In the domain of ontology design as well as in Knowledge Representation, modeling universals is a challenging problem.Most approaches that have addressed this problem rely on Description Logics (DLs) but many difficulties remain, due to under-constrained representation which reduces the inferences that can be drawn and further causes problems in expressiveness. In mathematical logic and program checking, type theories have proved to be appealing but, so far they have not been applied in the formalization of ontologies. To bridge this (...) gap, we present in this paper a theory for representing ontologies in a dependently typed framework which relies on strong formal foundations including both a constructive logic and a functional type system. The language of this theory defines in a precise way what ontological primitives such as classes, relations, properties, etc., and thereof roles, are. The first part of the paper details how these primitives are defined and used within the theory. In a second part, we focus on the formalization of the role primitive. A review of significant role properties leads to the specification of a role profile and most of the remaining work details through numerous examples, how the proposed theory is able to fully satisfy this profile. It is demonstrated that dependent types can model several non-trivial aspects of roles including a formal solution for generalization hierarchies, identity criteria for roles and other contributions. A discussion is given on how the theory is able to cope with many of the constraints inherent in a good role representation. (shrink)

Abstract The purpose of this paper is twofold: (i) we will argue that formal semantics might have faltered due to its failure in distinguishing between two fundamentally very different types of concepts, namely ontological concepts, that should be types in a strongly-typed ontology, and logical concepts, that are predicates corresponding to properties of, and relations between, objects of various ontological types; and (ii) we show that accounting for these differences amounts to a new formal semantics; one that (...) integrates lexical and compositional semantics in one coherent framework and one where formal semantics is embedded with a strongly typed ontology; an ontology that reflects our commonsense knowledge of the world and the way we talk about it in ordinary language. We will show how in such a framework a number of challenges in the semantics of natural language are adequately and systematically treated. (shrink)

In this article, we analyse the ontological import of adding classes to set theories. We assume that this increment is well represented by going from ZF system to NBG. We thus consider the standard techniques of reducing one system to the other. Novak proved that from a model of ZF we can build a model of NBG (and vice versa), while Shoenfield have shown that from a proof in NBG of a set-sentence we can generate a proof in ZF of (...) the same formula. We argue that the first makes use of a too strong metatheory. Although meaningful, this symmetrical reduction does not equate the ontological content of the theories. The strong metatheory levels the two theories. Moreover, we will modernize Shoenfields proof, emphasizing its relation to Herbrands theorem and that it can only be seen as a partial type of reduction. In contrast with symmetrical reductions, we believe that asymmetrical relations are powerful tools for comparing ontological content. In virtue of this, we prove that there is no interpretation of NBG in ZF, while NBG trivially interprets ZF. This challenges the standard view that the two systems have the same ontological content. (shrink)

Western philosophy and science have a strongly dualistic tradition regarding the mental and physical aspects of reality, which makes it difficult to understand their possible causal relations. In recent debates in cognitive neuroscience it has been common to claim on the basis of neural experiments that conscious experiences are causally inefficacious. At the same time there is much evidence that consciousness does play an important role in guiding behavior. The author explores whether a new way of understanding the causal (...) role of mental states and consciousness could be provided by the ontological interpretation of the quantum theory (Bohm and Hiley, Phys. Rep. 144:323–348, 1987; Bohm and Hiley, The undivided universe: An ontological interpretation of quantum theory. Routledge: London, 1993). This interpretation radically changes our notion of matter by suggesting that a new type of active information plays a causal role at the quantum level of reality. The author thus considers to what extent the alleged causal powers of consciousness involve information, and then moves on to consider whether information in (conscious) mental states can be connected to the information at the level of quantum physics. In this way he sketches how quantum theory might help to throw light upon one of the grand challenges facing the social sciences and the humanities, namely the question of whether consciousness plays any genuine causal role in the physical world. (shrink)

We argue that logical semantics might have faltered due to its failure in distinguishing between two fundamentally very different types of concepts: ontological concepts, that should be types in a strongly-typed ontology, and logical concepts, that are predicates corresponding to properties of and relations between objects of various ontological types. We will then show that accounting for these differences amounts to the integration of lexical and compositional semantics in one coherent framework, and to an embedding in our (...) logical semantics of a strongly-typed ontology that reflects our commonsense view of the world and the way we talk about it in ordinary language. We will show that in such a framework a number of challenges in natural language semantics can be adequately and systematically treated. (shrink)

