Objective – is to formulate a methodological discourse regarding the place and role of the language interconnected with the process of socialization of a person and develop a systemic idea of the corresponding functional features. -/- Materials & Methods – this discourse is formulated on the basis of a systemic idea of the personality socialization, which, in turn, is realized using the structural-ontological method of studying the subject matter field in interdisciplinary researches. This method involves the construction of special (...) visual-graphic matrices that reflect the interaction of the primary process and the material of the studied system. -/- Results. The work with the structural-ontological matrix made it possible to analyze the functions of the language in the context of such significant factors of socialization as complex psychodynamics, civilization space and the function of reflection. At the same time, reflection is considered at the level of two plans – primary (reflection-bond) and secondary (reflection-splitting). This made it possible to deduce the idea of the role of language beyond the traditional framework of working with text and analyze the place of the language in the context of activities to establish a connection between individuals, which is realized in a specific cooperative situation (Shchedrovitsky). In particular, the look at language as a specific tool of civilizational rationing, the mechanism of which is provided through reflection-communication. Thus, the language is examined through the prism of its systemic influence on the morphology of the psyche. -/- Conclusions – a structural-ontological analysis of the place and role of language in the process of personality socialization has led us to construction of a hypothesis about the phenomenon of language discontentment, as a tendency to distance away ego-consciousness in the process of individuation from linguistic ontology. The arguments were also advanced in favor of the assumption regarding the peculiarities of the influence of language discontentment on cultural activities and the psychodynamic contribution of this phenomenon in the midlife crisis (Jung). (shrink)

This paper discusses attributively limited concrete objects such as disturbances (holes, folds, scratches etc), tropes, and attitudinal objects, which lack the sort of spatial location or part structures expected of them as concrete objects. The paper proposes an account in terms of (quasi-Fregean) abstraction, which has so far been applied only to abstract objects.

This essay explores the possibility of constructing a structural realist interpretation of spacetime theories that can resolve the ontological debate between substantivalists and relationists. Drawing on various structuralist approaches in the philosophy of mathematics, as well as on the theoretical complexities of general relativity, our investigation will reveal that a structuralist approach can be beneficial to the spacetime theorist as a means of deflating some of the ontological disputes regarding similarly structured spacetimes.

Combinations of molecules, of biological individuals, or of chemical processes can produce effects that are not simply attributable to the constituents. Such non-redundant causality warrants recognition of those coherences as ontologically significant whenever that efficacy is relevant. With respect to such interaction, the effective coherence is more real than are the components. This ontological view is a variety of structural realism and is also a kind of process philosophy. The designation ‘process structural realism’ (PSR) seems appropriate.

In this paper I elicit a prediction from structural realism and compare it, not to a historical case, but to a contemporary scientific theory. If structural realism is correct, then we should expect physics to develop theories that fail to provide an ontology of the sort sought by traditional realists. If structure alone is responsible for instrumental success, we should expect surplus ontology to be eliminated. Quantum field theory (QFT) provides the framework for some of the (...) best confirmed theories in science, but debates over its ontology are vexed. Rather than taking a stand on these matters, the structural realist can embrace QFT as an example of just the kind of theory SR should lead us to expect. Yet, it is not clear that QFT meets the structuralist's positive expectation by providing a structure for the world. In particular, the problem of unitarily inequivalent representations threatens to undermine the possibility of QFT providing a unique structure for the world. In response to this problem, I suggest that the structuralist should endorse pluralism about structure. (shrink)

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

For a long time it was believed that it was impossible to be realist about quantum mechanics. It took quite a while for the researchers in the foundations of physics, beginning with John Stuart Bell [Bell 1987], to convince others that such an alleged impossibility had no foundation. Nowadays there are several quantum theories that can be interpreted realistically, among which Bohmian mechanics, the GRW theory, and the many-worlds theory. The debate, though, is far from being over: in what respect (...) should we be realist regarding these theories? Two diff erent proposals have been made: on the one hand, there are those who insist on a direct ontological interpretation of the wave function as representing physical bodies, and on the other hand there are those who claim that quantum mechanics is not really about the wave function. In this paper we will present and discuss one proposal of the latter kind that focuses on the notion of primitive ontology. (shrink)

