Barry Smith

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart.

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data.

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps.

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 truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis.

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.

One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psychological environments of cognitive subjects and the different sorts of external (physical, geographical, social) environments which they inhabit. The present essay addresses this environmental version of the problem of intentionality. It draws not only on the work of Husserl and Scheler but also on the Gestalt psychological writings of Kurt Koffka and Kurt Lewin. It considers the influential subjective idealist theory of animal environments put forward by J. von Uexküll and contrasts this with a realist theory of organism-environment interaction based on the work of the ecological psychologists J. J. Gibson and Roger Barker. This realist theory is then exploited as a basis for an ontology of social objects of a range of different sorts. (English translation is appended to the French text.)

This essay is a contribution to social ontology, drawing on the work of John Searle and of Hernando de Soto. At the center of the argument is the proposition advanced by de Soto in his Mystery of Capital to the effect that many of the entities which structure our contemporary social reality are entities which exist in virtue of the fact that there are (paper or digital) documents which support their existence. I here develop de Soto’s argument further, focusing specifically on the ontological problems raised by a family of new types of social phenomena – exemplified most dramatically in the domain of finance for example in the form of what are called ‘structured investment vehicles’ – made possible as a result of the employment of computer technology in entity creation. I address also Searle’s most recent work on social ontology, and conclude with an appendix on the theory of documentality advanced by Maurizio Ferraris.

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data.

We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral trauma, pain that is caused neuropathically (thus with no necessary peripheral stimulus), and pain reports arising through deception either of self or of others. We describe how our approach can answer some of the objections raised against the IASP definition, and sketch how it can be used to support more sophisticated discrimination of different types of pain resulting in improved data analysis that can help in advancing pain research.

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory

In what respects is Western civilization superior or inferior to its rivals? In raising this question we are addressing a particularly strong form of the problem of relativism. For in order to compare civilizations one with another we would need to be in possession of a framework based on principles of evaluation which would be acceptable, in principle, to all human beings. Morality will surely provide one axis of such a framework (and we note in passing that believers in Islam might quite reasonably claim that their fellow-believers are characteristically more moral than are many in the West). Criteria such as material wellbeing, too, will need to play a role, as also will happiness or pleasure. Even happiness (pace some proponents of the utilitarian philosophy) comes in different types, and to count in the civilization stakes the happiness involved would presumably need to be of the right kind. We propose a specification for what this ‘right kind’ of happiness might be.

One of the tasks of ontology in information science is to support the classification of entities according to their kinds and qualities. We hold that to realize this task as far as entities such as material objects are concerned we need to distinguish four kinds of entities: substance particulars, quality particulars, substance universals, and quality universals. These form, so to speak, an ontological square. We present a formal theory of classification based on this idea, including both a semantics for the theory and a provably sound axiomatization.

Where some have attempted to apply cognitive methods to the study of geography, the present paper is designed to serve as a starting point for applying methods of geographic ontology to the phenomena of cognition. Agglomerations are aggregates of entities that are dispersed through space on geographic scales. Examples include: plagues, biological species, major world religions. The paper applies standard mereotopological theories of spatial regions to agglomerations in this sense. It offers the beginnings of a general theory of the relations between social, cultural, ethnic and religious agglomerations on the one hand and territorially demarcated spatial objects on the other. In this way it serves as the basis for a general ontological theory of types of human groups and also of types of conflict between these groups. At the same time it provides ontological foundations for the epidemiological study of cognitive phenomena, and especially of cognitive phenomena in the sociopolitical realm.

The theory of speech acts put forward by Adolf Reinach in his "The A Priori Foundations of the Civil Law" of 1913 rests on a systematic account of the ontological structures associated with various different sorts of language use. One of the most original features of Reinach's account lies in hIs demonstration of how the ontological structure of, say, an action of promising or of commanding, may be modified in different ways, yielding different sorts of non-standard instances of the corresponding speech act varieties. The present paper is an attempt to apply this idea of standard and modified instances of ontological structures to the realm of judgement and cognition, and thereby to develop a Reinachian theory of how intentionality is mediated through language in acts of thinking and speaking.

When national borders in the modern sense first began to be established in early modern Europe, non-contiguous and perforated nations were a commonplace. According to the conception of the shapes of nations that is currently preferred, however, nations must conform to the topological model of circularity; their borders must guarantee contiguity and simple connectedness, and such borders must as far as possible conform to existing topographical features on the ground. The striving to conform to this model can be seen at work today in Quebec and in Ireland, it underpins much of the rhetoric of the P.L.O., and was certainly to some degree involved as a motivating factor in much of the ethnic cleansing which took place in Bosnia in recent times. The question to be addressed in what follows is: to what extent could inter-group disputes be more peacefully resolved, and ethnic cleansing avoided, if political leaders, diplomats and others involved in the resolution of such disputes could be brought to accept weaker geometrical constraints on the shapes of nations? A number of associated questions then present themselves: What sorts of administrative and logistical problems have been encountered by existing non contiguous nations and by perforated nations, and by other nations deviating in different ways from the received geometrical ideal? To what degree is the desire for continuity and simple connectedness a rational desire, and to what degree does it rest on species of political rhetoric which might be countered by, for example, philosophical argument? These and a series of related questions will form the subject- matter of the present essay

We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent.

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.

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.

The ontology of language is concerned with the relations between uses of language, both overt and covert, and other entities, whether in the world or in the mind of the thinking subject. We attempt a first survey of the sorts of relations which might come into question for such an ontology, including: relations between referring uses of expressions and their objects, relations between the use of a (true) sentence and that in the world which makes it true, relations between mental acts on the one hand and underlying mental states (attitudes, beliefs), on the other, relations between my acts and states, associated uses of language and overt actions on my part and on the part of those other subjects with whom I communicate.

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability.

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.

When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the relation between fetus and mother (connection, parthood, dependence).

From his groundbreaking book Speech Acts to his most recent studies of consciousness, freedom and rationality John Searle has been a dominant and highly influential figure amongst contemporary philosophers. This systematic introduction to the full range of Searle's work begins with the theory of speech acts and proceeds with expositions of Searle's writings on intentionality, consciousness and perception, as well as a careful presentation of the so-called Chinese Room argument. The volume considers Searle's recent work on social ontology and his views on the nature of law and obligation. It concludes with an appraisal of Searle's spirited defence of truth and scientific method in the face of the criticisms of Derrida and other postmodernists. This is the only comprehensive introduction to Searle's work, and as such it will be of particular value to advanced undergraduates, graduates and professionals in philosophy, psychology, linguistics, cognitive and computer science and literary theory.