Barry Smith

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.

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.

Defends a view of intentional directedness according to which those seemingly object-directed acts – involved for example in reading works of fiction – which lack existing objects as targets, are not intentional (thus: not directed towards any object). Rather, each such act seems to its subject as if it were so directed because it is associated with a belief of a certain special sort, whose intentional directedness is not towards any putative external object but rather towards the very act itself with which the belief is associated.

Human cognitive acts are directed towards objects extended in space of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. The theory of spatially extended objects should make room not only for the objects of physics but also for objects at higher levels, including the objects of geography and of related disciplines. It should leave room for different types of boundaries, including both the bona fide boundaries which we find in the physical world and the fiat (or human-demarcation-induced) boundaries with which much of geography has to deal. Two distinct axiomatic theories of boundaries are accordingly presented, and the need for both is examined in some detail. The resultant dual framework is shown to have application above all for our understanding of issues involving contact, division, and separation, issues which have posed serious difficulties for the ontological theories of boundaries that have been proposed hitherto.

The magisterial analyses of logic and meaning advanced in Husserl's Logical Investigations of 1900/01 have for a number of reasons been neglected by analytical philosophers in subsequent decades. This state of affairs has to do, in part, with the history of the editions and translations of Husserl's writings. Findlay's readable but imperfect translation appeared seventy years after the work itself was first published, and the editors and translators and expositors of Husserl's works have reflected the prevailing philosophical atmosphere on the Continent by concentration their energies on Husserl's later writings. Now, however, over eighty years after the appearance of Husserl's one true masterpiece, a critical edition of the work is at last available in completed form. We here analyze the structure and content of this new edition, published as part of the Husserliana series by the Husserl Archive in Louvain.

The paper seeks to indicate ways in which the crude distinction between Anglo-Saxon and Continental philosophy may have to be amended in light of recent developments in Eastern Europe. As is well known, the philosophy of science is to no small part a product of the universities of the Habsburg Empire (in Vienna, Prague, Lemberg/Lwow, etc.). Logic, too, has played a more significant role in Eastern Europe (not least in Poland) than in the philosophical cultures of Germany or France. For these and other reasons, a shift in the center of gravity of Continental philosophy is currently being realized, as younger Eastern European philosophers in newly liberalized institutions begin to return to their roots in their native pre-Communist intellectual traditions.

As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case study to show how these benefits are being achieved, and we describe our strategy for developing a suite of ontologies to serve the needs of the war-fighter in the ever more complex battlespace environments of the future.

The remarks which follow are intended to address a certain apparent asymmetry as between German and Anglo-Saxon philosophy. Put most simply, it is clear to every philosopher moving backwards and forwards between the two languages that the translation of an Anglo-Saxophone philosophical text into German is in general a much easier task than is the translation of a German philosophical text into English. The hypothesis suggests itself immediately that this is so because English philosophical writings are in the main clear and intelligible, and therefore easy to translate. The texts of German philosophy, on the other hand, both classical and contemporary, seem in many cases to be marked by stylistic obscurities or idiosyncracies of a sort which make them not translatable in the strict sense at all.

While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other hand, matters are more complex. We provide a brief overview of recent proposals concerning the ontology of species, dealing with species as sets, classes and as collections, the views of Ernst Meyr, and mereological views.

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions.

It is a truism that the attitude of deference to the text plays a lesser role in Anglo-Saxon philosophy than in other philosophical traditions. Works of philosophy written in English have, it is true, spawned a massive secondary literature dealing with the ideas, problems or arguments they contain. But they have almost never given rise to works of commentary in the strict sense, a genre which is however a dominant literary form not only in the Confucian, Vedantic, Islamic, Jewish and Scholastic traditions of the past, but also in relation to more recent German-language philosophy (thus for example in work on Hegel, Heidegger or Wittgenstein). Moreover Anglo-Saxon philosophers have themselves embraced the commentary form when dealing with Greek or Latin philosophers outside their own tradition. The paper seeks to establish the reasons for this imbalance by examining those factors which might be conducive to the growth of a commentary literature in a given culture.

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 K hler, 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 alla critique of the set-theory-based models of reality typically presupposed by contemporary work in common-sense ontology [1].

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration.

We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentionality; it provides an account of how cells and subcells relate to objects in reality. We define a notion of well-formedness for partitions, and we give an account of what it means for a partition to project onto objects in reality. We continue by classifying partitions along three axes: (a) in terms of the degree of correspondence between partition cells and objects in reality; (b) in terms of the degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) in terms of the degree of completeness with which a partition represents this domain.