The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies.[1] To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO).[2] With this project we aim to move (...) beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for (...) the model organism communities to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

Contrary to Sankey’s central assumption, incommensurability does not imply incomparability of content, nor threaten scientific realism by challenging the rationality of theory comparison. Moreover, Sankey equivocates between reference to specific entities by statements used to test theories and reference to kinds by theories themselves. This distinction helps identify and characterize the genuine threat that incommensurability poses to realism, which is ontological discontinuity as evidenced in the historical record: Successive theories reclassify objects into mutually exclusive sets of kinds to (...) which they refer. That is why claiming that scientific progress is an increasingly better approximation to truth is difficult to justify. Similarly, Sankey’s attack on neo-Kantian antirealist positions is based on his misunderstanding of some of the central terms of those positions, making most of his attack on them ineffectual, including his diagnosis of their incoherence. We conclude by reiterating our conviction that in this debate meta-incommensurability plays an important role.Keywords: Scientific realism; Incommensurability; Meta-incommensurability; Thomas Kuhn; Paul Feyerabend; Howard Sankey. (shrink)

The distinction between reference ontologies and application ontologies crept rather unobtrusively into the recent literature on knowledge engineering. A lot of the discourse surrounding this distinction – notably, the one framing the workshop generating this collection of papers – suggests the two types of ontologies are in some sort of opposition to one another. Thus, Borge et al. [3] characterize reference ontologies (more recently, foundational ontologies) as rich, axiomatic theories whose focus is to clarify the intended meanings of (...) terms used in specific domains. Application ontologies, by contrast, provide a minimal terminological structure to fit the needs of a specific community. Reflecting their minimal nature, Masolo et al. [7] refer to such ontologies as “lightweight” ontologies. An application ontology can be lightweight in a second respect as well, namely, that it may not necessarily take the form of fully-fledged axiomatic theory. Rather, it might only be a taxonomy of the relevant domain, a division of the domain into a salient collection of classes, perhaps ordered by the subclass relation. Importantly, though, for an application ontology to “fit the needs of a specific community” needn’t require representational accuracy. In the “worst” case (from a reference ontology perspective), to fit the needs of a community is just to represent uncritically what people in that community think about the ontology’s domain. (shrink)

In “Ontological realism: Methodology or misdirection?” I offered a detailed critique of the position referred to as “realism” taken by Barry Smith and Werner Ceusters. This position is claimed to serve as the basis for a “realist methodology” that they seek to impose on the development of scientific ontologies, particularly within the biomedical sciences. Here, in part responding to a reply to those criticisms by Smith and Ceusters, I return the focus to an examination of fundamental incoherencies in this realist (...) approach and propose an alternative that is amenable to much of what Smith and Ceusters hope to accomplish. And I sketch what I believe is needed to advance ontology theory and practice in the sciences. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute (...) class='Hi'>Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Contains the following contributions: -/- Ingvar Johansson: Ontologies and Concepts. Two Proposals -/- Christopher Menzel: Reference Ontologies - Application Ontologies: Either/Or or Both/And? -/- Luc Schneider: Foundational Ontologies and the Realist Bias -/- Guenther Goerz, Kerstin Buecher, Bernd Ludwig, Frank-Peter Schweinberger, and Iman Thabet: Combining a Lexical Taxonomy with Domain Ontology in the Erlangen Dialogue System -/- Vim Vandenberghe, Burkhard Schafer, John Kingston: Ontology Modelling in the Legal Domain - Realism Without Revisionism -/- A Proposed Methodology for (...) the Development of Application-Based Formal Ontologies Eric Little . (shrink)

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

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We (...) advance a proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

This is a book about the concept of a physical thing and about how the names of things relate to the things they name. It questions the prevalent view that names 'refer to' or 'denote' the things they name. Instead it presents a new theory of proper names, according to which names express certain special properties that the things they name exhibit. This theory leads to some important conclusions about whether things have any of their properties as a matter of (...) necessity. This will be an important book for philosophers in metaphysics and the philosophy of language, though it will also interest linguists concerned with the semantics of natural language. (shrink)