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)

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. This ontology has led to the development of an Ontology-Driven Conceptual Modeling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed in a number of academic, industrial and governmental settings to create conceptual models in a variety (...) of different domains. These experiences have pointed out to opportunities of improvement not only to the language itself but also to its underlying theory. In this paper, we take the first step in that direction by revising the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of the meta-types present in OntoUML (differentiating Kinds, Roles, Phases, Mixins, etc.) 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 a formal characterization of this fragment of the theory, which is then used to advance a metamodel for OntoUML 2.0. Finally, we propose a computational support tool implementing this updated metamodel. (shrink)

The aim of this essay is twofold. First, it outlines the concept of ontological frame. Secondly, two models are distinguished on this structure. The first one is connected to Kant’s concept of possible object and the second one relates to Leibniz’s. Leibniz maintains that the source of possibility is the mere logical consistency of the notions involved, so that possibility coincides with analytical possibility. Kant, instead, argues that consistency is only a necessary component of possibility. According to Kant, something is (...) possible if there is a cause capable of bringing it into existence; to this end consistency alone is not sufficient. Thus, while the Leibnizian notion of consistency is at the root of the concept of analytical possibility, the Kantian notion of possibility is the source of real possibility. This difference plays an important role in the discussion of Gödel’s ontological proof, which can be formally interpreted on the ontological frame of the pure perfections. While this proof, under some emendation condition, is conclusive in the context of Leibniz’s ontological model, it is not so within the Kantian one. This issue will be the subject of the second part of the present essay. (shrink)

The paper presents, a new large deviations principles (SLDP) of non-Freidlin-Wentzell type, corresponding to the solutions Colombeau-Ito’s SDE. Using SLDP we present a new approach to construct the Bellman function ????(????, ????) and optimal control ????(????, ????) directly by way of using strong large deviations principle for the solutions Colombeau-Ito’s SDE. As important application such SLDP, the generic imperfect dynamic models of air-to-surface missiles are given in addition to the related simple guidance law. A four, examples have been illustrated proposed (...) approach and corresponding numerical simulations have been illustrated and analyzed. Using SLDP approach, Jumps phenomena, in financial markets, also is considered. Jumps phenomena, in financial markets is explained from the first principles, without any reference to Poisson jump process. In contrast with a phenomenological approach we explain such jumps phenomena from the first principles, without any reference to Poisson jump process. (shrink)

In his article “The Ontology of Musical Versions: Introducing the Hypothesis of Nested Types,” Nemesio Puy raises a hypothesis that continuity of the purpose is both a necessary and a sufficient condition for musical work’s identity. Puy’s hypothesis is relevant to two topics in cognitive psychology and experimental philosophy. The first topic is the prevalence of teleological reasoning about various objects and its influence on persistence and categorization judgments. The second one is the importance of an artist’s intention in (...) the categorization of artworks. We tested the teleological hypothesis across three studies. Vignettes in these three studies describe a musical work being changed in some of these aspects: purpose either changed or retained; score either changed or retained; change is made either by the same or a different composer. The results suggest that teleological considerations impact judgments on the persistence of musical works, but this impact appears to be relatively weak. The results also suggest that persistence judgments strongly depend on whether acoustical properties were changed, while whether the change was made by the original composer seems to be relatively unimportant. (shrink)

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

In this paper, we support a continuistic reading of Joseph Margolis' philosophy, defending the claim that in the 1970s, Margolis tackled the issues suggested by the analytic philosophy of art from an original theoretical perspective and through conceptual tools exceeding the analytical framework. Later that perspective turned out to be a radically pragmatist one, in which explicitly tolerant realistic claims and non-reductive naturalism converged with radical historicism and contextualism. We will endorse this thesis by focusing on two important concepts appearing (...) in Margolis' aesthetics essays from the late 1950s to the 1970s: the type-token pair and the notion of cultural emergence. On the one hand, we will emphasise Margolis' indebtedness to Peirce's first formulation of the type-token distinction, involving a strong interdependence between the two elements of the pair, as well as an anti-essentialistic, historicised, and contextualised notion of type. On the other hand, we will delve into Margolis' exploration of the concept of emergence and cultural emergence, involving a genuinely pluralistic view of ontology, as well as a non-reductive, continuistic form of naturalism. Finally, we will connect the criticism of the so-called closure of the physical world with Margolis' anti-autonomistic stance in defining artworks. (shrink)

