18,408 research outputs found
A formal theory for spatial representation and reasoning in biomedical ontologies
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 individuals, called Basic Inclusion
Theory (BIT). Since biomedical ontologies are comprised of assertions
about classes of individuals (rather than assertions about individuals),
we define parthood and location relations among classes in the
extended theory BIT+Cl (Basic Inclusion Theory for Classes). We
then demonstrate the usefulness of this formal theory for making
the logical structure of spatial information more precise in two
ontologies concerned with human anatomy: the Foundational Model of
Anatomy (FMA) and GALEN.
Results: We find that in both the FMA and GALEN, class-level spatial
relations with different logical properties are not always explicitly
distinguished. As a result, the spatial information included in
these biomedical ontologies is often ambiguous and the possibilities
for implementing consistent automatic reasoning within or across
ontologies are limited.
Conclusion: Precise formal characterizations of all spatial relations
assumed by a biomedical ontology are necessary to ensure that the
information embodied in the ontology can be fully and coherently
utilized in a computational environment. This paper can be seen as
an important beginning step toward achieving this goal, but much
more work is along these lines is required
Geographical information retrieval with ontologies of place
Geographical context is required of many information retrieval tasks in which the target of the search may be documents, images or records which are referenced to geographical space only by means of place names. Often there may be an imprecise match between the query name and the names associated with candidate sources of information. There is a need therefore for geographical information retrieval facilities that can rank the relevance of candidate information with respect to geographical closeness of place as well as semantic closeness with respect to the information of interest. Here we present an ontology of place that combines limited coordinate data with semantic and qualitative spatial relationships between places. This parsimonious model of geographical place supports maintenance of knowledge of place names that relate to extensive regions of the Earth at multiple levels of granularity. The ontology has been implemented with a semantic modelling system linking non-spatial conceptual hierarchies with the place ontology. An hierarchical spatial distance measure is combined with Euclidean distance between place centroids to create a hybrid spatial distance measure. This is integrated with thematic distance, based on classification semantics, to create an integrated semantic closeness measure that can be used for a relevance ranking of retrieved objects
The Foundational Model of Anatomy Ontology
Anatomy is the structure of biological organisms. The term also denotes the scientific
discipline devoted to the study of anatomical entities and the structural and
developmental relations that obtain among these entities during the lifespan of an
organism. Anatomical entities are the independent continuants of biomedical reality on
which physiological and disease processes depend, and which, in response to etiological
agents, can transform themselves into pathological entities. For these reasons, hard copy
and in silico information resources in virtually all fields of biology and medicine, as a
rule, make extensive reference to anatomical entities. Because of the lack of a
generalizable, computable representation of anatomy, developers of computable
terminologies and ontologies in clinical medicine and biomedical research represented
anatomy from their own more or less divergent viewpoints. The resulting heterogeneity
presents a formidable impediment to correlating human anatomy not only across
computational resources but also with the anatomy of model organisms used in
biomedical experimentation. The Foundational Model of Anatomy (FMA) is being
developed to fill the need for a generalizable anatomy ontology, which can be used and
adapted by any computer-based application that requires anatomical information.
Moreover it is evolving into a standard reference for divergent views of anatomy and a
template for representing the anatomy of animals. A distinction is made between the FMA
ontology as a theory of anatomy and the implementation of this theory as the FMA
artifact. In either sense of the term, the FMA is a spatial-structural ontology of the
entities and relations which together form the phenotypic structure of the human
organism at all biologically salient levels of granularity. Making use of explicit
ontological principles and sound methods, it is designed to be understandable by human
beings and navigable by computers. The FMA’s ontological structure provides for
machine-based inference, enabling powerful computational tools of the future to reason
with biomedical data
'Natural concepts' in the spatial topological domain - adpositional meanings in crosslinguistic perspective: An exercise in semantic typology
Most approaches to spatial language have assumed that the simplest spatial notions are (after Piaget) topological and universal (containment, contiguity, proximity, support, represented as semantic primitives suchas IN, ON, UNDER, etc.). These concepts would be coded directly in language, above all in small closed classes suchas adpositions—thus providing a striking example of semantic categories as language-specific projections of universal conceptual notions. This idea, if correct, should have as a consequence that the semantic categories instantiated in spatial adpositions should be essentially uniform crosslinguistically. This article attempts to verify this possibility by comparing the semantics of spatial adpositions in nine unrelated languages, with the help of a standard elicitation procedure, thus producing a preliminary semantic typology of spatial adpositional systems. The differences between the languages turn out to be so significant as to be incompatible withstronger versions of the UNIVERSAL CONCEPTUAL CATEGORIES hypothesis. Rather, the language-specific spatial adposition meanings seem to emerge as compact subsets of an underlying semantic space, withcertain areas being statistical ATTRACTORS or FOCI. Moreover, a comparison of systems withdifferent degrees of complexity suggests the possibility of positing implicational hierarchies for spatial adpositions. But such hierarchies need to be treated as successive divisions of semantic space, as in recent treatments of basic color terms. This type of analysis appears to be a promising approachfor future work in semantic typology
Three Dimensional Software Modelling
Traditionally, diagrams used in software systems modelling have been two dimensional (2D). This is probably because graphical notations, such as those used in object-oriented and structured systems modelling, draw upon the topological graph metaphor, which, at its basic form, receives little benefit from three dimensional (3D) rendering. This paper presents a series of 3D graphical notations demonstrating effective use of the third dimension in modelling. This is done by e.g., connecting several graphs together, or in using the Z co-ordinate to show special kinds of edges. Each notation combines several familiar 2D diagrams, which can be reproduced from 2D projections of the 3D model. 3D models are useful even in the absence of a powerful graphical workstation: even 2D stereoscopic projections can expose more information than a plain planar diagram
Towards a Scalable Dynamic Spatial Database System
With the rise of GPS-enabled smartphones and other similar mobile devices,
massive amounts of location data are available. However, no scalable solutions
for soft real-time spatial queries on large sets of moving objects have yet
emerged. In this paper we explore and measure the limits of actual algorithms
and implementations regarding different application scenarios. And finally we
propose a novel distributed architecture to solve the scalability issues.Comment: (2012
Boundaries and Prototypes in Categorizing Direction
Projective terms such as left, right, front, back are conceptually interesting due to their flexibility of contextual usage and their central relevance to human spatial cognition. Their default acceptability areas are well known, with prototypical axes representing their most central usage and decreasing acceptability away from the axes. Previous research has shown these axes to be boundaries in certain non-linguistic tasks, indicating an inverse relationship between linguistic and non-linguistic direction concepts under specific circumstances. Given this striking mismatch, our study asks how such inverse non-linguistic concepts are represented in language, as well as how people describe their categorization. Our findings highlight two distinct grouping strategies reminiscent of theories of human categorization: prototype based or boundary based. These lead to different linguistic as well as non-linguistic patterns
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