The Heythrop Journal, Volume 63, Issue 2, Page 196-209, March 2022.

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)

One assumption of the new mechanistic approach is that there are two kinds of mechanistic explanations: etiological and constitutive ones. While the former explain phenomena in terms of their preceding causes, the latter are supposed to refer to mechanisms that constitute phenomena. Based on arguments by Kaiser and Krickel (Br J Philos Sci 68(3):745–779, 2017) and Krickel (The mechanical world, vol. 13, Springer International Publishing, 2018), I will show that this view is too narrow. Indeed, three different types of explanation (...) are usually subsumed under the label “constitutive explanation”. However, one of those types of explanation is not a version of constitutive explanation. Rather it is a variant of etiological explanation. As a result, I will show that there are four types of mechanistic explanation, two variants of etiological explanation—which I will call output mechanistic explanations and input-output mechanistic explanations—and two variants of constitutive explanation—which I will call filler mechanistic explanations and dimensioned mechanistic explanations. Keeping these apart is crucial as they come with different ontological implications. An evaluation of the mechanistic approach regarding its stance on reduction, levels, and interlevel causation crucially depends on which notion of mechanistic explanation one has in mind. (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)

Are works of music types of performance or are they continuants? Types are unchanging entities that could not have been otherwise; continuants can undergo change through time and could have been different. Picking up on this distinction, Guy Rohrbaugh has recently argued that musical works are continuants rather than performance-types. This paper replies to his arguments and, in the course of so doing, elaborates and defends the conception of musical works as types of performance. I end the article by arguing (...) that the conception of musical works as continuants is under-motivated and, ultimately, obscure. (shrink)

In 1982, Wolniewicz proposed a formal ontology of situations based on the lattice of elementary situations (cf. [7, 8]). In [3], I constructed some types of formal structure Porphyrian Tree Structures (PTS), Concepts Structures (CS) and the Structures of Individuals (U) that formally represent ontologically fundamental categories: species and genera (PTS), concepts (CS) and individual beings (U) (cf. [3, 4]). From an ontological perspective, situations and concepts belong to different categories. But, unexpectedly, as I shall show, some variants of (...) CS and Wolniewicz’s lattice are similar. The main theorem states that a subset of a modified concepts structure (called CS+) based on CS fulfils the axioms of Wolniewicz’ lattice. Finally, I shall draw some philosophical conclusions and state some formal facts. (shrink)

There are at least two passages in the jamesian corpus where he seems to establish a topology of "regional ontologies", or to set up multiple "language games". the first of these is "the principles of psychology" when he talks about "the many worlds", or "...sub-universes commonly discriminated from each other...", the second is in "pragmatism", where he notes that there "are...at least three well-characterized levels, stages, or types of thought about the world we live in..." two questions immediately come to (...) mind about these levels. first, is each of these areas of equal importance, epistemologically and ontologically speaking? second, how, if at all, are these regional areas related to each other? each of these questions has a seemingly obvious answer. to wit, the world of perception is more important than any of the other areas; and second, the regional areas are related in terms of the disjunctive and conjunctive transitions which james so strenuously upholds, resulting in an overall "concatenated" picture. i argue that both of these responses are insufficient, and that the issue is more complicated than it first appears. (edited). (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)

This paper explores the ontology of musical improvisation (MI). MI, as process in which creative and performing activities are one and the same generative occurrence, is contrasted with the most widespread conceptual resource used in inquiries about music ontology of the Western tradition: the type/token duality (TtD). TtD, which is used for explaining the relationship between musical works (MWs) and performances, does not fit for MI. Nonetheless MI can be ontologically related to MWs. A MW can ensue (...) from MI and MI can be required for performing a MW faithfully. As performance on a MW, MI can offer versions of a MW, manifest a MW, and, especially, use it as one of its ‘ingredients’. Recordings of MI present special challenges and an unexpected ontological revival. (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)

This paper presents a generalization of a proposal of van Benthem’s who has shown how to provide a canonical name for any object in propositional type theory. Van Benthem’s idea is to characterize any function in the hierarchy by the Boolean values the function takes for any sequence of arguments. The recursive definition of canonical names uses only the abstraction, functional application, the identity operator and the fact that we have a name for the true and the false. We (...) show that this result can be extended to the finite theory of types by the introduction of an algebra on individuals. (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.

