Viewing Literature References for the Association Network

 

When a literature search completes, the Query Matches panel will contain entries that correspond to the retrieved results from the various search engines.  These entries contain useful information about the source document for which the match was found, depending upon the search engine used.  For example, entries for matches in PubMed may display title, authors, journal or publication type of the document, first sentence in abstract, and a URL for the document (see figure below).

 

For those documents that specifically have mapped sentences to Cytoscape Node and Edges, you can highlight those Nodes and Edges in the Cytoscape window by clicking on the icon next to the entry.  Alternatively, you can bring up the context menu on a on an entry in the Query Matches panel (e.g. by right-clicking in Windows systems) and selecting the Highlight Match menu item.  Note that for documents that do not specifically have mappings to Cytoscape Node and Edges, the will not be displayed and the Highlight Match menu item will not appear on the context menu.  A Refresh button provide in the Query Matches panel synchronizes the in the Query Matches entries based upon the current network being viewed. 

For any Node in the Cytoscape network diagram and for any Edge between Nodes, you can access the sentences and abstracts in the scientific literature that were utilized by Agilent Literature Search in generating the association network related to that Node or Edge. 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 -> Show Sentences 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 -> Show Sentences from the Literature menu item

 

For either of these methods, a list of sentences will appear, as in the figure below, which displays sentences that were extracted from the earlier search related to melanoma. Concept lexicon terms identified in each sentence are shown in bold. If an alias matched, then the formal name is shown [formal name]. Multiple Nodes and Edges can be selected at once to visualize all the sentences that were used by the Agilent Literature Search plugin to create the association Edges for the selected Nodes and Edges.

 

 

Mouse-clicking on any of the sentences will bring up its associated literature abstract in the default Web browser, as shown in the figure below: