Interaction Lexicon

The interaction lexicon is an interactions-specific vocabulary, used by the literature search to identify potential interactions between the identified genes or proteins. Each of the "interesting" sentences, that has a potential gene or protein is analyzed to identify words matching terms present in the interaction lexicon. If a match is found, the sentence is marked as a potential "interaction" sentence.

The interaction lexicon consists of a file, named interaction-lexicon-map.txt, in the home folder, <user.home>/.cytoscape/<Cytoscape-version>/plugins/ <AgilentLiteratureSearch-version>/data, for example . 

This file is used to identify potential "interaction sentences".  It contains a TAB-delimited list of two columns where each row represents one lexicon mapping. The first column is the name of the interaction lexicon and represents the name displayed within the dropdown menu for Interaction Lexicon: in the Agilent Literature Search UI. The second column is the file path, relative to the home folder, that defines this lexicon.

Each lexicon contain lists of stemmed verbs.  Two files currently provided are verbNames.txt, and strictVerbNames.txt.  They are used to guide relaxed and limited search, respectively.  As with the concept lexicon files, you can edit these files to add, delete, and/or modify verb terms.  The figure below shows excerpts from verbNames.txt and strictVerbNames.txt files, respectively.