The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

We challenge the widespread presumption that matter and objects are ontologically prior to processes and events, and also the less widespread but increasingly popular view that processes and events...

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...) between them. (shrink)

This book is about matter. It involves our ordinary concept of matter in so far as this deals with enduring continuants that stand in contrast to the occurrents or processes in which they are involved, and concerns the macroscopic realm of middle-sized objects of the kind familiar to us on the surface of the earth and their participation in medium term processes. The emphasis will be on what science rather than philosophical intuition tells us about the world, and on chemistry (...) rather than the physics that is more usually encountered in philosophical discussions. It is the everyday science of matter characterised by differences of chemical substance that constitutes individuated macroscopic bodies of geological and biological complexity—the continuous matter of macroscopic theory and described by mass terms. -/- The discussion might be characterised as descriptive metaphysics, being content, to paraphrase Strawson’s use of the term, to describe the structure of our scientific thought about the actual world. The method in the central chapters dealing with the nature of matter will be to pursue key steps in the historical development of scientific thought about chemical substance and related concepts with a view to tracing the emergence of a systematic ontological interpretation. Aristotle’s and the Stoics’ discussions of elements and mixtures, based on a continuous view of matter, bear some resemblance to modern, macroscopic conceptions and therefore have some interest as precursors to modern views as well as being of conceptual interest in their own right. Some of the issues they raised are still reflected in modern discussions, despite the considerable increase in complexity of the subject. Other ideas, such as the intimate connection between what modern science distinguishes as substance and phase, maintained their grip on the understanding of matter until the end of the eighteenth century. These are some of the important aspects of the properties of matter that have been neglected by linguistic concerns that have dominated the recent study of mass terms and which the present study seeks to redress. It will be of interest to see how the bounds of possibility are delimited by the laws governing the appropriate use of concepts refined for the purpose of describing the behaviour of matter. But the concern with modality will not stretch to venturing into the realms of metaphysical possibility governed by philosophical speculation about individual essences and underlying natures. -/- Like many contemporary discussions of material objects, this one relies heavily on mereology. Unlike several such discussions, this one adheres to the classical principles of mereology governing the usual dyadic relations of part, overlapping, etc. and the operations of sum, product and difference. These principles apply to the mereological structure of regions of space, intervals of time, processes and quantities of matter. Material objects that gain and lose matter are not understood to gain and lose parts and don’t call for a modification of the classic dyadic mereological relations to triadic relations with the introduction of a third term referring to time. Rather, a distinction is drawn between quantities of matter, which don’t gain or lose parts over time, and individuals, which are typically constituted of different quantities of matter at different times. The proper treatment of the temporal aspect of the features of material objects is a central issue in this book. The topics falling under this heading are addressed by investigating the conditions governing the application of predicates relating time and other entities. Of particular interest here are relations between quantities of matter and times expressing substance kind, phase and mixture. (shrink)

Time is a pervasive notion of high impact in information systems and computer science altogether. Respective understandings of the domain of time are fundamental for numerous areas, frequently in combination with closely related entities such as events, changes and processes. The conception and representation of time entities and reasoning about temporal data and knowledge are thus significant research areas. Each representation of temporal knowledge bears ontological commitments concerning time. Thus it is important to base temporal representations on a foundational ontology (...) that covers general categories of time entities. In this article we introduce and discuss two consecutive ontologies of time that have been developed for the top-level ontology General Formal Ontology. The first covers intervals, named chronoids, and time boundaries of chronoids, as a kind of time points. One important specialty of time boundaries is their ability to coincide with other time boundaries. The second theory extends the first one by additionally addressing time regions, i.e., mereological sums of chronoids. Both ontologies are partially inspired by ideas of Franz Brentano, especially from his writings about the continuum. In particular, we view continuous time intervals as a genuine phenomenon which should not be identified with intervals of real numbers. On these grounds the resulting ontologies allow for proposing novel contributions to several problematic issues in temporal representation and reasoning, among others, the Dividing Instant Problem and the problem of persistence and change. Following our general approach to ontology development, both ontologies are axiomatized as formal theories in first-order logic and are analyzed metalogically. We prove the consistency of both ontologies, and completeness and decidability for one. Moreover, standard time theories with points and intervals are covered by both theories. (shrink)