Barry Smith

The paper seeks to develop an account of indexical phenomena based on the highly general theory of structure and dependence set forth by Husserl in his Logical Investigations. Husserl here defends an Aristotelian theory of meaning, viewing meanings as species or universals having as their instances certain sorts of concrete meaning acts. Indexical phenomena are seen to involve the combination of such acts of meaning with acts of perception, a thesis here developed in some detail and contrasted with accounts of indexicals suggested by Frege, Wittgenstein and by the later Husserl himself in his Ideas I. Implications are drawn also for our understanding of the categorial grammar sketched by Husserl in his 4th Logical Investigation, as also for our understanding of the nature of proper names and other candidate indexical expressions

Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.

It will be the thesis of this paper that there are among our mental acts some which fall into the category of real material relations. That is: some acts are necessarily such as to involve a plurality of objects as their relata or fundamenta. Suppose Bruno walks into his study and sees a cat. To describe the seeing, here, as a relation, is to affirm that it serves somehow to tie Bruno to the cat. Bruno's act of seeing, unlike his feeling depressed, his putative thinking-about-Santa-Claus or his musing, abstractedly, about the tallest spy, has at least two fundamenta: it is, as a matter of necessity, dependent for its existence upon both Bruno himself and the cat that he sees. This idea will naturally raise echoes of Russell's doctrine of knowledge by acquaintance. 'I am acquainted with an object', Russell tells us, 'when I have a direct cognitive relation to that object, i. e. when I am directly aware of the object itself' (1918, p. 209). And indeed a distinction in many ways like that between acquaintance and description will find a place within the theory here projected, but there are crucial differences.

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning.

Imagine that your body has become attached, without your permission, to that of a sick violinist. The violinist is a human being. He will die if you detach him. Such detachment seems, nonetheless, to be morally permissible. Thomson argues that an unwantedly pregnant woman is in an analogous situation. Her argument is considered by many to have established the moral permissibility of abortion even under the assumption that the foetus is a human being. Another popular argument is that presented by Singer and Unger to the effect that even those who are moderately prosperous are morally obliged to help the poor if they can do so at relatively small cost to themselves. The paper (published under the pseudonym 'Nicola Bourbaki') considers the question whether these two arguments can be simultaneously valid.

In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed partitions along three axes: (a) degree of correspondence between partition cells and objects in reality; (b) degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) degree of completeness and exhaustiveness with which a partition represents reality. This classification is used to characterize three types of partitions that play an important role in spatial information science: cadastral partitions, categorical coverages, and the partitions involved in folk categorizations of the geospatial domain.

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth.

What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas were developed prior to the scientific discoveries of the modern era, he approached the objects and relations of everyday reality with the same ontological seriousness with which scientists today approach the objects of physics. We shall seek to show that what Aristotle has to say about these commonsensical objects and relations can, when translated into more formal terms, be of use also to contemporary ontologists. More precisely, we shall argue that his ideas can contribute to the development of a rigorous theory of those social and institutional components of everyday reality – the settings of human behavior – which are the subject of this volume. When modern-day philosophers turn their attentions to ontology they begin not with Aristotle but rather, in almost every case, with a set-theoretic ontology of the sort which is employed in standard model-theoretic semantics. Set-theoretic ontology sees the world in atomistic terms: it postulates a lowest level of atoms or urelements, from out of which successively higher levels of set-theoretic objects are then constructed. The approach to ontology to be defended here, in contrast, starts not with atoms but with the mesoscopic objects by which we are surrounded in our normal day-to-day..

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure.

There are some who defend a view of vagueness according to which there are intrinsically vague objects or attributes in reality. Here, in contrast, we defend a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extension. We provide a new formulation of these ideas in terms of a theory of granular partitions. We show that this theory provides a general framework within which we can understand the relation between vague terms and concepts on the one hand and correlated portions of reality on the other. We also sketch how it might be possible to formulate within this framework a theory of vagueness which dispenses with the notion of truth-value gaps and other artifacts of more familiar approaches.

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data.

The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an effort called Industrial Ontologies Foundry (IOF) has been formed to pursue the same goal for the industrial manufacturing domain. However, developing a coherent ontology covering the entire industrial manufacturing domain has been known to be a mountainous challenge because of the multidisciplinary nature of manufacturing. To manage the scope and expectations, the IOF community kicked-off its effort with a proof-of-concept (POC) project. This paper describes the developments within the project. It also provides a brief update on the IOF organizational set up.

We review an influential series of lectures on analytic philosophy published in 1976 by the West German philosopher Ernst Tugendhat focusing on Tugendhat's treatment of Husserl, and particularly on issues connected with the notion of dependence or Abhängigkeit central to Husserl's philosophy. These issues are of interest not only because Tugendhat's work is one of the few contributions to contemporary analytic philosophy in which they are confronted explicitly, but also because what he has to say about Husserl and dependence illustrates well both the positive and the negative thrust of his argument.

The project of a naive physics has been the subject of attention in recent years above all in the artificial intelligence field, in connection with work on common-sense reasoning, perceptual representation and robotics. The idea of a theory of the common-sense world is however much older than this, having its roots not least in the work of phenomenologists and Gestalt psychologists such as Kohler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit from a knowledge of these historical roots of their discipline, which are shown to imply above all a critique of the set-theory-based models of reality typically presupposed by contemporary work in common-sense ontology.

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data.

