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
This is illustrated in the figure below.
The second way to view literature references is to:
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: