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Source Code Biol Med. 2011 Apr 7;6:7. doi: 10.1186/1751-0473-6-7.

WordCloud: a Cytoscape plugin to create a visual semantic summary of networks.

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Department of Computer Science, Brown University, Providence, RI, USA.



When biological networks are studied, it is common to look for clusters, i.e. sets of nodes that are highly inter-connected. To understand the biological meaning of a cluster, the user usually has to sift through many textual annotations that are associated with biological entities.


The WordCloud Cytoscape plugin generates a visual summary of these annotations by displaying them as a tag cloud, where more frequent words are displayed using a larger font size. Word co-occurrence in a phrase can be visualized by arranging words in clusters or as a network.


WordCloud provides a concise visual summary of annotations which is helpful for network analysis and interpretation. WordCloud is freely available at

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