Transitive Closure of GO Ontology
Oral Defence Date:
Professors Margaritte Murphy, Dragutin Petkovic and C. Smith (Biology)
Visualization of ontology terms is useful for understanding the underlying semantics and structure of data as well as to gain better domain knowledge. The Controlled Vocabulary Module of the Chado database schema makes use of ontologies from the OBO consortium, in particular the Gene Ontology (GO) family: Biological Process, Molecular Function and Cellular Component. Ontology terms in GO are linked by typed relationships that are transitive in nature (e.g. synonym, part-of). Genomic data stored in Chado is annotated using GO terms to describe genome and protein properties. This paper presents the design and implementation of the GO2 Visual Browser: an interactive and user-friendly Web application. The GO Ontology contents and genome feature data is assumed to be stored in a standard Chado formatted database. The GO2 Visual Browser assists biologists in navigating between ontology terms and genomic data stored in the backend database. This tool can be used for visualization of terms as well as for the computation of transitive closure of terms. The selected term and its related terms are displayed in a radial graphical layout, and genomic sequence data associated with each term can be viewed interactively. The generated graph is dynamic and any term in the graph can be made the center of the graph by clicking on it; all the other terms are automatically rearranged around the new central node. A zoom in and zoom out feature is provided and panning can be done by clicking and dragging on any point within the graph. These features are useful when the associated terms and the level of relations displayed is large. The genomic features and related sequence information associated with the terms in the graphical layout can be viewed at any time. A usability study was conducted to evaluate the GO2 Visual Browser. The results of this study indicate that the layout and performance of the application were found to be satisfactory. The GO2 Visual Browser is fully functional and is platform independent; it is being distributed as Open Source software.
OBO: Open Biomedical Foundry, GO: Gene Ontology, SO: Sequence Ontology, RO: Relation Ontology, CV: Controlled vocabulary, transitive closure