Agilent Literature Search Software is a meta-search tool for automatically querying multiple text-based search engines (both public and proprietary) in order to aid biologists faced with the daunting task of manually searching and extracting associations among genes/proteins of interest.
Agilent Literature Search Software can be used in conjunction with Cytoscape, which provides a means of generating an overview network view of gene/protein associations.
Agilent Literature Search Software provides an easy-to-use interface to its powerful querying capabilities. When a query is entered, it is submitted to multiple user-selected search engines, and the retrieved results (documents) are fetched from their respective sources. Each document is then parsed into sentences and analyzed for protein-protein associations. Agilent Literature Search Software uses a set of "context" files (lexicons) for defining protein names (and aliases) and association terms (verbs) of interest. Associations extracted from these documents are collected into a Cytoscape network. The sentences and source hyperlinks for each association are further stored as attributes of the corresponding Cytoscape edges.
Agilent Literature Search is a registered Cytoscape plugin and can be installed via the Cytoscape Plugin Manager. Just click the plugins->Manage Plugins menu item and then look under Network Inference.
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Aditya Vailaya , Peter Bluvas , Robert Kincaid , Allan Kuchinsky , Michael Creech , and Annette Adler, "An architecture for biological information extraction and representation," Bioinformatics, 2005, 21(4):430-438.
King JY, Ferrara R, Tabibiazar R, Spin JM, Chen MM, Kuchinsky A, Vailaya A, Kincaid R, Tsalenko A, Deng DX, Connolly A, Zhang P, Yang E, Watt C, Yakhini Z, Ben-Dor A, Adler A, Bruhn L, Tsao P, Quertermous T, Ashley EA., “Pathway analysis of coronary atherosclerosis”, Physiol Genomics. 2005 Sep 21;23(1):103-18.
Ashley EA, Ferrara R, King JY, Vailaya A, Kuchinsky A, He X, Byers B, Gerckens U, Oblin S, Tsalenko A, Soito A, Spin JM, Tabibiazar R, Connolly AJ, Simpson JB, Grube E, Quertermous T. Related Articles, “Network analysis of human in-stent restenosis”, Circulation. 2006 Dec 12;114(24):2644-54.
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