This week I would like you to present to the class a review of the following journal article:
Biodynamic Ontology: Applying BFO in the Biomedical Domain
Download Biodynamic Ontology: Applying BFO in the Biomedical Domain
Then write about the following:
- Summarize the article
- Discuss the article’s strengths and weaknesses in terms of the study
- Could this methodology be applied to your ontology creation? Explain why or why not.
- One primary post (minimum 300 words)
- and two commentary posts (minimum 100 words each)
Microsoft Word - grenon-smith-goldberg.doc From D. M. Pisanelli (ed.), Ontologies in Medicine, Amsterdam: IOS Press, 2004, 20–38 Biodynamic Ontology: Applying BFO in the Biomedical Domain Pierre GRENON,1 Barry SMITH1,2 and Louis GOLDBERG1,3 1Institute for Formal Ontology and Medical Information Science, University of Leipzig 2Department of Philosophy, University at Buffalo 3Department of Oral Diagnostic Sciences, University at Buffalo Abstract. We propose a modular formal ontology of the biomedical domain with two components, one for biological objects, corresponding broadly to anatomy, and one for biological processes, corresponding broadly to physiology. The result constitutes what might be described as a joint venture between two perspectives – of so-called three-dimensionalism and four-dimensionalism – which are normally regarded as incompatible. We outline an approach which allows them to be combined together, and provide examples of its application in biomedicine. Introduction 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. 1. Background 1.1 Methodology The methodology presupposed in what follows and developed in [10, 33] is realist, fallibilist, perspectivalist, and adequatist: (i) Realism holds that reality and its constituents exist independently of our (linguistic, conceptual, theoretical, cultural) representations thereof. (ii) Fallibilism accepts that our theories and classifications can be subject to revision. (iii) Perspectivalism maintains that there exists a plurality of alternative, equally legitimate perspectives on reality. (iv) Adequatism maintains that these alternative views are not reducible to any single basic view. Thus adequatism is opposed to reductionism, i.e. to the thesis that there is some one privileged perspective to which all other representations of reality can be reduced. These four axes of our methodology are not independent of each other. Thus perspectivalism is constrained by realism, which means that it does not amount to the thesis that just any view of reality is legitimate. To establish which views are legitimate we must weigh them against their ability to survive critical tests above all when confronted with reality in scientific experiments. Those perspectives which survive are deemed in the spirit of realism to be transparent to reality: it is however a fact that apparent scientific certainties are sometimes abandoned over time, and so each given perspective is accepted always in a way which leaves open the possibility of future revision. The biomedical sciences are themselves in considerable flux, a fact that is well illustrated by the recent radical reorganization of science departments in medical schools [21], reflecting an increasing emphasis in the biomedical sciences on subcellular processes and modes of organization. Perspectivalism and realism combined with adequatism generate the view that we need (and do not merely have as an option) a plurality of alternative theories to reflect the different perspectives which cover complex domains of reality like that of biomedicine. Reality is like cheese: it can be cut in many ways. Our methodology endorses the need for views of entities belonging to different domains (neurology, cardiology, urology) all of which coexist within a single organism. The progress of science often involves appeal to the reductionistic methodology for instrumental reasons: scientific explanations often take the form of a demonstration of how coarse-grained phenomena can be reduced to finer- grained phenomena, for example at the level of microphysical particles. But the purposes of building ontologies are distinct from those of empirical science, and experience has shown that an adequate representation of reality of the sort needed for purposes of biomedical ontology must take account of a plurality of different views, all of which are equally veridical. This is because the central purpose of ontology lies precisely in its ability to assist in the communication between the perspectives associated with different scientific disciplines. A perspectivalist approach to biomedical ontology with ambitions to remain consistent with science and to cope with its reductionistic tendencies will need to find ways to do justice above all to a plurality of perspectives on different levels of granularity. Granularity is indeed here understood as reflecting those specific ways of carving up domains of reality we associate with different scientific theories. One perspective might focus on whole