ABSTRACT: In its strongest unqualified form, the principle of wholistic reference is that in any given discourse, each proposition refers to the whole universe of that discourse, regardless of how limited the referents of its non-logical or content terms. According to this principle every proposition of number theory, even an equation such as "5 + 7 = 12", refers not only to the individual numbers that it happens to mention but to the whole universe of numbers. This principle, its (...) history, and its relevance to some of Oswaldo Chateaubriand's work are discussed in my 2004 paper "The Principle of Wholistic Reference" in Essays on Chateaubriand's "Logical Forms". In Chateaubriand's réplica (reply), which is printed with my paper, he raised several important additional issues including the three I focus on in this tréplica (reply to his reply): truth-values, universes of discourse, and formal ontology. This paper is self-contained: it is not necessary to have read the above-mentioned works. The principle of wholistic reference (PWR) was first put forth by George Boole in 1847 when he espoused a monistic fixed-universe viewpoint similar to the one Frege and Russell espoused throughout their careers. Later, Boole elaborated PWR in 1854 from the pluralistic multiple-universes perspective. (shrink)

This is a book about the concept of a physical thing and about how the names of things relate to the things they name. It questions the prevalent view that names 'refer to' or 'denote' the things they name. Instead it presents a new theory of proper names, according to which names express certain special properties that the things they name exhibit. This theory leads to some important conclusions about whether things have any of their properties as a matter of (...) necessity. This will be an important book for philosophers in metaphysics and the philosophy of language, though it will also interest linguists concerned with the semantics of natural language. (shrink)

Eli Hirsch argues that certain ontological disputes involve a conflict between “equivalent” languages, and that the principle of charity compels each disputant to interpret the other as speaking truly in their own language. For Hirsch, a language’s semantics maps sentences (in context) onto sets of possible worlds but assigns no role to reference. I argue that this method leads to an overly uncharitable portrayal of the disputes at issue – whereby ontologists who speak “equivalent” languages can only argue about (...) syntax. Lack of charity stems from the fact that this portrayal likely fails to uphold the self-conception of the disputants – and particularly what I will call “the weak self-conception”. As a result, Hirsch’s deflationism falls victim of the same principle of charity that informs it. (shrink)

relations between events both require a more complex structure on the domain underlying the meaning representations than is commonly assumed. This paper proposes an ontology based on such notions as causation and consequence, rather than on purely temporal primitives. A central notion in the ontology..

This study in fundamental ontology calls for rethinking some pedestrian assumptions about what there is and provides the motivation for a new theory of reference. It contains clear, crisp discussions of mereology, identity, reference, and necessity and should be valuable to metaphysicians and philosophers of language.

I argue that Amie Thomasson’s recent theory of the methodology to be applied to find the truth-conditions for claims of existence faces serious objections. Her account is based on Devitt and Sterelny’s solution to the qua problem for theories of reference fixing; however, such a solution cannot be also applied to analyze existential claims.

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

The transience of being in the Chinese context—and specifically within Daoist texts—has been the subject of scholarly attention both as a philosophical theme and as a social phenomenon. Dao is the mystery that makes nature “the way it is.” It can mean process, pattern, or existence. Eastern thinkers tend to find truth in every perspective, pursuing the middle way, and they stress mutual dependence—Zhuangzi’s “equality of things,” the “axis of Dao,” etc. The Chinese sages tend to harbor an optimistic outlook (...) that, however opposed divergent views may appear, in the end they are bound to harmonize and complement one another. Humans can unite themselves with the way they live. There are three threads at work in Zhuangzi’s thought:(1) The principle of equality: all things are equal or have relative parity. Each has its own merit, even that which seems deformed or useless to humans.(2) The principle of difference: each thing is unique and exists in itself in accordance with the Dao.(3) The principle of transformation. The only constant is that myriad beings are always transforming and becoming. (shrink)

I have been interested for quite some time in the relevance of reference to ontology. Another who has shown equal interest is W. V. Quine. Surprisingly, because of many other disagreements, there is a large area in which we agree about reference and ontology, namely, that there is some reason to think that both are “inscrutable.” Not so surprisingly, there is a crucial point where we disagree, namely, concerning the relativity of reference and ontology. (...) Although it is not clear, it seems that Quine holds that both reference and ontology are relative to what he calls a “background language” in a way that results in metaphysical questions, as I describe them, being senseless or meaningless. He argues for this relativity from inscrutability. I, however, explain it by postulating that ontological problems and certain referential problems are in a certain sense, “external.” In this paper I propose to lay out what I take to be the relevance of reference to ontological problems, show where Quine’s claims of inscrutability agree with my view, clarify Quine’s claims about relativity, and finally show that, given the inscrutability we both find acceptable, it is reasonable to reject the relativity only Quine accepts. (shrink)

