29 January 2007 A visualization method for ontology based distance measure on relation network
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Proceedings Volume 6495, Visualization and Data Analysis 2007; 649502 (2007); doi: 10.1117/12.704782
Event: Electronic Imaging 2007, 2007, San Jose, CA, United States
Abstract
Relation network is constructed by discovering relations between objects. Discovering relations is challenging and usually time consuming job. For example, most relation in protein-protein interaction networks has been discovered one by one empirically. However, if we know some objects have similar functions, we can make inference of the relationship between objects. And these inferences can avoid false trial and errors in discovering relations. Ontology is a structured representation of conceptual knowledge. This hierarchical knowledge can be applied at inference of relation between objects. Objects with similar functions share similar ontology terms. Therefore, combining relation network with ontology makes it possible to reflect that kind of knowledge and we can infer unknown relations. In this paper, we propose a visualization method in 3D space, to examine specific relation network based on a proper ontology structure. To gather related ontology terms, we added a degree of freedom to conventional layered drawing algorithm so that the position of the term in an ontology tree can move like a mobile. And we combined it with modified spring embedder model to map relation network onto the ontology tree. We have used protein-protein interaction data from Ubiquitination Information System for relation network, and Gene Ontology for ontology structure. The proposed method lays out the protein relation data in 3D space with a meaningful distance measure. Finally, we have designed experiments to verify the relationship between Euclidean distance of each protein and existence of interaction. The results support that our method provides a means to discover new relation based on visualization.
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Seongyoon Cho, Jinah Park, "A visualization method for ontology based distance measure on relation network", Proc. SPIE 6495, Visualization and Data Analysis 2007, 649502 (29 January 2007); doi: 10.1117/12.704782; https://doi.org/10.1117/12.704782
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KEYWORDS
Proteins

Visualization

Distance measurement

Databases

Bioinformatics

3D modeling

3D visualizations

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