Extend Network for Nodes in Cytoscape

 

You can gather fresh evidence for selected Nodes in a Network from the scientific literature. There are two ways do this. The first way is to
  1. bring up the context menu on a Node in the Network (e.g. by right-clicking in Windows systems).
  2. select the Evidence from Literature->Extend Network from the Literature menu item.

This is illustrated in the figure below.

The second way to view literature references is to:

  1. select either a Node in the Network
  2. On the Select menu, select the Evidence from Literature-> Extend Network from the Literature menu item.

For either of these methods, a list of query terms (one for each selected Node) will be sent to Pubmed, up to 10 abstracts (you can vary the number of abstracts fetched for each query by changing the Max Engine Matches: entry in the Search Controls window of the plugin GUI) fetched for each query, and any associations impinging among one of the selected Nodes will be added along with its evidence to the Network. By default the canonicalName attribute is used to identify the gene symbol.   

You can select a different attribute by editing the preferences (via Edit->Preferences…), and changing the attribute name associated with the litSearchEvidenceAttributeName entry. If the attribute doesn't exist, you may create a new attribute. Please note that the attribute name is case sensitive.