organisms, another on cellular assemblies. Yet another might seek to do justice to the very same reality in terms of complexes of atoms or molecules. A fourth might talk in terms of changes and invariants in an associated continuum of metabolic pathways, or of behavior (of walking, eating, drinking, sweating) on a whole-organism scale. Our approach allows that all of these views can be tenable within their respective boundaries, and that there need be no privileged approach which could justify the reduction of one to another. It allows us also simultaneously to embrace both commonsensical and scientific perspectives on reality; that is, it allows us to endorse the view that both common sense and science at different levels of detail and granularity can give us genuine knowledge of the world. 1.2 Basic Formal Ontology in Context Basic Formal Ontology (BFO) is a theory of the basic structures of reality currently being developed at the Institute for Formal Ontology and Medical Information Science (IFOMIS) at the University of Leipzig. BFO is a formal ontology whose construction follows the methodological maxims presented above. The enterprise of building BFO is thus motivated on the one hand by the desire to be faithful to reality, and on the other hand by the need to accept a multiplicity of perspectives upon reality which may be skew to each other. Such perspectives can be organized along two dimensions, reflecting (i) the opposition between different levels of granularity, from single molecules to whole populations of organisms, and (ii) the opposition between objects and processes. The bacterium in the Petri dish on your desk can be apprehended either as an object in its own right or as a structured group of molecules and either in terms of objects such as the cell and its components, or in terms of processes such as the movements of the cell, the interactions of its components. As to (i), we refer the reader to [4, 35, 37]. Here, we shall concentrate primarily on (ii). Our focus, more precisely, will be the reconciliation of the dynamic approach to biological phenomena with the orientation of biology around objects (molecules, cells, organs, organisms, species). It should be borne in mind throughout that what is said about objects and processes in what follows can be applied, in principle, at all of the different levels of granularity which are relevant to the enterprise of biomedical research. In practice, each material application of BFO will be restricted to some given level of granularity, and each resultant granular ontology will respect the two-component structure here presented. 1.3 Continuants and Occurrents The central dichotomy between objects and processes concerns two distinct modes of existence in time. BFO endorses first of all a view according to which there are entities in the world that endure through time: entities which persist self-identically even while undergoing changes of various sorts. Such continuant or endurant entities come in several kinds. Examples are: you, your hippocampus, your kidneys, your chromosomes; but also: your bone mass, your cranial cavity, the surface of your skin. You are, for instance, the same person today as you were yesterday and as you will be tomorrow. In the terms of Zemach [45], continuants are said to be bound with respect to space. This means that if we segment the region of space occupied by a continuant, then we segment the continuant also. Continuants are not, however, bound with respect to time. This means that however we segment the interval of time during which a continuant exists, we find this continuant itself in every segment. This is what it means to endure. [19, 20, 25, 41] BFO endorses in addition a view according to which the world contains occurrents, more familiarly referred to as processes, events, activities, changes. Occurrents include: your breathing, her coughing, my drinking, the spreading of an epidemic through a population and the chemical synthesis of proteins. Occurrents have, in addition to their spatial dimensions also a fourth, temporal dimension, and they are, in contradistinction to continuants, bound with respect to time. This means that if we segment the interval of time during which an occurrent occurs then we segment the occurrent also. Occurrents occur in time and they unfold themselves through a period of time in such a way that they can be divided into temporal parts or phases. Not all entities are segmentable in this way. This is because there are beginnings and endings and other boundaries in the realm of occurrents, which are instantaneous: they are analogous to the edges and surfaces of objects in the realm of continuants. Just as the latter can exist only as the boundaries of three-dimensional spatially extended objects, so the former can exist only as the boundaries of temporally extended processes. Typically, the beginning and ending of an occurrent, as well as everything that takes place between these two points, are parts of the occurrent itself. The beginning and ceasing to exist