Application of Spatial Concepts to Genome Data

This project will investigate the application of geographic information science concepts and methods to the modeling and analysis of genome data. The primary objective of the research is to develop a data model for genomes that supports the graphical exploration of the higher order spatial arrangement of genome features through spatial queries and spatial data analysis tools. The spatial genome model formalizes topological and order relationships among genome features (before, after, overlap), uses metric properties to refine spatial topologies, and includes representations of features that have uncertain metric properties. The genome spatial model enhances the integrative and comparative potential of genome data by providing the foundation for more powerful spatial reasoning and inferences than can be achieved by data models that incorporate only a small subset of possible temporal-spatial relationships among genome features (e.g. order and distance). The research represents a logical extension from current feature by feature analytical approaches of genome studies to one that allows biologists to ask questions about the contextual and organizational significance of the spatial arrangement of genome features. These functional capabilities should, in turn, aid in the automation of repetitive analytical tasks associated with the mapping of genome features and drive the discovery of biologically significant aspects of genome organization and function

Qualitative Spatial Reasoning with Holed Regions

The intricacies of real-world and constructed spatial entities call for versatile spatial data types to model complex spatial objects, often characterized by the presence of holes. To date, however, relations of simple, hole-free regions have been the prevailing approaches for spatial qualitative reasoning. Even though such relations may be applied to holed regions, they do not take into consideration the consequences of the existence of the holes, limiting the ability to query and compare more complex spatial configurations. To overcome such limitations, this thesis develops a formal framework for spatial reasoning with topological relations over two-dimensional holed regions, called the Holed Regions Model (HRM), and a similarity evaluation method for comparing relations featuring a multi-holed region, called the Frequency Distribution Method (FDM). The HRM comprises a set of 23 relations between a hole-free and a single-holed region, a set of 152 relations between two single-holed regions, as well as the composition inferences enabled from both sets of relations. The inference results reveal that the fine-grained topological relations over holed regions provide more refined composition results in over 50% of the cases when compared with the results of hole-free regions relations. The HRM also accommodates the relations between a hole-free region and a multi-holed region. Each such relation is called a multi-element relation, as it can be deconstructed into a number of elements—relations between a hole-free and a singleholed region—that is equal to the number of holes, regarding each hole as if it were the only one. FDM facilitates the similarity assessment among multi-element relations. The similarity is evaluated by comparing the frequency summaries of the single-holed region relations. The multi-holed regions of the relations under comparison may differ in the number of holes. In order to assess the similarity of such relations, one multi-holed region is considered as the result of dropping from or adding holes to the other region. Therefore, the effect that two concurrent changes have on the similarity of the relations is evaluated. The first is the change in the topological relation between the regions, and the second is the change in a region’s topology brought upon by elimination or addition of holes. The results from the similarity evaluations examined in this thesis show that the topological placement of the holes in relation to the hole-free region influences relation similarity as much as the relation between the hole-free region and the host of the holes. When the relations under comparison have fewer characteristics in common, the placement of the holes is the determining factor for the similarity rankings among relations. The distilled and more correct composition and similarity evaluation results enabled by the relations over holed regions indicate that spatial reasoning over such regions differs from the prevailing reasoning over hole-free regions. Insights from such results are expected to contribute to the design of future geographic information systems that more adequately process complex spatial phenomena, and are better equipped for advanced database query answering

Qualitative Spatial Reasoning with Holed Regions

The intricacies of real-world and constructed spatial entities call for versatile spatial data types to model complex spatial objects, often characterized by the presence of holes. To date, however, relations of simple, hole-free regions have been the prevailing approaches for spatial qualitative reasoning. Even though such relations may be applied to holed regions, they do not take into consideration the consequences of the existence of the holes, limiting the ability to query and compare more complex spatial configurations. To overcome such limitations, this thesis develops a formal framework for spatial reasoning with topological relations over two-dimensional holed regions, called the Holed Regions Model (HRM), and a similarity evaluation method for comparing relations featuring a multi-holed region, called the Frequency Distribution Method (FDM). The HRM comprises a set of 23 relations between a hole-free and a single-holed region, a set of 152 relations between two single-holed regions, as well as the composition inferences enabled from both sets of relations. The inference results reveal that the fine-grained topological relations over holed regions provide more refined composition results in over 50% of the cases when compared with the results of hole-free regions relations. The HRM also accommodates the relations between a hole-free region and a multi-holed region. Each such relation is called a multi-element relation, as it can be deconstructed into a number of elements—relations between a hole-free and a singleholed region—that is equal to the number of holes, regarding each hole as if it were the only one. FDM facilitates the similarity assessment among multi-element relations. The similarity is evaluated by comparing the frequency summaries of the single-holed region relations. The multi-holed regions of the relations under comparison may differ in the number of holes. In order to assess the similarity of such relations, one multi-holed region is considered as the result of dropping from or adding holes to the other region. Therefore, the effect that two concurrent changes have on the similarity of the relations is evaluated. The first is the change in the topological relation between the regions, and the second is the change in a region’s topology brought upon by elimination or addition of holes. The results from the similarity evaluations examined in this thesis show that the topological placement of the holes in relation to the hole-free region influences relation similarity as much as the relation between the hole-free region and the host of the holes. When the relations under comparison have fewer characteristics in common, the placement of the holes is the determining factor for the similarity rankings among relations. The distilled and more correct composition and similarity evaluation results enabled by the relations over holed regions indicate that spatial reasoning over such regions differs from the prevailing reasoning over hole-free regions. Insights from such results are expected to contribute to the design of future geographic information systems that more adequately process complex spatial phenomena, and are better equipped for advanced database query answering