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2006
IEEE

On Data and Visualization Models for Signaling Pathways

11 years 5 months ago
On Data and Visualization Models for Signaling Pathways
Signaling pathways are chains of interacting proteins, through which the cell converts a (usually) extracellular signal into a biological response. The number of known signaling pathways in the biological literature and on the web has been increasing at a very high rate, thus demanding a need for efficient ways of storing, visualizing, querying, and mining signaling pathways. In this paper, first we briefly compare the data modeling and visualization capabilities of existing signaling pathways systems. Then, we present a signaling pathway data model and its visualization that subsumes the existing models. Our model visualizes a signaling pathway (a) as a nested graph, (b) with explicit location information (e.g., cell, tissue, organelle, nucleus, etc.), and (c) in four abstraction levels, namely, the levels of molecule-tomolecule signaling steps, collapsed sub-pathways, molecule-to-pathway connections, and pathway-to-pathway connections. We model (1) the effects of specific signaling ...
Nattakarn Ratprasartporn, Ali Cakmak, Gultekin &Ou
Added 12 Jun 2010
Updated 12 Jun 2010
Type Conference
Year 2006
Where SSDBM
Authors Nattakarn Ratprasartporn, Ali Cakmak, Gultekin Özsoyoglu
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