Document Type

Report

Publication Date

2006

Abstract

Ontologies build the backbone for many life-sciences applications. These ontologies, however, are represented in XML based languages that are meant for machine-consumption and hence are difficult for humans to comprehend. For a meaningful visualization of these ontologies, it is important that the display of entities and relationships captures the cognitive representation of the domain as perceived by the domain experts. In this paper we present OntoVista, an ontology visualization tool that is adaptable to the needs of different domains, especially in the life sciences. While keeping the graph structures as the predominant model, we provide a semantically enhanced graph display that gives users a more intuitive way of interpreting nodes and their relationships. Additionally, OntoVista provides comfortable interfaces for searching, semantic edge filtering and quick-browsing of ontologies. To this end, we extended the Jambalaya plugin for Protege to allow for customization and integration of different layouts. As a use case, we demonstrate how the ontology encoding of complex carbohydrate structures is transformed into a standard graphical representation (David Goldberg 2005) of carbohydrates familiar to biochemists.

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