Graduated: January 1, 2006
Ontology Recapitulates Phylogeny: Design, Implementation and Potential for Usage of a Comparative Anatomy Information System
Building on our previous design work in the development of the Structural Difference Method (SDM) for symbolically modeling anatomical similarities and differences across species, we describe the design and implementation of the associated comparative anatomy information system (CAIS) knowledge base and query interface, and provide scenarios from the literature for its use by research scientists. Our work includes several relevant informatics contributions. The first one is the application of the structural difference method (SDM), a formalism for symbolically representing anatomical similarities and differences across species. We also present 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. The design of the internal syntax and semantics of the query language underlies 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. We also contributed to the expansion of the domain knowledge by identifying medically-relevant structural questions for humans, mice, and rats. Finally, we carried out a preliminary validation of the application and its content by means of user questionnaires, software testing, and other feedback.
Last Known Position:
Research Scientist, University of Washington
Linda G. Shapiro (Chair), Ira J. Kalet, Billie J. Swalla, John H. Gennari, Willie J. Swanson (GSR)