Nanogen, Inc.

Thomas J Macke

James P O'Connell

Bill F Butler

A system and method for processing, searching, and performing in-context searches on named annotated text string databases. The system and method provides users with a means for interactively refining database searches in order to account for differences in keywords used to describe similar phenomena. The system and method provides a means for performing searches for particular predefined target strings in context of particular predefined context strings. Data is represented using data types referred to as Hits and E-Hits. Hits data contains locations of search results and the E-Hits data contains text of search results. Hits lists are sorted and duplicate entries are discarded. Context search results are segregated from non-context search results by sorting the Hits lists. The Search module operates on a Hits list and selects those elements that match one or more search key(s). The output from a Search module is a Results Hits list. The Context Search module accepts two inputs in addition to the search key(s), a Context Hits list and a Target Hits list. The output of the Context Search module is a Hits list that contains matches found within the specified context. The Select module accepts a stream of Hits as input parameters and can be used to add or subtract annotations to the results of a search, remove base text sub-strings from the results of a search, or perform additional processing on Hits that may be useful for context searching. The Extract module is used to extract actual data from a Hits list, typically for display to a user and/or for converting results to keywords used for a subsequent search.

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Las Vegas, NV, United States of America

Thomas J Macke