Holes are a good example of the sort of entity that down-to-earth philosophers would be inclined to expel from their ontological inventory. In this work we argue instead in favor of their existence and explore the consequences of this liberality—odd as they might appear. We examine the ontology of holes, their geometry, their part-whole relations, their identity and their causal role, the ways we perceive them. We distinguish three basic kinds of holes: blind hollows, perforating tunnels, and internal cavities, treating (...) these uniformly as immaterial bodies. We develop a morphology of holes, focusing on the way a hole can be filled, and then look at the main properties of the resulting conceptual framework: holes are parasitic upon the surfaces of their hosts; holes can move, fuse into each other, split; they can be born, develop, and die. Finally, we examine how some morphological features of holes are represented in perception, including the conditions whereby we have the impression that we see, feel, or even hear a hole. The book has over 150 pictures and is completed by a formal appendix, a section with puzzles and exercises, and a extensive annotated bibliography. (shrink)

The paper argues that causal systems and spatial patterns are species of the same genus, namely pattern, and that a clear view of spatial patterns throws light on some aspects of the ontological nature of causal systems. In particular, it is argued that all patterns (and systems) depend on a fiat delimitation of something which in itself is a unity without borders. Pattern realism is true.

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and (...) formal ontological principles as a first step towards finding answers to this question. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these are (...) two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine. (shrink)