Quick Tour

 

Agilent Literature Search uses text mining technology to generate an "association" network from information extracted from the scientific literature. This can be useful in understanding how genes and proteins may interact in the context of a disease or other biological process. Agilent Literature Search can also be used to create a knowledge base for a set of genes and proteins.  In this case, the network diagram can serve as a visual "table of contents" for the knowledge base.   We refer to these networks as "association networks" because they represent associations in the literature between biological entities. The Agilent Literature Search tool can be invoked in Cytoscape by selecting the Agilent Literature Search item on the Plugins menu. When you do this, the Agilent Literature Search control panel will appear, as shown in the figure below.

To execute a search, you enter a set of search terms and, optionally, context words. You can also restrict search results to a particular species by checking the Concept lexicon limits search box.  For each search term entered, a query line is constructed in the Query Editor panel, incorporating aliases and context, if desired.  You can also manually edit the query lines in the Query Editor to specify more advanced search options, such as an "author" field.   When you press the  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 .

The networks can be viewed and manipulated in Cytoscape v2.3.

 

The Agilent Literature Search control panel consists of several panels:

 

Menu Bar File submenu Load loads a previously saved result
Save saves a search
Edit submenu Preferences allows you to edit preferences, such as proxy server
View submenu Engine Selections

invokes a popup checkbox menu that will allow you to select the search engines you would like to use for the literature search. Engines available in the current version are

  • PubMed
  • OMIM
  • USPTO
Help submenu    contains interactive help documentation and an "About" dialog
Terms       enables you to enter search terms of interest, such as a list of names of highly regulated genes
Context       enables you to enter terms related to the context of your inquiry, such as a disease or therapeutic drug.
Search Controls Max Engine Searches                                         set the maximum number of "hits" per query line per search engine used.
Query Controls Use aliases    augment the query to include aliases for the terms in the "Terms" subpanel
Use context    toggle between using and not using context in the search
Concept Lexicon limits search    toggle between using and not using the name of the concept lexicon as context in the search. This would be used if you wanted to restrict search results to a particular species.
Extraction Controls Concept Lexicon     set the concepts used for the search and extraction , e.g. homo sapiens
Interaction Lexicon    set the level of stringency used by the text mining algorithm when generating putative interactions from sentences of interest, ranging from limited to relaxed..
Query Editor       allows you to manually edit the query that is to be sent to the search engine(s). This query string is built up automatically as you enter terms into the Terms and Context subpanels and modify settings in the Match controls subpanel. The Query Editor subpanel gives you the opportunity to fine-tune the query string, add new terms, modify aliases and context, etc.
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
Query Matches        displays a list of references found by the search, including the actual sentences where matches were found.   Selecting one of the displayed sentences will result in a display, in the Web browser, of the literature document or abstract from which the sentence was extracted.
Reanalyze reanalyzes a saved (and loaded) search result with respect to the current Extraction Control settings
Refresh refreshes the icon in the Query Matches window with respect to the currently viewed Cytoscape network

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The figure below shows an Agilent Literature Search control panel with information filled in for a set of genes related to melanoma, using Human concept lexicon to resolve aliases, limiting results to 'human' concept lexicon, and limiting search engine "hits" to 5 per search engine per query line. The stringency level is set to "limited".

 

The  figure below shows the Literature Search control panel, with entries in the Query Matches panel that correspond to the sentences found in the literature.   Note that you may see a different network due to additions to PubMed since this query was run. 

  

 

This figure below shows the resulting network from the example melanoma search, displayed in Cytoscape. The thickness of an edge is mapped (via Cytoscape VizMapper) to the number of sentences stored as a property on the edge. The network nodes containing user-entered search terms are highlighted in yellow.

 

 

A closer look at a zoomed-in area of the network is shown in the figure below.

 

For each of the Nodes and Edges, you can view the literature references that were used to generate them.