Whitehead’s cosmology centers on the self-creation of actual occasions that perish as they come to be, but somehow do combine to constitute societies that are persistent agents and/or patients. “Instance Ontology” developed by D.W. Mertz concerns unification of relata into facts of relatedness by specific intensions. These two conceptual systems are similar in that they both avoid the substance-property distinction: they differ in their understanding of how basic units combine to constitute complex unities. “Process Structural Realism” (PSR) draws (...) from both of these approaches in developing an account of how combinations of processes may produce ontologically significant coherences. When a group of processes achieves such closure that a set of states recurs continually, the effects of that coherence differ from what would occur in the absence of that closure. Such altered effectiveness is an attribute of the system as a whole, and would have consequences. This indicates that the network of processes, as a unit, has ontological significance. The closed network of processes, together with the conditions that prevail, constitute the form of definiteness of the coherence. That form continues to obtain as long as the coherence persists. Constituents contribute to, rather than share, that characteristic. Aspects of some recent research in systems biology, microeconomics, and social psychology illustrate the application of PSR. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO (...) relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

In this chapter, we propose an ecological hermeneutic phenomenology to study both the ontic and ontological structures of new and emerging technologies. In section 2, we first consult the traditional concept of phenomenology to find an entry point for our methodological considerations. It will become clear that Heidegger provides a progressive concept of hermeneutic phenomenology, although we are critical of his essentialism and linguistic focus in which there seems to be no room for the phenomenological consideration of ontic phenomena. The (...) discussion of Heidegger results in a methodological concept of an empirically informed ecological hermeneutic phenomenology that enables us to research how new and emerging technologies impact the World in which we live and act. Subsequently, we critically reflect on the epoché of phenomenology and show that a methodological concept of ecological hermeneutic phenomenology engages in an ecological transduction from technology as thematic artefact to technology as co-thematic ontological structure in which each and every artefact is grounded. (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)

Could space consist entirely of extended regions, without any regions shaped like points, lines, or surfaces? Peter Forrest and Frank Arntzenius have independently raised a paradox of size for space like this, drawing on a construction of Cantor’s. I present a new version of this argument and explore possible lines of response.

Types are fundamental for conceptual modeling and knowledge representation, being an essential construct in all major modeling languages in these fields. Despite that, from an ontological and cognitive point of view, there has been a lack of theoretical support for precisely defining a consensual view on types. As a consequence, there has been a lack of precise methodological support for users when choosing the best way to model general terms representing types that appear in a domain, and for building sound (...) taxonomic structures involving them. For over a decade now, a community of researchers has contributed to the development of the Unified Foundational Ontology (UFO) - aimed at providing foundations for all major conceptual modeling constructs. At the core of this enterprise, there has been a theory of types specially designed to address these issues. This theory is ontologically well- founded, psychologically informed, and formally characterized. These results have led to the development of a Conceptual Modelling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed on conceptual model design in a variety of domains including academic, industrial, and governmental settings. These experiences exposed improvement opportunities for both the OntoUML language and its underlying theory, UFO. In this paper, we revise the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of OntoUML’s meta-types (e.g. kind, role, phase, mixin) should be considered not as restricted to substantial types but instead should be applied to model endurant types in general, including relator types, quality types, and mode types. We also contribute with a formal characterization of this fragment of the theory, which is then used to advance a new metamodel for OntoUML (termed OntoUML 2). To demonstrate that the benefits of this approach are extended beyond OntoUML, the proposed formal theory is then employed to support the definition of UFO-based lightweight Semantic Web ontologies with ontological constraint checking in OWL. Additionally, we report on empirical evidence from the literature, mainly from cognitive psychology but also from linguistics, supporting some of the key claims made by this theory. Finally, we propose a computational support for this updated metamodel. (shrink)

In this paper I discuss the ontological status of actants. Actants are argued as being the basic constituting entities of networks in the framework of Actor Network Theory (Latour, 2007). I introduce two problems concerning actants that have been pointed out by Collin (2010). The first problem concerns the explanatory role of actants. According to Collin, actants cannot play the role of explanans of networks and products of the same newtork at the same time, at pain of circularity. The second (...) problem is that if actants are, as suggested by Latour, fundamentally propertyless, then it is unclear how they combine into networks. This makes the nature of actants inexplicable. -/- I suggest that both problems rest on the assumption of a form of object ontology, i.e. the assumption that the ontological basis of reality consists in discrete individual entities that have intrinsic properties. I argue that the solution to this problem consists in the assumption of an ontology of relations, as suggested within the framework of Ontic Structural Realism (Ladyman & Ross, 2007). Ontic Structural Realism is a theory concerning the ontology of science that claims that scientific theories represent a reality consisting on only relation, and no individual entities. -/- Furthermore I argue that the employment of OSR can, at the price of little modification for both theories, solve both of the two problems identified by Collin concerning ANT. -/- Throughout the text I seek support for my claims by referring to examples of application of ANT to the context of networked learning. As I argue, the complexity of the phenomenon of networked learning gives us a convenient vantage point from which we can clearly understand many important aspects of both ANT and OSR. -/- While my proposal can be considered as an attempt to solve Collin's problems, it is also an experiment of reconciliation between analytic and constructivist philosophy of science. -/- In fact I point out that on the one hand Actor Network Theory and Ontic Structural Realism show an interesting number of points of agreement, such as the naturalistic character and the focus on relationality. On the other hand, I argue that all the intuitive discrepancies that originates from the Science and Technology Studies’ criticism against analytic philosophy of science are at a closer look only apparent. (shrink)

'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and familiarizing (...) the reader with concrete examples of the latest research in the field. The basic sub-fields of ontology are covered here via an accessible and captivating exposition: events, properties, universals, abstract objects, possible worlds, material beings, mereology, fictional objects. -/- The guide's modular structure allows for a flexible approach to the subject, making it suitable for both undergraduates and postgraduates looking to better understand and apply the exciting developments and debates taking place in ontology today. (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)

: To address the question “on what there is” raised by Quine, and to accomplish the task of comprehending exhaustively the many ontological units that populate the great province of Being, we propose as an alternative to Puntel’s ontology a new ontology designated as “Structural Ontology” (SO). Such ontology is based on systematic-structural theoretical foundations, but leads to a diverse view in which structured factual units, structural configurations (dynamics), as well as apparent ontological (...) units (objects), all encompassed by the temporal sub-dimension that interconnects them, understood as an internal sub-dimension of the macro-dimension of Being, co-subsist. In this sense, we begin by situating the ontological theme in current philosophical discussion from a Quinean perspective. We then present a concept of truth derived from our reading of puntelian philosophy, which will be the point of connection between language and the world. Subsequently, we show how from the concept of truth, after a brief foray into philosophical semantics, we arrive at the ontological field from the ontological categories of structure and ontological state. Finally, we outline, in its general features, our structural ontology, which includes its own ontological notions that give new directions to philosophical understanding of this great theme. (shrink)

The article proposes systematisation and development of the discourse of the East European methodological traditions regarding application of the systematic approach as a way of subject localisation in psychological research. In particular, the author’s version of systematic localisation of psychological research subjects by means of structural and ontological visualisations has been developed. The procedure proposed for systematic localisation of the researched subject includes four subsequent stages: 1) fixation of the borders and structure of the ontological field which is being (...) studied; 2) segment analysis of the obtained structure; 3) study of specifics and contents of structural and functional ties; 4) visual mapping of genesis of the core processes. The article describes specifics of application of systematic localisation of the subject of research at the example of such researched object as personal socialisation. (shrink)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ is often used by philosophers as a synonym for ‘metaphysics’ (literally: ‘what comes after the Physics’), a term which was used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. The term ‘ontology’ (or ontologia) was itself coined in 1613, independently, by two (...) philosophers, Rudolf Göckel (Goclenius), in his Lexicon philosophicum and Jacob Lorhard (Lorhardus), in his Theatrum philosophicum. The first occurrence in English recorded by the OED appears in Bailey’s dictionary of 1721, which defines ontology as ‘an Account of being in the Abstract’. (shrink)

Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these (...) are two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine. (shrink)

The given is the state of a mind in its primary engagement with the world. A satisfactory epistemology—one, it turns out, that is foundationalist and includes a naïve realist view of perception—requires a certain account of the given. Moreover, knowledge based on the given requires both a particular view of the world itself and a heterodox account of judgment. These admittedly controversial claims are supported by basic ontological considerations. I begin, then, with two contradictory views of the world per se (...) and the structure one experiences. I draw out the consequences of these two views for what intentionality is. The two views yield incompatible accounts of the given. The definitive spontaneity of the one account, and passivity of the other, can be understood in terms of the structure (or lack thereof) in the given. In defense of the claim that a structured given is not an apt epistemic basis, I examine an attempt to found an epistemology on such an account in light of the so-called myth of the given. I maintain that the given, if it is to provide some justification for taking the world to be a particular way, must be unstructured. To support this, I first discuss a significant problem with traditional foundationalism. I then argue that a satisfactory (foundationalist) epistemology requires the rejection of the orthodox propositional view of judgment in favor of a non-propositional, reistic view. (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)

In this article, the results of conceptualization of the definition of mind as an object of interdisciplinary applied research are described. The purpose of the theoretical analysis is to generate a methodological discourse suitable for a functional understanding of the mind in the context of the problem of natural language processing as one of the components of developments in the field of artificial intelligence. The conceptual discourse was realized with the help of the author's method of structural-ontological analysis, and (...) developed in the mainstream of the system-methodological tradition of the school of G.P. Shchedrovitsky and intended for descriptive research of subject areas of interdisciplinary objects of scientific study. As a result of the structural and ontological analysis of the super-system, the relevant place and role of the directly studied system (mind) are determined, and its primary process and material are localized and structural and functional connections are described. At the basic level, the mind is conceptualized as an energy process unfolding in a spatio-temporal environment and accompanied by archetypal structuring of neural impulses into images. The genesis of the system is separately analyzed by constructing a structural-ontological matrix that reflects the initial stage of the development of the mind. The primary process is concretized with the help of hetero- and homeostatic dichotomy, and also the most significant features of the consistent transformation of the material of the system and its ascent to verbal morphology are described. The structural-ontological comparison of the functioning of the verbal intelligence with the preverbal level has been carried out. The transformation of neural impulses of needs into words, as verbal units fixing semiotic values is analyzed. Structural-ontological connections that determine the reactive and prospective characteristics of the functioning of the system are disclosed. The position of the chronological primacy of "semiotic readiness" for language with respect to the debut of the latter as an information-sign model of the environment is argued. The hypothesis of domination at the initial stage of the development of the mind of exopsychic functions over endopsychic ones is formulated. The theoretical substantiation of the hypothesis of the inevitability of the ontology of language in the functional understanding of the mind is given, corresponding structural and ontological arguments are given, including those based on the ideas about the information relationship between affects and needs, according to the views of P.V. Simonov. The arguments are presented in favor of the non-alternative methodology of A. Turing in studies of artificial intelligence. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

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

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 greatly benefits application ontologies. To this end r®, 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 project we aim to move (...) beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

A version of the growing block theory of time is developed based on the choice of both consciousness and mathematics as fundamental substances, while dismissing the reality/semantics distinction usually assumed by works on time theory. The well-analyzable growing block structure of mathematical ontology revealed by mathematical logic, is used as a model for a possible deeper working of conscious time. Physical reality is explained as emerging from a combination of both substances, with a proposed specific version of the Consciousness (...) Causes Collapse interpretation. This leads to new solutions to old problems, including the epistemic problem and issues with Relativity. (shrink)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those (...) who created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant (...) science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

An ontology of geographic kinds is designed to yield a better understanding of the structure of the geographic world, and to support the development of geographic information systems that are conceptually sound. This paper first demonstrates that geographical objects and kinds are not just larger versions of the everyday objects and kinds previously studied in cognitive science. Geographic objects are not merely located in space, as are the manipulable objects of table-top space. Rather, they are tied intrinsically to space, (...) and this means that their spatial boundaries are in many cases the most salient features for categorization. The ontology presented here will accordingly be based on topology (the theory of boundary, contact and separation) and on mereology (the theory of extended wholes and parts). Geographic reality comprehends mesoscopic entities, many of which are best viewed as shadows cast onto the spatial plane by human reasoning and language. Because of this, geographic categories are much more likely to show cultural differences in category definitions than are the manipulable objects of table-top space. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and (...) developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

While contemporary philosophers have devoted vast amounts of attention to the language we use in describing and finding our way about the world of everyday experience, they have, with few exceptions, refused to see this world itself as a fitting object of theoretical concern. In what follows I shall seek to show how the commonsensical world might be treated ontologically as an object of investigation in its own right. At the same time I shall seek to establish how such a (...) treatment might help us better philosophically to understand the structures of both physical reality and cognition. (shrink)

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

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of (...) certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

Fictionalism in ontology is a mixed bag. Here I focus on three main variants—which I label after the names of Pascal, Berkeley, and Hume—and consider their relative strengths and weaknesses. The first variant is just a version of the epistemic Wager, applied across the board. The second variant builds instead on the fact that ordinary language is not ontologically transparent; we speak with the vulgar, but deep down we think with the learned. Finally, on the Humean variant it’s the (...) structure of the ontological inventory, not its content, that may turn out to involve fictional elements. That is, for the Humean the fiction lies, not in the reality of common-sense ontology, but in the laws—of unity, identity, causation, etc.—in terms of which we articulate our experience of that reality. In the end, this is the kind of fictionalism that I find most interesting, sensible, and tenable. And I argue that it is even compatible with the sort of “naive” realism we have all come to appreciate in the work of Paolo Bozzi, to whom the paper is dedicated. (shrink)

Theorising the interplay of structure and agency is the quintessential focus of sociological endeavour. This paper aims to be part of that continuing endeavour, arguing for a stratified social ontology, where structure and agency are held to be irreducible to each other and causally efficacious, yet necessarily interdependent. It thus aims not to be part of that on-going journey in search of the 'ontological holy grail'. Instead, it offers a way of linking structure and agency which enables the practical (...) education researcher concretely to examine their relative interplay over time. The methodological key to teasing out their relative interplay is held to be analytical dualism. It will be argued that such a methodological device is precluded by Giddens' structuration theory. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

Formal ontology as it is presented in Husserl`s Third Logical Investigation can be interpreted as a fundamental tool to describe objects in a formal sense. It is presented one of the main sources: chapter five of Carl Stumpf`s Ûber den psycholoogischen Ursprung der Raumovorstellung (1873), and then it is described how Husserlian Formal Ontology is applied in Fifth Logical Investigation. Finally, it is applied to dramatic structures, in the spirit of Roman Ingarden.

This paper motivates taking seriously the possibility that brains are basically protean: that they make use of neural structures in inventive, on-the-fly improvisations to suit circumstance and context. Accordingly, we should not always expect cognition to divide into functionally stable neural parts and pieces. We begin by reviewing recent work in cognitive ontology that highlights the inadequacy of traditional neuroscientific approaches when it comes to divining the function and structure of cognition. Cathy J. Price and Karl J. Friston, and (...) Colin Klein identify the limitations of relying on forward and reverse inferences to cast light on the relation between cognitive functions and neural structures. There is reason to prefer Klein’s approach to that of Price and Friston’s. But Klein’s approach is neurocentric - it assumes that we ought to look solely at neural contexts to fix cognitive ontology. Using recent work on mindreading as a case study, we motivate adopting a radically different approach to cognitive ontology. Promoting the Protean Brain Hypothesis, we posit the possibility that we may need to look beyond the brain when deciding which functions are being performed in acts of cognition and in understanding how the brain contributes to such acts by adapting to circumstance. (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)

In the ontology of music the Aristotelian theory of musical works is the view that musical works are immanent universals. The Aristotelian theory (hereafter Musical Aristotelianism) is an attractive and serviceable hypothesis. However, it is overlooked as a genuine competitor to the more well-known theories of Musical Platonism and nominalism. Worse still, there is no detailed account in the literature of the nature of the universals that the Aristotelian identifies musical works with. In this paper, I argue that the (...) best version of Musical Aristotelianism identifies musical works with structural universals. I first motivate the view by outlining its explanatory benefits. I then argue that Musical Aristotelianism is preferable to Musical Platonism and present a novel account of musical works as structural universals by developing D. M. Armstrong’s theory of structural universals. I discuss the consequences of Musical Aristotelianism with respect to on-going issues in debates about musical works and defend the view against an influential objection, concluding that Musical Aristotelianism is a genuine competitor in debates about the nature of musical works. (shrink)

In this paper I present the common structure of quantum theories with a primitive ontology, and discuss in what sense the classical world emerges from quantum theories as understood in this framework. In addition, I argue that the primitive ontology approach is better at answering this question than the rival wave function ontology approach or any other approach in which the classical world is nonreductively ‘emergent:’ even if the classical limit within this framework needs to be fully (...) developed, the difficulties are technical rather than conceptual, while this is not true for the alternatives. (shrink)

In contrast to individualistic explanations of social injustice that appeal to implicit attitudes, structural explanations are unintuitive: they appeal to entities that lack clear ontological status, and the explanatory mechanism is similarly unclear. This makes structural explanations unappealing. The present work proposes a structural explanation of one type of injustice that happens in conversations, discursive injustice. This proposal meets two goals. First, it satisfactorily accounts for the specific features of this particular kind of injustice; and second, it (...) articulates a structural explanation that overcomes their unattractiveness. The main idea is that discursive injustice is not the result of biased interlocutors, but of problematic discursive norms. (shrink)

How should scientists carve up cognition to generate good predictions, explanations, and models of cognition? This chapter argues that cognitive categories should be constructed the same way that biological categories are: in terms of homology. The chapter adapts a developmental account of trait identity from evolutionary-developmental biology to make sense of the notion of “cognitive homology.” The consequence is that both brain structures and the organism’s ongoing interactions with the environment are crucial for individuating cognitive homologies, and thus for cognitive (...) ontology. (shrink)

Ontologies are being used by information scientists in order to facilitate the sharing of meaningful information. However, computational ontologies are problematic in that they often decontextualize information. The semantic content of information is dependent upon the context in which it exists and the experience through which it emerges. For true semantic interoperability to occur among diverse information systems, within or across domains, information must remain contextualized. In order to bring more context to computational ontologies, we introduce culture as an essential (...) concept for information science. Culture helps to focus our attention on and make meaning of relevant extrapersonal structures and their qualities and dimensions that comprise the context and background of the world. In our approach, culture is integral to the study of semantics and, consequently, the study of ontologies and information technologies. The meaning we make of entities and phenomena in the world is always shaped by our cultural experience. If we understand culture as the emergent interplay of intrapersonal cognitive structures and extrapersonal structures of the world, then the notion of cognitive and cultural schemas becomes essential to understanding ontology and the ways in which we might achieve authentic semantic interoperability among diverse information systems. We explore the nature of ontologies and reconceptualize them as cultural schemas. Our proposal is an alternative to the historical path from philosophical ontology to computational ontologies as one that adheres primarily to the notion of ontology as a categorization and classification system. The obvious implication for ontology as categorization is that there is a single objective world that exists and that it can be described as entirely separate from the person observing it. We draw upon Heidegger’s examination of ontology to ground ontology in a phenomenological perspective, enabling it to remain flexible and adaptable and to accommodate context. (shrink)

Quine's views on ontology and naturalism are well-known but rarely considered in tandem. According to my interpretation the connection between them is vital. I read Quine as a global epistemic structuralist. Quine thought we only ever know objects qua solutions to puzzles about significant intersections in observations. Objects are always accessed descriptively, via their roles in our best theory. Quine's Kant lectures contain an early version of epistemic structuralism with uncharacteristic remarks about the mental. Here Quine embraces mitigated anomalous (...) monism, allowing introspection and the availability in principle of full physical descriptions of the perceptual states which get science off the ground. Later versions abandon these ideas. My epistemic-structural interpretation explains why. I argue first-personal introspective access to mental states is incompatible with global epistemic structuralism. (shrink)

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

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

The paper argues that digital ontology (the ultimate nature of reality is digital, and the universe is a computational system equivalent to a Turing Machine) should be carefully distinguished from informational ontology (the ultimate nature of reality is structural), in order to abandon the former and retain only the latter as a promising line of research. Digital vs. analogue is a Boolean dichotomy typical of our computational paradigm, but digital and analogue are only “modes of presentation” of (...) Being (to paraphrase Kant), that is, ways in which reality is experienced or conceptualised by an epistemic agent at a given level of abstraction. A preferable alternative is provided by an informational approach to structural realism, according to which knowledge of the world is knowledge of its structures. The most reasonable ontological commitment turns out to be in favour of an interpretation of reality as the totality of structures dynamically interacting with each other. The paper is the first part (the pars destruens) of a two-part piece of research. The pars construens, entitled “A Defence of Informational Structural Realism”, is developed in a separate article, also published in this journal. (shrink)

This essay examines the difficulties faced by the claim that artworks are simple physical objects (or, in the case of non-visual art forms, simple structures of another sort) and examines alternative proposals regarding their ontological nature.