Visualizing the temporal distribution of terminologies for biological ontology development

Tak-eun Kim; Hodong Lee; Jinah Park; Jong C. Park

doi:10.1117/12.773263

28 January 2008 Visualizing the temporal distribution of terminologies for biological ontology development

Tak-eun Kim, Hodong Lee, Jinah Park, Jong C. Park

Proceedings Volume 6809, Visualization and Data Analysis 2008; 68090G (2008) https://doi.org/10.1117/12.773263
Event: Electronic Imaging, 2008, San Jose, California, United States

Abstract

Communities in biology have developed a number of ontologies that provide standard terminologies for the characteristics of various concepts and their relationships. However, it is difficult to construct and maintain such ontologies in biology, since it is a non-trivial task to identify commonly used potential member terms in a particular ontology, in the presence of constant changes of such terms over time as the research in the field advances. In this paper, we propose a visualization system, called BioTermViz, which presents the temporal distribution of ontological terms from the text of published journal abstracts. BioTermViz shows such a temporal distribution of terms for journal abstracts in the order of published time, occurrences of the annotated Gene Ontology concepts per abstract, and the ontological hierarchy of the terms. With a combination of these three types of information, we can capture the global tendency in the use of terms, and identify a particular term or terms to be created, modified, segmented, or removed, effectively developing biological ontologies in an interactive manner. In order to demonstrate the practical utility of BioTermViz, we describe several scenarios for the development of an ontology for a specific sub-class of proteins, or ubiquitin-protein ligases.

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Tak-eun Kim, Hodong Lee, Jinah Park, and Jong C. Park "Visualizing the temporal distribution of terminologies for biological ontology development", Proc. SPIE 6809, Visualization and Data Analysis 2008, 68090G (28 January 2008); https://doi.org/10.1117/12.773263

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KEYWORDS

Visualization

Proteins

Biology

Human-machine interfaces

Standards development

Data modeling

Visibility

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