Modal ontological arguments are often claimed to be immune to the flqqperfect islandfrqq objection of Gaunilo, because necessary existence does not apply to material, contingent things. But Gaunilo’s strategy can be reformulated: we can speak of non-contingent beings, like quasi-Gods or evil God. The paper is intended to show that we can construct ontological arguments for the existence of such beings, and that those arguments are equally plausible as theistic modal argument. This result does not show that this argument is (...) fallacious, but it shows that it is dialectically ineffective as an argument for theism. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that (...) is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

"The main aim of the paper is to compare two types of abstractionistic accounts of fictional objects, and to analyze their consequences for interpretation of existential quantification. According to a proponent of general abstractionistic theory, fictional objects have abstract nature in a way similar to contracts, marriages, and the likes. This view is an alternative to strongly realistic accounts of fictional objects, defended by Terence Parsons or David Lewis. Within abstractionistic theories, as in all philosophical areas, one can find (...) divergences of opinions. The main differences between two of them – Peter van Inwagen's and Edward Zalta's – are connected with the interpretation of existential quantification. According to van Inwagen, “being” is the same as “existence” and its sense is captured by the existential quantifier. Edward Zalta's theory is much closer to the Meinongian Theory of Objects. He argues for the need of distinguishing between “being” and “existence” and for invoking nonexistent objects. Because of that he suggests an alternative interpretation of quantification. Admittedly, there is one abstractionistic source for both theories, but their ontological consequences are different - van Inwagen is a staunch opponent of nonexistent objects, and Zalta describes his own theory as "Meinongian".". (shrink)

What are words? What makes two token words tokens of the same word-type? Are words abstract entities, or are they (merely) collections of tokens? The ontology of words tries to provide answers to these, and related questions. This article provides an overview of some of the most prominent views proposed in the literature, with a particular focus on the debate between type-realist, nominalist, and eliminativist ontologies of words.

A crucial question for both philosophy and for science concerns the kind of relationship that obtains between entities—objects, properties, states, processes, kinds and so on—that exist at apparently higher and lower ‘levels’ of reality. According to reductionism, seeming higher-level entities can in fact be fully accounted for by more fundamental, lower-level entities. Conversely, emergentists of various stripes hold that whilst higher-level entities depend in some important sense on lower-level entities, they are nevertheless irreducible to them. This introductory paper outlines the (...) context of the debate between emergentists and reductionists; offers a broad characterisation of ‘strong’ or ontological emergence, and provides summaries of each of the papers to come in this special issue. (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 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)

Standard approaches to ontological simplicity focus either on the number of things or types a theory posits or on the number of fundamental things or types a theory posits. In this paper, I suggest a ground-theoretic approach that focuses on the number of something else. After getting clear on what this approach amounts to, I motivate it, defend it, and complete it.

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)

Foundational ontologies, central constructs in ontological investigations and engineering alike, are based on ontological categories. Firstly proposed by Aristotle as the very ur- elements from which the whole of reality can be derived, they are not easy to identify, let alone partition and/or hierarchize; in particular, the question of their number poses serious challenges. The late medieval philosopher Dietrich of Freiberg wrote around 1286 a tutorial that can help us today with this exceedingly difficult task. In this paper, I discuss (...) ontological categories and their importance for foundational ontologies from both the contemporary perspective and the original Aristotelian viewpoint, I provide the translation from the Latin into English of Dietrich's De origine II with an introductory elaboration, and I extract a foundational ontology–that is in fact a single-category one–from this text rooted in Dietrich's specification of types of subjecthood and his conception of intentionality as causal operation. (shrink)

Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find (...) self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But these ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, we shall argue, ontologies such as the GO are comparable to scientific theories, to scientific databases, or to scientific journal publications. Such a view implies a radically new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a radically new approach to the evaluation of ontologies and to the training of ontologists. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. (...) In a SNAP (snapshot) ontology we have enduring entities such as substances, qualities, roles, functions as these exist to be inventoried at a given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontological theory are required, together with the metaontology which joins them together, in order to give a non-reductionistic account of both static and dynamic aspects of the geospatial world. (shrink)

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

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)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical (...) data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

I develop a view of the common factor between subjectively indistinguishable perceptions and hallucinations that avoids analyzing experiences as involving awareness relations to abstract entities, sense-data, or any other peculiar entities. The main thesis is that hallucinating subjects employ concepts (or analogous nonconceptual structures), namely the very same concepts that in a subjectively indistinguishable perception are employed as a consequence of being related to external, mind-independent objects or property-instances. These concepts and nonconceptual structures are identified with modes of presentation types. (...) Since a hallucinating subject is not related to any such objects or property-instances, the concepts she employs remain empty. I argue that the phenomenology of hallucinations and perceptions can be identified with employing concepts and analogous nonconceptual structures. By doing so, I defend an ontologically minimalist view of the phenomenology of experience that (1) vindicates Aristotelianism about types and (2) amounts to a naturalized view of the phenomenology of experience. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

Commonplace syntactic constructions in natural language seem to generate ontological commitments to a dazzling array of metaphysical categories - aggregations, sets, ordered n-tuples, possible worlds, intensional entities, ideal objects, species, intensive and extensive quantities, stuffs, situations, states, courses of events, nonexistent objects, intentional and discourse objects, general objects, plural objects, variable objects, arbitrary objects, vague kinds and concepts, fuzzy sets, and so forth. But just because a syntactic construction in some natural language appears to invoke a new category of entity, (...) are we theoreticians epistemically justified in holding that there are such entities? This would hardly seem sufficient. To be epistemically justified, the ontology to which we theoreticians are committed must pass strict standards: the entities must be of the sort required by our best comprehensive theory of the world. The thesis of this paper is that fine-grained type-free intensional entities are like this. If the thesis is right, these entities have a special objective status perhaps not possessed by some of the other ontological categories associated with special syntactic constructions in natural language. In fact, it is plausible to hold that fine-grained type-free intensional entities provide the proper minimal framework for constructing logical and linguistic theories. In this paper my strategy will be to survey the competing conceptions of fine-grained type-free intensionality and to present arguments in support of one of them. Following this narrowing down process, I will go on to the indicated epistemological considerations. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

Naturalism has typically been entangled with a physicalist view. Physicalism, on the other hand, falls short of accounting for qualitative states of mental phenomena. The hard problem of consciousness seems to be a natural epistemic boundary in such a way that we do not even have any conceptualization as to how we can possibly account for mental states in physicalist terms in the future, which leads us to some version of causal/ontological plurality in the sense that it does not seem (...) possible to explain everything with the same parameters even though the world fundamentally consists in a single substance. If plurality in multiple levels of scientific explanation is necessary, I argue that strong emergentism is, as a metaphysical framework, the best candidate to account for this fact. I will tackle two major physicalist views by Kim and Sider. Kim shows us that non-reductive physicalism is a bankrupt project whereas Sider’s physicalism that postulates a pure and complete fundamental level renders higher-level phenomena (including mental reality) metaphysically spurious. In relation to Kim and Sider’s accounts, I will try to elaborate on my view that physicalism, when pursued to the end, is inherently reductive and ultimately falls short of accounting for the mental reality. I emphasize that the causal identification of brain and mind rests on an arbitrary carving of world, namely a description of the world which cannot be intrinsic to nature. These are the main reasons why I conclude that our revised naturalism should be disentangled from physicalism and embrace the causal/ontological plurality of strong emergentism without falling for substance dualism. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve (...) the representation of contractual obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