We defend a view according to which Austrian economics rests on what can most properly be called an Aristotelian methodology. This implies a realist perspective, according to which the world exists independently of our thinking and reasoning activities; an essentialist perspective, according to which the world contains certain simple essences or natures which may come together in law-like ways to form more complex static and dynamic wholes, and an apriorist perspective, according to which given essences and essential structures are intelligible, in the sense that they ca be grasped non-inductively in our thinking. We show the consequences of this view for an analysis of the thinking of Mises and Hoppe, both of which – we claim – incorporate what we believe to be foreign mixtures of Kantianism in their account of the foundations of Austrian economics.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions.

Analytic philosophers have until recently been reluctant to pursue historical investigations into the Central European roots of their own philosophical tradition. The most recent book by Michael Dummett, however, entitled Origins of Analytic Philosophy, shows how fruitful such investigations can be, not only as a means of coming to see familiar philosophical problems in a new light, but also as a means of clarifying what, precisely, ‘analytic philosophy’ might mean. As Dummett points out, the newly fashionable habit of referring to analytic philosophy as ‘Anglo-American’ leads to a ‘grave historical distortion’. If, he says, we take into account the historical context in which analytic philosophy developed, then such philosophy ‘could at least as well be called "Anglo-Austrian"’ (p. 7). We here show the implications of this assertion for a more adequate understanding of the relations between analytic and Continental philosophy.

Both ‘Sachverhalt’ and ‘state of affairs’ seem to have been derived from the juridical ‘status’ in the sense of 'status rerum' meaning: state or constitution of things. ‘Status’ signifies also in an extended sense ‘the way things stand, the condition or peculiarity of a thing in regard to its circumstances, position, order’. We describe the history of usage of ‘Sachverhalt’ from these beginnings, addressing the role of Goclenius, Lotze, Stumpf, Husserl and Adolf Reinach, whose theory of the relations between judgment and Sachverhalt served as one starting point for the development of Reinach’s theory of speech acts in 1913.

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering.

Disaster response is a highly collaborative and critical process that requires the involvement of multiple emergency responders (ERs), ideally working together under a unified command, to enable a rapid and effective operational response. Following the 9/11 and 11/13 terrorist attacks and the devastation of hurricanes Katrina and Rita, it is apparent that inadequate communication and a lack of interoperability among the ERs engaged on-site can adversely affect disaster response efforts. Within this context, we present a scenario-based terrorism case study to highlight the challenges of operational disaster command and response. In this article, which is based on the French emergency response doctrine, we outline a semantics-based common operational command system that is designed to guarantee an efficient information flow among ERs. Our focus is on offering to all ERs, a real-time operational picture of the situation in order to enable multilevel coordination among firefighters, police, healthcare units, public authorities, and other stakeholders. Our approach consolidates information to promote timely sharing of data among ERs. The proposed system is based on an ontology that has been developed to represent the different types of knowledge on the part of ERs, providing a shared vocabulary that covers a variety of interoperability concerns.

Le présent article est une tentative nouvelle d’articuler le rôle d’une théorie des vérifacteurs. Nous soutenons que la théorie de la vérifaction constitue une pierre angulaire dans une bonne méthodologie en métaphysique, mais que l’amalgame entre la théorie de la vérifaction et la théorie de la vérité a été responsable de certains excès associés aux approches vérifactionnistes dans la littérature récente. Nous montrons que la théorie de la vérifaction conserve son attrait comme instrument d’investigation métaphysique, et ce, malgré notre accord avec les doctrines déflationnistes telles que celles défendues par Ayer, Quine, Field et Horwich (ou, du moins, malgré notre neutralité à leur égard). Nous soutenons en outre que les intuitions sous-jacentes à la théorie de la vérifaction s’éclairent quand nous les dissocions d’une théorie de la vérité et, par-dessus tout, de la tentative de fournir une définition de la vérité.

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summarizes what is known about Kafka’s relations to the Brentanist movement. It draws on Brentanian ideas on the evidence of inner perception, on oblique consciousness, on active introspection, on correct and incorrect judgment, and on consciousness as a species of inner tribunal, in order to throw light on central features of Kafka’s writings, including stylistic features. Special attention is directed towards Die Verwandlung and Der Prozess, and a reading of the latter is offered according to which the trial of Joseph K. occurs entirely within the mind of K. himself. The revisions in the 1997 version of the paper relate especially to the treatment of Kafka and Brentano in Arnold Heidsieck’s book The Intellectual Contexts of Kafka’s Fiction: Philosophy, Law, Religion of 1994.

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway.

The author attempts to show how mereology, taken together with certain topological notions, can yield the foundations for future investigations in formal ontology. He also attempts to show how the mereological framework allows for the direct and natural formulation of a series of theses - for example pertaining to the concept of a boundary - which can be only indirectly formulated (if at all) in set-theoretic terms. The far-reaching ain of the present framework is to serve as a basis for a formal ontology of the common-sense world. The author is interested in producing formally precise theories of structures of certain sorts in such a way that it is the structures themselves that intrest him and not formal machinery that has been set up to describe them. Hence the axioms are chosen primarily for the sake of the light they throw on the intended subject-matters (and not for their logical independence). The world itself - or its picture given in ordinary experience - is the only model the paper concentrates upon. Thus for example the presented system allows to prove that every boundary is the boundary of something, and that in particular no point exists in isolation from a large extended whole that is its boundary

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.