Abstract: We propose a dichotomy between object-entities and meaning-entities. The former are entities such as molecules, cells, organisms, organizations, numbers, shapes, and so forth. The latter are entities such as concepts, propositions, and theories belonging to the realm of logic. Frege distinguished analogously between a ‘realm of reference’ and a ‘realm of sense’, which he presented in some passages as mutually exclusive. This however contradicts his assumption elsewhere that every entity is a referent (even Fregean senses can be referred (...) to by means of suitably constructed expressions). We apply the meaning/object dichotomy to mathematical and fictional entities, and develop a view of mathematical and other abstract objects as the results of certain types of demarcation – as for example the North Sea is the result of demarcations built into naval charts. Such demarcations reflect demarcatory acts, which presuppose complex cognitive and social structures enabling the creation of maps, of theories (of mathematics, of natural science), and of novels. (shrink)

Julian Dodd has characterized the default position in metaphysics as meta-ontologically realist: the answers to first-order ontological questions are thought to be entirely independent of the things we say and think about the entities at issue. Consequently, folk ontologies are liable to substantial error. But while this epistemic humility is commendable where the ontology of natural kinds is concerned, it seems misplaced with respect to social kinds since their ontology is dependent upon the human social world. Using art (...) and art-kinds as paradigmatic examples of social kinds, I argue that meta-ontological realism sets conditions that are too strict to apply to social kinds. Nevertheless, I argue that we should not be too quick to embrace the conclusion that our folk theories of social kinds cannot err substantially. By modelling the reference of social kind-terms on that of natural kind-terms, it becomes clear that in both cases, our sole epistemic privilege lies in our ability to pinpoint the subject of our inquiries. (shrink)

When we use a directly referential expression to denote an object, do we incur an ontological commitment to that object, as Russell and Barcan Marcus held? Not according to Quine, whose regimented language has only variables as denoting expressions, but no constants to model direct reference. I make a case for a more liberal conception of ontological commitment—more wide-ranging than Quine’s—which allows for commitment to individuals, with an improved logical language of regimentation. The reason for Quine’s prohibition on commitment (...) to individuals, I argue, is that his choice of regimented language is heavily informed by his holist epistemology, in which objects are introduced via a description of their explanatory role. But non-holists can coherently attempt to commit to individuals using directly referential expressions, modelled in a formal language as constants. While holding on to the insight that a logical language is a helpful medium for ontology, I propose instead a more permissive language of regimentation, one expanded to permit the use of constants to record attempts to commit to individuals, which allows us to make sense of non-holist theories with alternative name-based or name-and-variable-based criteria of ontological commitment as well as Quinean theories. (shrink)

This chapter contains sections titled: Abstract Introduction Semantics, Cross ‐ Cultural Style Metalinguistic and Linguistic Intuitions Speaker's Reference and Semantic Reference The Vacuity of Ontological Disagreements Conclusion References.

I argue that Amie Thomasson’s recent theory of the methodology to be applied to find the truth-conditions for claims of existence faces serious objections. Her account is based on Devitt and Sterelny’s solution to the qua problem for theories of reference fixing; however, such a solution cannot be also applied to analyze existential claims.

According to the propositional view of belief, a belief situation involves a believer’s standing in the relation of belief to a proposition. It is argued that the propositional view has unacceptable implications concerning the identity conditions of belief situations involving beliefs with indexical contents, especially where such beliefs are held over a period of time during which background circumstances change. After a critical discussion of Perry’s alternative to the propositional view, a version of the adverbial theory of belief, which accounts (...) satisfactorily for the identity conditions of belief situations, is advanced. This theory, which avoids the standard objections to adverbialism, is defended against the charge that it cannot provide an account of the semantics of sentences attributing the same belief to two or more believers. In the course of this defense it is argued that the standard propositional account of such sentences is insensitive to everyday language. (shrink)

The essays address a wide range of topics, including normativity and naturalized epistemology, holism, consciousness, the philosophy of logic, perception, value ...

The Analysis of Perception i Moore's most systematic attempt to handle the problems of in- tentionality occurs in connection with his analysis of perception in Some Main Problems of Philosophy . He begins the book with the following ...

