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| The Semantic Network Summary Cytoscape Plugin allows you to visualize a selected set of nodes in a network as a word tag cloud. It will operate on any Cytoscape network. The tag cloud can be built based up the words in the node ID's or the words appearing in any node attribute that is comprised of Strings, or a List of Strings. The size of the words appearing in the word tag cloud is representative of the word's importance for the node selection as a function of both the number of times the word appears in the selected nodes and the entire network for the selected node attribute. There are also options for viewing a clustered version of the word tag cloud. | The Semantic Network Summary is a Cytsocape plugin that generates a word tag cloud from a user-defined node selection, summarizing an attribute of choice. For instance, if selected nodes are proteins, and the string attribute "full protein name" is selected, every string will be broken down into words, which will be plotted on a panel with size proportional to their frequency. It is also possible to use the plugin to cluster words that appear together in the selected nodes. For instance, if node A has name attribute "Origin Recognition Complex 1" and node B has name attribute "Origin Recognition Complex 2", then the words "Origin", "Recognition" and "Complex" will be clustered together, following the order in which they appear. The plugin operates on any network and on any selected attributes, although it has been specifically designed for string attributes such as gene names or gene ontology annotations. |
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| Coming soon! | Updated 7/20/2010 * [[attachment:SemanticNetworkSummary_v0.5.zip]] == Sample Data Download == [[attachment:AlzheimerEM.cys]] * [[GSoC2010_UseExamples|Guided tutorial]] on the basic functioning of the Semantic Network Summary plugin. * [[GSoC2010_ParameterTutorial|Parameter tutorial]] on using all of the parameters available for the Semantic Network Summary plugin. |
Semantic Network Summary Plugin Download Page
Brief Description
The Semantic Network Summary is a Cytsocape plugin that generates a word tag cloud from a user-defined node selection, summarizing an attribute of choice. For instance, if selected nodes are proteins, and the string attribute "full protein name" is selected, every string will be broken down into words, which will be plotted on a panel with size proportional to their frequency.
It is also possible to use the plugin to cluster words that appear together in the selected nodes. For instance, if node A has name attribute "Origin Recognition Complex 1" and node B has name attribute "Origin Recognition Complex 2", then the words "Origin", "Recognition" and "Complex" will be clustered together, following the order in which they appear. The plugin operates on any network and on any selected attributes, although it has been specifically designed for string attributes such as gene names or gene ontology annotations.
Plugin Download
Updated 7/20/2010
Sample Data Download
Guided tutorial on the basic functioning of the Semantic Network Summary plugin.
Parameter tutorial on using all of the parameters available for the Semantic Network Summary plugin.