9 research outputs found
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Implementing a comparative anatomy information system for the foundational model of anatomy and the mouse anatomy ontology
This thesis describes the implementation of an interface for querying established correspondences between anatomical structures across species. I was the main developer of this query engine, called the Comparative Anatomy Information System. My work involved developing methods to query the knowledge base, perform the specified comparison, display the anatomical hierarchies and results, and implement features to make the application user-friendly. The comparisons are based on the Structural Difference Method (SDM) for finding similarities and differences, developed in previous work. Since the CAIS knowledge base is sparsely populated, it has thus far been difficult to conduct extensive user testing, but I include two usage scenarios proposed by one of my mentors that outline some proposed uses of the application. These scenarios reflect the need for a system like CAIS that communicates anatomical correspondences to researchers who work on animal modeling of disease with a background other than traditional comparative anatomy
A Graphical User Interface for a Comparative Anatomy Information System: Design, Implementation and Usage Scenarios
Building on our previous design work in the development of the Structural Difference Method (SDM) for describing anatomical similarities and differences across species, we describe the design and implementation of the associated comparative anatomy information system (CAIS) interface and provide scenarios from the literature for its use by research scientists
An ontology-based comparative anatomy information system
Introduction: This paper describes the design, implementation, and potential use of a comparative anatomy information system (CAIS) for querying on similarities and differences between homologous anatomical structures across species, the knowledge base it operates upon, the method it uses for determining the answers to the queries, and the user interface it employs to present the results. The relevant informatics contributions of our work include (1) the development and application of the structural difference method, a formalism for symbolically representing anatomical similarities and differences across species; (2) the design of the structure of a mapping between the anatomical models of two different species and its application to information about specific structures in humans, mice, and rats; and (3) the design of the internal syntax and semantics of the query language. These contributions provide the foundation for the development of a working system that allows users to submit queries about the similarities and differences between mouse, rat, and human anatomy; delivers result sets that describe those similarities and differences in symbolic terms; and serves as a prototype for the extension of the knowledge base to any number of species. Additionally, we expanded the domain knowledge by identifying medically relevant structural questions for the human, the mouse, and the rat, and made an initial foray into the validation of the application and its content by means of user questionnaires, software testing, and other feedback