This paper defends an ontology of weak entity realism for homeostatic property cluster (HPC) theories of natural kinds, adapted from Bird’s (Synthese 195(4):1397–1426, 2018) taxonomy of such theories. Weak entity realism about HPC kinds accepts the existence of natural kinds. Weak entity realism denies two theses: that (1) HPC kinds have mind-independent essences, and that (2) HPC kinds reduce to entities, such as complex universals, posited only by metaphysical theories. Strong entity realism accepts (1) and (2), whereas moderate entity (...) realism accepts only (1). Given its commitment to (2), strong entity realism is more theoretically complex than weak entity realism, with little explanatory payoff. Given their commitment to (1), moderate and strong entity realisms cannot explain how the identity conditions of HPC kinds are to be straightforwardly knowable. I argue that weak entity realism avoids such epistemic difficulties. I further rebut two plausible criticisms of weak entity realism, namely that weak entity realism cannot account for quantification over kinds, and that weak entity realism cannot provide identity conditions for HPC kinds which are both scientifically useful and objective. Given the theoretical costs of strong and moderate entity realism, and weak entity realism’s adequate response to its most plausible challenges, weak entity realism about HPCs is to be preferred, especially for biological and chemical kinds. (shrink)

The book is a collection of papers and aims to unify the questions of syntax and semantics of language, which are included in logic, philosophy and ontology of language. The leading motif of the presented selection of works is the differentiation between linguistic tokens (material, concrete objects) and linguistic types (ideal, abstract objects) following two philosophical trends: nominalism (concretism) and Platonizing version of realism. The opening article under the title “The Dual Ontological Nature of Language Signs and the Problem (...) of Their Mutual Relations” provides a broad introduction into the problem area connected with this differentiation, while the logic-formal characteristics of the distinction are framed in the work entitled “On the Type-Token Relationships” (Chapter 1). The basic part of the book deals with issues relating to syntax (Chapters 2-4) and semantics of language (Chapters 5-6), as well as pertaining to syntactic-semantic pragmatic questions (Chapters 7-13). Throughout the book, language, categorial language, is characterized syntactically as generated by classical categorial grammar (Chapter 2) and formalized on two opposing levels: as language of expression-tokens (level of tokens) and language of expression-types (level of types). The author’s considerations contained in Chapters 2 and 4 lead to the important philosophical conclusion that in formal-logical syntactic studies on language the assumption that expression-types constitute the primary language layer while expression-tokens make the secondary one, can be neglected; thus, this speaks in favour of the opposing standpoint—the concretistic one—in the ontology of language syntax. In the works “Meaning and Interpretations”, Parts I and II (Chapters 5 and 6), it is underlined, however, that such semantic concepts as: meaning, denotation and interpretation are defined on the types level, yet their formal definitions require making use of notions of the tokens level. The semantic notions introduced in the above-mentioned articles are also used in the following works of the present selection, under the titles: “Three Principles of Compositionality” and “On Metaknowledge and Truth” (Chapters 7 and 8). They formalize two principles of compositionality that are well known in the literature on the subject, deriving from Frege, i.e. those of meaning and of denotation; they are related to the syntactic principle of compositionality which was introduced by the author. All the three principles are, at the same time, three conditions of homomorphism of categorial language algebra into three kinds of non-standard models of language (one syntactic and two semantic ones: intensional and extensional), which allows introducing three definitions of truthfulness into these models. The next two works in the collection, entitled: “On Language Adequacy” and “What is the Sense in Logic and Philosophy of Language” (Chapters 9 and 10) concern adequacy of categorial language syntax along with its dual semantics: intensional and extensional, and categorial compatibility of any of its syntactic categories with two corresponding semantic categories: intensional and extensional, based on the compatibility the syntactic category of each language expression with the ontological category assigned to its denotatum. The well-known problem of categorial compatibility for first-order quantifiers finds its solution in the paper “Categories of First-Order Quantifiers” (Chapter 11). In the work “Logic and Ontology of Language” (Chapter 12), being in a sense a summary of the considerations presented in the preceding chapters of the book, language is treated as an ontological being, characterized in compliance with the logical conception of language proposed by Ajdukiewicz. Application—like throughout the book—of tools of classical logic and set theory has resulted in emergence of a general formal logical theory of syntax, semantics and pragmatics of language, which takes into account duality in the understanding of linguistic expressions as tokens (concretes) and types (abstract objects). In terms that take into account a functional approach to language itself, there comes out an ontological neutrality of logic with respect to existential assumptions relating to the ontological nature of linguistic expressions and their extra-linguistic ontological counterparts. The issues connected with applying logic while explaining the manner of using linguistic tokens and linguistic types to determine notions of language communication are raised and illustrated in the last chapter of the work, bearing the title “A Logical Conceptualization of Knowledge on the Notion of Language Communication”. (shrink)