Thought, Fact, and Reference was first published in 1978.Against a background of criticism of alternative accounts, Professor Hochberg presents an analysis of thought, reference, and truth within the tradition of logical atomism. He analyzes G. E. Moore's early attack on idealism and examines the influence of Moore on the development of Bertrand Russell's and Ludwig Wittgenstein's logical atomism. He traces an early divergence between Russell and Wittgenstein, on the one side, and Moore and Gottlob Frege on the other, (...) into variants recently advocated by Wilfrid Sellars, Gustav Bergmann, and others. The work will be of interest to professional philosophers, graduate students in philosophy, and linguists with interests in philosophy. (shrink)

Analytic philosophers apply the term ‘object’ both to concreta and to abstracta of certain kinds. The theory of objects which this implies is shown to rest on a dichotomy between object-entities on the one hand and meaning-entities on the other, and it is suggested that the most adequate account of the latter is provided by Husserl’s theory of noemata. A two-story ontology of objects and meanings (concepts, classes) is defended, and Löwenheim’s work on class-representatives is cited as an indication (...) of how the need for higher types may be obviated, even in mathematical contexts. The paper concludes with a sketch of the taxonomy of the object realm which results from the above. (shrink)

A. Meinong’s views are usually associated with an highly inflated ontology including various kinds of nonexistent objects, incomplete and impossible ones among others. Around the turn of the century B. Russell strongly criticised this ontology accusing it of inconsistency. And perhaps because of this criticism Meinong’s views have been forgotten for a long time. Only recently some philosophers have created theories of objects which are formalisations of Meinong’s ontology or which are directly inspired by the ontology (...) 1 . However there still remains a need to discuss the problem of ways of reference to Meinongian objects regarding their specific structure of predication, and the interrelated problem of ontological commitment of those theories. Meinong’s ontological theory seems to be not so bizzare if we interpret it as a theory of possible intentional objects, i.e. possible objects of consciousness. And this interpretation perfectly agrees with phenomenological tradition from Brentano to Husserl and with the contemporary philosophy of mind. Needless to say reference is a special form of intentional relation so semantical investigations into these objects are of great relevance for general theory of intentionality. (shrink)

Enterprise Risk Management and security have become a fundamental part of Enterprise Architecture, so several frameworks and modeling languages have been designed to support the activities associated with these areas. Archi- Mate’s Risk and Security Overlay is one of such proposals, endorsed by The Open Group. We investigate the capabilities of the proposed security-related con- structs in ArchiMate with regard to the necessities of enterprise security modeling. Our analysis relies on a well-founded reference ontology of security to uncover (...) ambiguity, missing modeling elements, and other deficiencies of the security mod- eling capabilities in ArchiMate. Based on this ontologically-founded analysis, we propose a redesign of security aspects of ArchiMate to overcome its original limitations. (shrink)

Enterprise Risk Management involves the process of identification, evaluation, treatment, and communication regarding risks throughout the enterprise. To support the tasks associated with this process, several frameworks and modeling languages have been proposed, such as the Risk and Security Overlay (RSO) of ArchiMate. An ontological investigation of this artifact would reveal its adequacy, capabilities, and limitations w.r.t. the domain of risk and security. Based on that, a language redesign can be proposed as a refinement. Such analysis and redesign have been (...) executed for the risk elements of the RSO grounded in the Common Ontology of Value and Risk. The next step along this line of research is to address the following research problems: What would be the outcome of an ontological analysis of security-related elements of the RSO? That is, can we identify other semantic deficiencies in the RSO through an ontological analysis? Once such an analysis is provided, can we redesign the security elements of the RSO accordingly, in order to produce an improved artifact? Here, with the aid of the Reference Ontology for Security Engineering (ROSE) and the ontological theory of prevention behind it, we address the remaining gap by proceeding with an ontological analysis of the security-related constructs of the RSO. The outcome of this assessment is an ontology-based redesign of the ArchiMate language regarding security modeling. In a nutshell, we report the following contributions: (1) an ontological analysis of the RSO that identifies six limitations concerning security modeling; (2) because of the key role of the notion of prevention in security modeling, the introduction of the ontological theory of prevention in ArchiMate; (3) a well-founded redesign of security elements of ArchiMate; and (4) ontology-based security modeling patterns that are logical consequences of our proposal of redesign due to its underlying ontology of security. As a form of evaluation, we show that our proposal can describe risk treatment options, according to ISO 31000. Finally, besides presenting multiple examples, we proceed with a real-world illustrative application taken from the cybersecurity domain. (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)