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Bridging levels of "granularity" and "scale" are frequently cited as key problems for biomedical informatics. However, detailed accounts of what is meant by these terms are sparse in the literature. We argue for distinguishing two notions: "size range," which deals with physical size, and "collectivity," which deals with aggregations of individuals into(More)
Reasoning about the location of regions in 2-dimensional space is necessarily based on nite approximations to such regions. These nite approximations are often derived by describing how a region (the gure) relates to a frame of reference (the ground). The frame of reference generally consists of regions, or cells, forming a partition of the space under(More)
OBJECTIVE The objective of this paper is to demonstrate how a formal spatial theory can be used as an important tool for disambiguating the spatial information embodied in biomedical ontologies and for enhancing their automatic reasoning capabilities. METHOD AND MATERIALS This paper presents a formal theory of parthood and location relations among(More)
This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category(More)
We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occur-rents) and the enduring entities (continuants) that participate therein. The theory is divided into two major categories of sub-theories: (sub-) theories of type SPAN and (sub-)theories of type SNAP. These theories represent two complementary(More)
Parthood, componenthood, and containment relations are commonly assumed in biomedical ontolo-gies and terminology systems, but are not usually clearly distinguished from another. This paper contributes towards a unified theory of parthood, com-ponenthood, and containment relations. Our goal in this is to clarify distinctions between these relations as well(More)
This paper proposes a qualitative coordinate language of regional individuals. It is shown that representing a configuration of regions using a coordinate language of regional individuals supports a primary breakup of a spatial configuration into primary objects of focus and secondary objects of reference, i.e., in figure and ground. We define the notion of(More)
We develop a formal theory of mereology that includes relations that change over time. We show how this theory formalizes reasoning over domains of material objects, which include not only integral objects (my computer, your liver) but also portions of stuff (the water in your glass, the blood in a vial). In particular, we use different mereological(More)