Executing the Search

A search can be launched and execution controlled by the use of a set of control buttons, which operate much in the manner of media control buttons, as in Windows Media Player(tm), or RealPlayer(tm).  The figure below shows the control buttons, as they would appear immediately after execution of a search.

When you press the Fetch    button, the set of queries in the Query Editor is submitted to multiple user-selected search engines.  The retrieved results (documents) are fetched from their respective sources and each document is then parsed into sentences and analyzed for concept associations (e.g. protein-protein associations). Agilent Literature Search uses a set of lexicons for defining concept names (and aliases) and association terms (verbs) of interest. The concept lexicon supplied with this version of Agilent Literature Search contains gene/protein names and aliases.  An association is extracted for every sentence containing at least two concept names and one verb.  Associations  are then converted into interactions, which are further grouped into a network. The sentences and source hyperlinks for each association are further stored as attributes of the corresponding interactions .

At any point in the search operation, you can Abort the operation by pressing the  button.  This terminates the source with no possibility of recovery.

Once the documents are fetched from their respective sources, you have the additional option to Pause the operation while document parsing and analysis is underway.  You will see a Pause button , in the place where the Fetch button was displayed.   If you press this button, Agilent Literature Search interrupts the search in progress, with the possibility to Continue .   If you then press the Continue button , then Agilent Literature Search resumes execution.

When you are finished with a search operation, the contents of the Terms, Context, and Query Editor panels remain intact.  You can edit them for subsequent refined searches or modified searches.  Or you can clear the contents of the Terms, Context, and Query Editor panels by pressing the Clear   button.   The Clear button can also be used to clear the contents of the Terms, Context, and Query Editor panels while you are building up your query strings prior to your initial search.

 

The table below summarizes the functionality of the search control buttons.

Clear           Clear clears the Terms, Context, and Query Editor subpanels
Abort         Abort aborts the search operation with no possibility of recovery
Fetch/Pause/Continue toggle         Fetch    invokes the literature search operation
       Pause interrupts the search in progress, with the possibility to Continue or save intermediate results and exit.   If intermediate results are saved, then when Agilent Literature Search is invoked again later, the interrupted search is resumed from the point of saving
    Continue resumes execution of a search after a Pause