Dombrowski and Murdoch offer versions of the ontological argument which aim to avoid two types of objection – those concerned with the nature of the divine, and those concerned with the move from an abstract concept to a mind-independent reality. For both, the nature of the concept of God/Good entails its instantiation, and both supply a supporting argument from experience. It is only Murdoch who successfully negotiates the transition from an abstract concept to the instantiation of that concept, however, and (...) this is achieved by means of an ontological argument from moral experience which, in a reversal of the Kantian doctrine, depends ultimately on a form of the cosmological argument. (shrink)

Many philosophers use “physicalism” and “naturalism” interchangeably. In this paper, I will distinguish ontological naturalism from physicalism. While broad versions of physicalism are compatible with naturalism, naturalism doesn't have to be committed to strong versions of physical reductionism, so it cannot be defined as equivalent to it. Instead of relying on the notion of ideal physics, naturalism can refer to the notion of ideal natural science that doesn't imply unity of science. The notion of ideal natural science, as well as (...) the notion of ideal physics, will be vindicated. I will shortly explicate the notion of ideal natural science, and define ontological naturalism based on it. (shrink)

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

The two-fold ontological character of linguistic objects revealed due to the distinction between “type” and “token” introduced by Ch. S. Peirce can be a base of the two-fold, both theoretical and axiomatic, approach to the language. Referring to some ideas included in A. A. Markov’s work [1954] (in Russian) on Theory of Algorithms and in some earlier papers of the author, the problem of formalization of the concrete and abstract words theories raised by J. Słupecki was solved. The construction of (...) the theories presented here has two levels. The axiomatic theory of label-tokens: material, physical linguistic objects, constitutes the first one. Label-types, according to the literature of the subject, are defined on the other level as equivalence classes of equiform label-tokens. Assuming the opposite point of view, one can accept that theory of label-types: abstract labels, formalized on the first level, in which it is possible to define the notion of label-token as well as the derivative notions on the second level, should become the basis of formalization of the theory of linguistic expressions and the theory of language in general. The axioms and definitions of both theories of labels: T k and T p representing the other approach to the ontology of language are included in the sequel of the abstract. The foundations of the theory of labels T k in which the primary assumption as to the label-types existence is superfluous have been referred on the basis of the author's monography "Teorie Języków Syntaktycznie Kategorialnych" ( "The Theories of Syntactically Categorial Languages"), PWN, Warszawa-Wrocław 1985. The basis of the theory of labels T p which takes into account the other position has to be presented here for the first time. Some extended ideas of the paper will also be presented in author's paper "Logiczne podstawy ontologii składni Języka" ("Logical foundations of language syntax ontology), Studia Filozoficzne 6-7 (271-272), (1988), pp. 263-284. (shrink)

The aim of this paper is to address a longstanding concern about the linguistic ‘relativ- ity’ of ontological categories, and resulting limitations in the scope of ontological theo- ries. Given recent evidence on the influence of language on cognitive dispositions, do we have empirical reasons to doubt that there are ontological categories that have uni- versal scope across languages? I argue that this is the case, at least if we retain the stan- dard ‘inferential’ approach within analytical ontology, i.e., (...) if we evaluate ontological interpretations of L-sentences relative to certain material inferences in L. Research in linguistic typology suggests that types of entities postulated for the domain of Indo- European languages cannot capture the ontological commitments of the (much larger group of) non-Indo-European languages. Ontological category theory thus seems to have three options. The first option is to abandon the standard ‘inferential’ approach to ontological category theory. Alternatively, if we stay with the inferential approach, we face the following choice. Either ontology must let go of its ambitions to provide general domain descriptions for any language and settle for the more modest project of reconstructing the ontological commitments of a group of natural languages. Or else analytical ontologists should turn to linguistic typology in order to accommodate the diversity of inferential structures embedded in natural languages. I recommend and ex- plore this third option, illustrating a strategy for how to construct a domain theory that can be used across languages. In a first step I show how linguistic research on the se- mantics of verbs and nouns (studies on so-called “Aktionsarten” and “Seinsarten”) can be used to identify the inferential patterns of ten basic concepts of modes of existence in time and space. In a second step I show how these inferential data can be inter- preted ontologically within General Process Theory, an ontological framework based on nonparticular individuals (“dynamics”). -/- . (shrink)