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)

I introduce a new version of Moral Error Theory, which I call Type-B Moral Error Theory. According to a Type-B theorist there are no facts of the kind required for there to be morality instricto sensu, but there can be irreducible ‘normative’ properties which she deems, strictly speaking, to be morally irrelevant. She accepts that there areinstrumentalall things considered oughts, andcategoricalpro tanto oughts (both of which she deems morally irrelevant), but denies that there arecategoricalall things considered oughts on (...) pain of requiring ‘queer’ facts to obtain. I detail the most central motivation of this version of the theory against its more traditional rival, according to which there are no irreducible normative properties at all. The motivation is that it, unlike its rival, can successfully be defended against the notorious charge of self-defeat. (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)

The way society is organised means that we all get made into members of various types of people, such as judges, wives, or women. These ‘human social kinds’ may be brought into being by oppressive social arrangements, and people may suffer oppression in virtue of being made into a member of a certain human social kind. This book argues that we should pay attention to the ways in which the very fact of being made into a member of a certain (...) human social kind can be oppressive in and of itself. For example, someone who becomes a wife under circumstances where husbands have unjust powers over their wives has suffered a wrong, even if her husband never in fact exercises these powers. The book argues that social movements against racial and gendered oppression, including efforts to advance trans liberation, must get to grips with this phenomenon, and it supplies the conceptual tools needed to do so. The first tool is an analysis of this general form of wrong, termed ‘ontic injustice’. The second tool is an account of ‘ontic oppression’, a particular kind of ontic injustice in which the wrong amounts to a form of oppression, in the sense of being structural and pervasive. The third tool is a pluralist account of race and gender kinds, according to which there is no single social kind that corresponds to a gender category such as ‘woman’, but, rather, there are various different social kinds, each of which is explanatory for different purposes. (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)

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)

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)

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)

Even the most Parmenidean-minded of people recognize that quotidian objects somehow undergo change. This claim, nonetheless, is as clearly intuitive as it is apparently incompatible with one of our most widely believed logical principles, namely, Leibniz's Law. This paper focuses briefly on the metaphysical issue underlying this alleged incompatibility in order to provide elements for exploring its semantical counterpart: the analysis of the logical form of sentences attributing complementary temporal properties to current objects. Four analyses are presented, and the ability (...) of each to account for the linguistic data is explained. The semantical issue is preceded by some introductory remarks on the role of temporal references in the evaluation of declarative sentences. (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)

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

The ontological model framework for an operational theory has generated much interest in recent years. The debate concerning reality of quantum states has been made more precise in this framework. With the introduction of generalized notion of contextuality in this framework, it has been shown that completely mixed state of a qubit is preparation contextual. Interestingly, this new idea of preparation contextuality has been used to demonstrate nonlocality of some \(\psi \) -epistemic models without any use of Bell’s inequality. In (...) particular, nonlocality of a non maximally \(\psi \) -epistemic model has been demonstrated from preparation contextuality of a maximally mixed qubit and Schrödinger’s steerability of the maximally entangled state of two qubits (Leifer and Maroney, Phys Rev Lett 110:120401, 2013). In this paper, we, show that any mixed state is preparation contextual. We, then, show that nonlocality of any bipartite pure entangled state, with Schmidt rank two, follows from preparation contextuality and steerability provided we impose certain condition on the epistemicity of the underlying ontological model. More interestingly, if the pure entangled state is of Schmidt rank greater than two, its nonlocality follows without any further condition on the epistemicity. Thus our result establishes a stronger connection between nonlocality and preparation contextuality by revealing nonlocality of any bipartite pure entangled states without any use of Bell-type inequality. (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.

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)

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)

In this article we describe two core ontologies of law that specify knowledge that is common to all domains of law. The first one, FOLaw describes and explains dependencies between types of knowledge in legal reasoning; the second one, LRI-Core ontology, captures the main concepts in legal information processing. Although FOLaw has shown to be of high practical value in various applied European ICT projects, its reuse is rather limited as it is rather concerned with the structure of legal (...) reasoning than with legal knowledge itself: as many other “legal core ontologies”, FOLaw is therefore rather an epistemological framework than an ontology. Therefore, we also developed LRI-Core. As we argue here that legal knowledge is based to a large extend on common-sense knowledge, LRI-Core is particularly inspired by research on abstract common-sense concepts. The main categories of LRI-Core are: physical, mental and abstract concepts. Roles cover in particular social worlds. Another special category are occurrences; terms that denote events and situations. We illustrate the use of LRI-Core with an ontology for Dutch criminal law, developed in the e-Court European project. (shrink)

