Gather Evidence for Nodes and Edges in Cytoscape

 

For any Node in the Cytoscape network diagram and for any Edge between Nodes, you can gather fresh evidence for the corresponding Edges from the scientific literature. There are two ways do this. The first way is to
  1. bring up the context menu on a Node or Edge in the Network (e.g. by right-clicking in Windows systems).
  2. select the Evidence from Literature->Gather Evidence 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 or an Edge in the Network
  2. On the Select menu, select the Evidence from Literature-> Gather Evidence from the Literature menu item.

For either of these methods, a list of query terms (one for each selected Edge or one for each Edge  adjacent to each selected Node) will be sent to Pubmed, up to 10 abstracts fetched for each query, and any associations among the Nodes impinging on the corresponding Edges will be attached as evidence on the respective Edge. 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.