The Unified Foundational Ontology (UFO) was developed over the last two decades by consistently putting together theories from areas such as formal ontology in philosophy, cognitive science, linguistics, and philosophical logics. It comprises a number of micro-theories addressing fundamental conceptual modeling notions, including entity types and relationship types. The aim of this paper is to summarize the current state of UFO, presenting a formalization of the ontology, along with the analysis of a number of cases to illustrate (...) the application of UFO and facilitate its comparison with other foundational ontologies in this special issue. (The cases originate from the First FOUST Workshop – the Foundational Stance, an international forum dedicated to Foundational Ontology research.). (shrink)

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

Forgetting is importantly related to remembering, evidence possession, epistemic virtue, personal identity, and a host of highly-researched memory conditions. In this paper I examine the nature of forgetting. I canvass the viable options for forgetting’s ontological category, type of content, characteristic relation to content, and scale. I distinguish several theories of forgetting in the philosophy and psychology of memory literatures, theories that diverge on these options. The best theories from the literature, I claim, fail two critical tests that I develop (...) (the metacognition and prospection tests), underwriting arguments against the theories. I introduce a new theory about the state of forgetting—the learning, access failure, dispositional (LEAD) theory: to forget is to fail to access something that is both learned and either inaccessible or intended to be accessed. I argue that the LEAD theory of forgetting is the lead theory of forgetting. It passes the metacognition and prospection tests, and has several further virtues at no cost. Finally, I advocate reductionism about the process of forgetting; the process reduces wholly to states of forgetting. In particular, a process of forgetting is just a sequence of increasingly strong states of forgetting. (shrink)

The aim of this paper is to propose a systematic classification of emotions which can also characterize their nature. The first challenge we address is the submission of clear criteria for a theory of emotions that determine which mental phenomena are emotions and which are not. We suggest that emotions as a subclass of mental states are determined by their functional roles. The second and main challenge is the presentation of a classification and theory of emotions that can account for (...) all existing varieties. We argue that we must classify emotions according to four developmental stages: 1. pre-emotions as unfocussed expressive emotion states, 2. basic emotions, 3. primary cognitive emotions, and 4. secondary cognitive emotions. We suggest four types of basic emotions (fear, anger, joy and sadness) which are systematically differentiated into a diversity of more complex emotions during emotional development. The classification distinguishes between basic and non-basic emotions and our multi-factorial account considers cognitive, experiential, physiological and behavioral parameters as relevant for constituting an emotion. However, each emotion type is constituted by a typical pattern according to which some features may be more significant than others. Emotions differ strongly where these patterns of features are concerned, while their essential functional roles are the same. We argue that emotions form a unified ontological category that is coherent and can be well defined by their characteristic functional roles. Our account of emotions is supported by data from developmental psychology, neurobiology, evolutionary biology and sociology. (shrink)

It is widely recognized that accurately identifying and classifying competitors is a challenge for many companies and entrepreneurs. Nonetheless, it is a paramount activity which provide valuable insights that affect a wide range of strategic decisions. One of the main challenges in competitor identification lies in the complex nature of the competitive relationships that arise in business envi- ronments. These have been extensively investigate over the years, which lead to a plethora of competition theories and frameworks. Still, the concept of (...) competition remains conceptually complex, as none of these approaches properly formalized their assumptions. In this paper, we address this issue by means of an ontological analysis on the notion of competition in general, and of business competition, in particular, leveraging theories from various fields, including Marketing, Strategic Management, Ecology, Psychology and Cognitive Sciences. Our analysis, the first of its kind in the literature, is grounded on the Unified Foundational Ontology (UFO) and allows us to formally characterize why competition arises, as well as to distinguish between three types of business competitive relationships, namely market-level, firm-level and potential competition. (shrink)

s Gibson (1982) correctly points out, despite Quine’s brief flirtation with a “mitigated phenomenalism” (Gibson’s phrase) in the late 1940’s and early 1950’s, Quine’s ontology of 1953 (“On Mental Entities”) and beyond left no room for non-physical sensory objects or qualities. Anyone familiar with the contemporary neo-dualist qualia-freak-fest might wonder why Quinean lessons were insufficiently transmitted to the current generation.