Words form a fundamental basis for our understanding of linguistic practice. However, the precise ontology of words has eluded many philosophers and linguists. A persistent difficulty for most accounts of words is the type-token distinction [Bromberger, S. 1989. “Types and Tokens in Linguistics.” In Reflections on Chomsky, edited by A. George, 58–90. Basil Blackwell; Kaplan, D. 1990. “Words.” Aristotelian Society Supplementary Volume LXIV: 93–119]. In this paper, I present a novel account of words which differs from the atomistic (...) and platonistic conceptions of previous accounts which I argue fall prey to this problem. Specifically, I proffer a structuralist account of linguistic items, along the lines of structuralism in the philosophy of mathematics [Shapiro, S. 1997. Philosophy of Mathematics: Structure and Ontology. Oxford University Press], in which words are defined in part as positions in larger linguistic structures. I then follow Szabò [1999. “Expressions and Their Representations.” The Philosophical Quarterly 49 (195): 145–163] and Parsons [1990. “The Structuralist View of Mathematical Objects.” Synthese 84: 303–346] in further defining words as quasi-concrete objects according to a representation relation. This view aims for general correspondence with contemporary generative linguistic approaches to the study of language. (shrink)

In their paper “Sixteen Days” Barry Smith and Berit Brogaard try to answer the question: when does a human being begin to exist? In this paper we will address some methodological issues connected with this exercise in ontology. We shall begin by sketching the argument of “Sixteen Days”. We shall then attempt to characterize what is special about the ontological realism of “Sixteen Days” as contrasted to the linguistic constructivism which represents the more dominant current in contemporary analytic philosophy. (...) This will allow us to infer guidelines for assessing the quality of ontological theories of various types. We shall argue that ontological parsimony, groundedness, faithfulness to ordinary language, consistency with science, coherence, and fruitfulness are at least part of the adequacy criteria for such theories. These criteria will then be applied to the theory presented in “Sixteen Days”, and they will lead us to some revisions of this theory as well as to some reflections on its ethical implications. (shrink)

Do Web devices (addresses, tags, networks, and the rest) have counterparts in classical ontology? Yes, but they allow us also to introduce more refined distinctions. In addition, their dynamic use could inspire a dynamic reconception of classical ontology. In the process of making explicit ontological types, different types can be undistinguished at the first step (considered as “floating types”) to be defined only in a further step, one in which their function as distinguishers of other kinds of entities (...) has to be made explicit. The fact that the ontological import of some node in a network of tags and addresses could evolve with the transformation of the network can most easily find an interpretation in this dynamic conception of ontology. (shrink)

In a series of papers over a period of several years Barry Smith andWerner Ceusters have offered a number of cogent criticisms of historical approaches to creating, maintaining, and applying biomedical terminologies and ontologies. And they have urged the adoption of what they refer to as a “realism-based” approach. Indeed, at times they insist that the realism-based approach not only offers clear advantages and a well-founded methodological basis for ontology development and evaluation, but that such a realist perspective is (...) in fact necessary for understanding and using terminologies and ontologies in science. -/- This paper explores a number of questions surrounding such claims, provides a careful characterization of the type of realism recommended by Smith and Ceusters, and evaluates the role that realism plays in the critiques and recommendations that they offer. The conclusion reached is that while Smith’s and Ceusters’ criticisms of prior practice in the treatment of ontologies and terminologies in medical informatics are often both perceptive and well founded, and while at least some of their own proposals demonstrate obvious merit and promise, none of this either follows from or requires the brand of realism that they propose. (shrink)

An ontology is a domain of knowledge structured through formal rules so that it can be interpreted and used by computers. Ontologies are becoming increasingly important in bioinformatics because they can be linked to the information in databases and their knowledge then used to query the databases. Typical examples in current use are the Gene Ontology, which incorporates much of our knowledge about gene products, and ontologies of developmental anatomy, which, for example, facilitate tissue‐based queries to gene expression (...) databases both textually and spatially. This article considers the production, formulation and types of bio‐ontologies together with the reasons why they are so useful. © BioEssays 25:501–506, 2003. © 2003 Wiley Periodicals, Inc. (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)

"An ontology may be described as consisting of three kinds of statements: those that set the problems; those that list the kinds of entities that exist; those that show how the existents solve the problems. Ontologies may thus differ in different ways. The most decisive way concerns the kinds of entities deemed to exist. With respect to this way, there are but two types of ontology. One is lavish, cluttered; the other, frugal, sparse. The ontologies of Plato, Meinong, (...) and Frege are lavish; those of Hume, Brentano, and Wittgenstein are frugal. Gustav Bergmann has propounded both types of ontology in the course of his thirty years of philosophizing. The Bergmann of The Metaphysics of Logical Positivism (1954) and Meaning and Existence (1959) propounds a frugal ontology. The Bergmann of Logic and Reality (1964) and Realism: A Critique of Brentano and Meinong (1967) propounds a lavish ontology. In a way of speaking that Bergmann himself has used, the world of the early Bergmann is a desert, the world of the later Bergmann a jungle. In a way of speaking that is suggestive, speculative, had the early Bergmann written Realism, he would have dedicated it to Brentano rather than to Meinong, as did the.. (shrink)