserves their source-specific informational content. (shrink)

Ontology engineering is a hard and error-prone task, in which small changes may lead to errors, or even produce an inconsistent ontology. As ontologies grow in size, the need for automated methods for repairing inconsistencies while preserving as much of the original knowledge as possible increases. Most previous approaches to this task are based on removing a few axioms from the ontology to regain consistency. We propose a new method based on weakening these axioms to make (...) them less restrictive, employing the use of refinement operators. We introduce the theoretical framework for weakening DL ontologies, propose algorithms to repair ontologies based on the framework, and provide an analysis of the computational complexity. Through an empirical analysis made over real-life ontologies, we show that our approach preserves significantly more of the original knowledge of the ontology than removing axioms. (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?

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)

As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field (such as, in the first place, the Web Ontology Language - OWL) do not allow for the representation of concepts (...) in terms of typical traits. The need of representing concepts in terms of typical traits concerns almost every domain of real world knowledge, including medical domains. In particular, in this article we take into account the domain of mental disorders, starting from the DSM-5 descriptions of some specific disorders. We favour a hybrid approach to concept representation, in which ontology oriented formalisms are combined to a geometric representation of knowledge based on conceptual space. As a preliminary step to apply our proposal to mental disorder concepts, we started to develop an OWL ontology of the schizophrenia spectrum, which is as close as possible to the DSM-5 descriptions. (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)

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)

dolce, the first top-level ontology to be axiomatized, has remained stable for twenty years and today is broadly used in a variety of domains. dolce is inspired by cognitive and linguistic considerations and aims to model a commonsense view of reality, like the one human beings exploit in everyday life in areas as diverse as socio-technical systems, manufacturing, financial transactions and cultural heritage. dolce clearly lists the ontological choices it is based upon, relies on philosophical principles, is richly formalized, (...) and is built according to well-established ontological methodologies, e.g. OntoClean. Because of these features, it has inspired most of the existing top-level ontologies and has been used to develop or improve standards and public domain resources. Being a foundational ontology, dolce is not directly concerned with domain knowledge. Its purpose is to provide the general categories and relations needed to give a coherent view of reality, to integrate domain knowledge, and to mediate across domains. In these 20 years dolce has shown that applied ontologies can be stable and that interoperability across reference and domain ontologies is a reality. This paper briefly introduces the ontology and shows how to use it on a few modeling cases. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. (...) Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Aristotle, in Chapter 7 of his Categories, classifies habits and dispositions, as well as knowledge, among relatives. However, in Chapter 8 of the Categories, he affirms that habits, including knowledge, and dispositions, including unstable knowledge, are qualities. Thus, habits and dispositions in general, and knowledge in particular, seem to be subject to a ‘dual categorization’. At the end of Chapter 8 of the treatise, the issue of the dual categorization is explicitly raised. How can one and (...) the same thing be a quality and a relative? Aristotle gives two distinct solutions to this problem. Both have been criticized by some modern commentators : these solutions would amount to a rejection of the basic principles of the categorial system and, as such, to a sort of philosophical suicide. However, Aristotle’s early commentators, notably the Greek Neoplatonists and Boethius, made attempts to render both solutions plausible and compatible with the rest of the doctrine. Their attempts are not only of exegetical interest, they also contain some significant philosophical analyses concerning the categories. In what follows, I will present the abovementioned problem of dual categorization in Aristotle and the two solutions offered to it in Categories, 8, 11a20-38. I will then turn to the early reception of this text, and focus on the way the Greek Neoplatonists and Boethius tried to make Aristotle’s solutions more plausible. Throughout, I will try to establish in what sense habits and dispositions in general, and knowledge in particular, are relative. I will conclude with some remarks on the later reception of Categories, 8, 11a20-38 and on the problem of the ontological status of mental acts and states. (shrink)

The gulf between philosophical and formal ontology can and should be bridged. In this Editorial, I elaborate briefly on this subject.

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)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T (...) as a standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results (...) of protein research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)