The paper offers an interpretation of a disputed portion of Plato’s Theaetetus that is often called the Secret Doctrine. It is presented as a process ontology that takes two types of processes, swift and slow motions, as fundamental building blocks for ordinary material objects. Slow motions are powers which, when realized, generate swift motions, which, in turn, are subjectively bundled to compose sensible objects and perceivers. Although the reading of the Secret Doctrine offered here—a new version of the “Causal (...) Theory interpretation”—is not without problems, these problems are acknowledged in Plato’s text, confirming that this interpretation is correct. (shrink)

W. V. Quine famously defended two theses that have fallen rather dramatically out of fashion. The first is that intensions are “creatures of darkness” that ultimately have no place in respectable philosophical circles, owing primarily to their lack of rigorous identity conditions. However, although he was thoroughly familiar with Carnap’s foundational studies in what would become known as possible world semantics, it likely wouldn’t yet have been apparent to Quine that he was fighting a losing battle against intensions, due in (...) large measure to developments stemming from Carnap’s studies and culminating in the work of Kripke, Hintikka, and Bayart. These developments undermined Quine’s crusade against intensions on two fronts. First, in the context of possible world semantics, intensions could after all be given rigorous identity conditions by defining them (in the simplest case) as functions from worlds to appropriate extensions, a fact exploited to powerful and influential effect in logic and linguistics by the likes of Kaplan, Montague, Lewis, and Cresswell. Second, the rise of possible world semantics fueled a strong resurgence of metaphysics in contemporary analytic philosophy that saw properties and propositions widely, fruitfully, and unabashedly adopted as ontological primitives in their own right. This resurgence — happily, in my view — continues into the present day. -/- For a time, at any rate, Quine experienced somewhat better success with his second thesis: that higher-order logic is, at worst, confused and, at best, a quirky notational alternative to standard first-order logic. However, Quine notwithstanding, a great deal of recent work in formal metaphysics transpires in a higher-order logical framework in which properties and propositions fall into an infinite hierarchy of types of (at least) every finite order. Initially, the most philosophically compelling reason for embracing such a framework since Russell first proposed his simple theory of types was simply that it provides a relatively natural explanation of the paradoxes. However, since the seminal work of Prior there has been a growing trend to consider higher-order logic to be the most philosophically natural framework for metaphysical inquiry, many of the contributors to this volume being among the most important and influential advocates of this view. Indeed, this is now quite arguably the dominant view among formal metaphysicians. -/- In this paper, and against the current tide, I will argue in §1 that there are still good reasons to think that Quine’s second battle is not yet lost and that the correct framework for logic is first-order and type-free — properties and propositions, logically speaking, are just individuals among others in a single domain of quantification — and that it arises naturally out of our most basic logical and semantical intuitions. The data I will draw upon are not new and are well-known to contemporary higher-order metaphysicians. However, I will try to defend my thesis in what I believe is a novel way by suggesting that these basic intuitions ground a reasonable distinction between “pure” logic and non-logical theory, and that Russell-style semantic paradoxes of truth and exemplification arise only when we move beyond the purely logical and, hence, do not of themselves provide any strong objection to a type-free conception of properties and propositions. -/- Most of my arguments in §1 are largely independent of any specific account of the nature of properties and propositions beyond their type-freedom. However, I will in addition argue that there are good reasons to take propositions, at least, to be very fine-grained. My arguments are thus bolstered significantly if it can be shown that there are in fact well-defined examples of logics that are not only type-free but which comport with such a conception of propositions. It is the purpose of §2 to lay out a logic of this sort in some detail, drawing especially upon work by George Bealer and related work of my own. With the logic in place, it will be possible to generalize the line of argument noted above regarding Russell-style paradoxes and, in §3, apply it to two propositional paradoxes — the Prior-Kaplan paradox and the Russell-Myhill paradox — that are often taken to threaten the sort of account developed here. (shrink)